Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain–Domain Interactions Mediating Protein–Protein Interactions

Abstract

Recent advances in functional genomics have helped generate large-scale high-throughput protein interaction data. Such networks, though extremely valuable towards molecular level understanding of cells, do not provide any direct information about the regions (domains) in the proteins that mediate the interaction. Here, we performed co-evolutionary analysis of domains in interacting proteins in order to understand the degree of co-evolution of interacting and non-interacting domains. Using a combination of sequence and structural analysis, we analyzed protein–protein interactions in F1-ATPase, Sec23p/Sec24p, DNA-directed RNA polymerase and nuclear pore complexes, and found that interacting domain pair(s) for a given interaction exhibits higher level of co-evolution than the noninteracting domain pairs. Motivated by this finding, we developed a computational method to test the generality of the observed trend, and to predict large-scale domain–domain interactions. Given a protein–protein interaction, the proposed method predicts the domain pair(s) that is most likely to mediate the protein interaction. We applied this method on the yeast interactome to predict domain–domain interactions, and used known domain–domain interactions found in PDB crystal structures to validate our predictions. Our results show that the prediction accuracy of the proposed method is statistically significant. Comparison of our prediction results with those from two other methods reveals that only a fraction of predictions are shared by all the three methods, indicating that the proposed method can detect known interactions missed by other methods. We believe that the proposed method can be used with other methods to help identify previously unrecognized domain–domain interactions on a genome scale, and could potentially help reduce the search space for identifying interaction sites.

Introduction

Post-genomic advances in molecular biology have helped uncover the intricate interplay between proteins in metabolic, signaling and regulatory pathways. Identification of protein–protein interactions is an essential step towards a better understanding of various cellular processes. Various high-throughput experimental techniques such as mass spectrometry, yeast two-hybrid, and tandem affinity purification have been used to discover and generate large scale protein interaction data.^1–8 In addition, several computational approaches towards predicting protein–protein interactions have been proposed in an effort to complement experimental methods.^9–23

Protein–protein interaction networks, though extremely valuable towards molecular level understanding of cells, do not provide insights on interaction specificity at the domain level. Most often, it is only a fraction of a protein that directly interacts with its biological partners. Since two thirds of proteins in prokaryotes and four fifths of proteins in eukaryotes are multidomain proteins,^24,25 interaction between two proteins (either stably or transiently) often involves binding of pair(s) of domains. Importantly, understanding interaction at the domain level is a critical step towards a thorough understanding of the protein–protein interaction networks and their evolution.

Statistical analysis of domain co-occurrence in interacting proteins (known as the Association Method) have been used towards predicting protein–protein interactions.^26–29 The underlying idea behind this type of approach is to identify domain pairs that co-occur significantly more often in interacting proteins than in non-interacting proteins, and use this information to identify new protein–protein interactions. Deng et al.³⁰ applied the Maximum Likelihood Estimation (MLE) method to infer domain–domain interactions from a given protein interaction network. They estimated the probability of interaction between every domain pair, and used it to predict protein–protein interactions. Instead of identifying domain interactions with the goal of predicting new protein–protein interactions, Nye et al.³¹ proposed the lowest p-value method, which focuses on identifying domain–domain interactions that are most likely to mediate a given protein–protein interaction. They performed a comprehensive comparative analysis of the association,²⁶ MLE,³⁰ and the lowest p-value³¹ methods and showed that (i) the overall prediction accuracy of the MLE and the lowest p-value methods is only as good as a random method, which is about 55%, and (ii) the association method was the worst among the four with a prediction accuracy of about 52%. Chen and Liu³² used Random Decision Forest Framework (RDFF) to predict domain–domain interactions, which are then used to predict protein–protein interactions. Recently, Riley et al.³³ extended ideas from earlier methods^26–28,30 by adding a likelihood ratio test to assess the contribution of each potential domain–domain interaction to the likelihood of a given set of protein–protein interactions. They demonstrated that their method performs considerably better than the association and MLE methods.

At the structural level, considerable amount of work has been done to understand protein/domain interactions. Littler and Hubbard ³⁴ performed a comprehensive analysis of domain–domain interactions observed in protein structures in an effort to understand comparative orientation and interacting surfaces of structurally unsolved domain pairs. Gong et al.³⁵ used geometric properties/tools such as accessible surface area and Voronoi diagram on Protein Data Bank (PDB) crystal structures of protein complexes to detect domain interaction interfaces. Shoemaker et al.³⁶ used a conserved binding mode analysis on domain–domain interactions inferred from PDB crystal structures to detect binding surfaces of biological relevance. Neduva et al.³⁷ studied interactions that involve binding between a globular domain in one protein and a short linear motif (pattern of three to eight residues), and proposed a systematic approach to discover these motifs. For a comprehensive review of structure-based interaction studies, we refer the reader to Aloy and Russell's recent review on protein interactions.³⁸

Structural information is necessary and critical for a full understanding of molecular/domain level interaction. However, as the number of interactions with known protein structures is far fewer than the number of interactions, it makes it difficult to understand domain level interactions at the genomic scale. Here, we attempt to understand domain–domain interactions at the sequence level. Specifically, we investigate the relative degree of co-evolution of domains in interacting proteins to understand whether or not interacting domain pairs exhibit higher level of co-evolution that those that are non-interacting. The concept of co-evolution has been widely applied in predicting protein–protein interactions solely based on sequence information^{14,16,39–44} as well as the gene expression data.^45,46 The underlying assumption behind this concept is that the interacting partners must co-evolve so that changes in a protein's binding surface are complemented in the interface of its partner.^14,47,48 We use co-evolutionary analysis to study protein–protein interactions in F1-ATPase, Sec23p/Sec24p, DNA-directed RNA polymerase, and nuclear pore complexes, and show that the degree of co-evolution of interacting domain pair(s) between two interacting proteins is higher than that of non-interacting domain pairs. We then develop a computational method, Relative Co-evolution of Domain Pairs (RCDP), to test the generality of the observed behavior, and to predict large-scale domain–domain interactions using the yeast inter-actome. The proposed method, given a pair of interacting proteins, predicts the domain pair(s) that is most likely to mediate the interaction. Predicted domain–domain interactions are validated against a set of known domain–domain interactions found in PDB⁴⁹ crystal structures (as reported in iPfam⁵⁰). We finally compare RCDP's prediction results with those from two other methods, and show that the RCDP method can predict known domain interactions that are missed by the other methods.

Results and Discussion

Co-evolution of domain pairs in interacting proteins

To assess the degree of co-evolution of domain pairs in interacting proteins, we considered protein–protein interactions in the Saccharomyces cerevisiae (yeast) genome. A schematic overview of assessing the degree of co-evolution between two protein/ domain families is shown in Figure 1. In this type of analysis, multiple sequence alignments of two proteins/domains for a common set of species are used to construct phylogenetic trees and similarity matrices. The degree of co-evolution of the two domains is measured by computing a linear correlation coefficient of the two similarity matrices, which implicitly compares the evolutionary histories of the two domains.

Figure 1.

A schematic overview of the co-evolutionary analysis. Multiple sequence alignments of two yeast proteins for a common set of species are constructed, followed by the construction of their phylogenetic trees and similarity matrices. The extent of agreement between the evolutionary histories of the two yeast proteins is assessed by computing a linear correlation coefficient between the two similarity matrices.

To study the relative degree of co-evolution of domain pairs in interacting proteins, interacting proteins are first assigned with Pfam Hidden Markov Model (HMM)⁵¹ profiles. Then, as shown in Figure 2, the correlation (agreement) scores, measuring the degree of co-evolution of all possible domain pairs between the two interacting proteins, are computed. Multiple sequence alignment for domain D in protein P is constructed by extracting those regions in P's multiple sequence alignment that correspond to D (see Materials and Methods for more details). Under the co-evolution hypothesis, which assumes that interacting domains undergo correlated mutations, domain pairs that are mediating the interaction between two proteins are expected to have co-evolved, and thus are expected to have high correlation score. To test this hypothesis, we began by examining yeast interactions supported by at least one PDB crystal structure. For a given protein–protein interaction, correlation scores of the interacting domain pairs (inferred from crystal structures) are compared against those domain pairs not known to interact to see whether or not the interacting domain pairs do really exhibit relatively high level of co-evolution. If two interacting proteins, P and Q, have two domains each, then there are a total of four domain–domain interaction possibilities between them.

Figure 2.

Relative degree of co-evolution of domains in interacting proteins. (a) Domain architecture of proteins P and Q (shown using gray boxes) that are known to interact (interaction sites are shown as black boxes). (b) Correlation (agreement) scores, measuring the degree of co-evolution, for all possible domain pairs in P and Q. Domain pairs that mediate the interaction between proteins P and Q are expected to have co-evolved, and thus are expected to have a high correlation score.

Interactions in F1-ATPase complex

The F1-ATP synthase is a five-subunit catalytic core (in a stoichiometry of 3α, 3β, 1γ, 1δ, and 1ɛ), which uses transmembrane proton motive force generated by photosynthesis or oxidative phosphorylation to drive the synthesis of ATP from ADP and inorganic phosphate. The central stalk, comprising 3α, 3β, and 1γ subunits, links F1 complex to the nine-subunit transmembrane channel through which the protons are pumped (F0 complex). The rod-shaped asymmetrical γ-subunit rotates inside a cylinder made of three α and β-subunits, arranged alternately^52–56, making contacts with α and β-subunits.

In this complex, we focused our attention on three interactions among the α, β, and γ chains (genes ATP1, ATP2, ATP3, respectively). The corresponding yeast proteins for the α, β, and γ chains (YBL099w, YJR121w, YBR039w, respectively) were assigned with Pfam domains. The α-subunit (YBL099w) was inferred to contain three domains: beta-barrel domain (PF02874, 2e-18), nucleotide-binding domain (PF00006, 3e-122), and C-terminal domain (PF00306, 2e-37). The β-subunit (YJR121w), a close homolog of the α-subunit, was inferred to contain the same three domains as well. The γ-subunit (YBR039w) contained just the ATP synthase domain (PF00231, 1e-130). Figure 3(a) depicts the domain architecture of the sequences along with the true domain–domain interactions between the subunits. The results from co-evolutionary analysis (using orthologs from 22 species) are listed as tables in Figure 3(b), which clearly shows that those domain pairs that interact do, in fact, have relatively high correlation scores. A cartoon of one of several bovine mitochondrial F1-ATPase crystal structures (PDB: 1h8e), supporting the interactions, is shown in Figure 3(c). Despite the complexity of this system, it is remarkable that the degree of co-evolution among the interacting domain pairs is clearly higher than that among the non-interacting domain pairs. In particular, between the α and the β chains, seven out of the nine domain pairs that are known to interact have higher correlation than the two noninteracting domain pairs. In comparison, an approach that picks seven domain pairs out of the nine possibilities at random (without replacement) will have a 0.028 probability (p-value) of getting all its seven picks correct (truly interacting domain pairs).

Figure 3.

Interactions among alpha (ATP1), beta (ATP2), and gamma (ATP3) chains of the ATPase. (a) Protein sequences are shown using thick colored lines: red for the alpha chain, green for the beta chain, blue for the gamma chain, and black for alpha or beta chain. Pfam domain annotations are shown using rectangular boxes (not drawn to scale). The names of the protein sequences are to the left of the domain architecture. Inter-chain domain–domain interactions, which are known to be true from PDB crystal structures (as inferred in iPfam), are shown using double-arrow lines in the domain architecture. (b) The correlation scores of all possible domain pairs between two proteins, sorted in descending order, are listed as tables. Domain pairs that are known to interact, denoted with Y, have high correlation scores exhibiting high degree of co-evolution. (c) A bottom view of the cartoon of bovine mitochondrial F1-ATPase PDB crystal structure (PDB: 1h8e), supporting the interactions, is shown with alpha, beta, and gamma chains colored in red, green, and blue, respectively.

Yeast Sec23p/Sec24p heterodimer

Sec23p (YPR181c) and Sec24p (YIL109c) are components of the Sec23p-Sec24p heterodimeric complex of the COPII vesicle, which carries proteins from the endoplasmic reticulum (ER) to the Golgi complex.⁵⁷ YPR181c and YIL109c are structurally related proteins, consisting of five distinct Pfam domains: zinc finger (PF04810,<1e-19), alpha/beta trunk domain (PF04811,<1e-124), beta-barrel domain (PF08033,<2e-36), helical domain (PF04815, <1e-43), and C-terminal gelsolin-like domain (PF00626, 1e-17). The domain architectures for both the proteins are given in Figure 4(a), showing the lone inter-chain domain–domain interaction between the two alpha/beta trunk domains.

Figure 4.

Interaction between Sec23 (YPR181c) and Sec24 (YIL109c) components of the COPII coat of ER-golgi vesicles. (a) Protein sequences are shown using thick gray lines, and Pfam domain annotations are shown using colored rectangular boxes (not drawn to scale). The names of the protein sequences are to the left of the domain architecture. An inter-chain domain–domain interaction, which is known to be true from a PDB crystal structure (as inferred in iPfam), is shown using a double arrow line. (b) The correlation scores of all possible domain pairs between the two proteins, sorted in descending order, are listed as a table. The domain pair that is known to interact, denoted with Y, has a high correlation score, exhibiting high degree of co-evolution. (c) A cartoon of PDB crystal structure (PDB: 1m2v), supporting the interaction, is shown with domain colors consistent with the domain architecture.

There are several intra-chain domain–domain interactions within each chain, involving all five domains (not shown in the Figure). Since, our analysis considers only inter-chain domain pairs (one in each chain), we considered only the lone inter-chain interaction between the alpha/beta trunk domains of the Sec23p and Sec24 chains. The correlation scores for all possible inter-chain domain pairs are listed as a table in Figure 4(b), and the cartoon of the PDB crystal structure (PDB: 1m2v), supporting the interaction, is shown in Figure 4(c). It is evident from our analysis that the interacting domain pair indeed has relatively high correlation. However, it was not the pair with the highest correlation. The domain pair of beta-barrel domain (PF04811) of Sec23p and alpha/beta trunk domain (PF08033) of Sec24p had the highest correlation. Since the trunk and beta-barrel domains interact within each chain, and both chains are remarkably conserved through evolution and are related, it may not be unreasonable to expect them to have a high correlation. Considering the fact that the lone true interacting domain pair has the second highest correlation score, an approach that picks two domain pairs out of the 25 possibilities at random (without replacement) will have a 0.04 probability (p-value) of picking the lone interacting domain pair.

Interactions in DNA-directed RNA polymerase complex

From the DNA-directed RNA polymerase complex in yeast, we considered two protein–protein interactions involving subunit Rpb8. There are several PDB crystal structures that show Rpb8 subunit interacting with smaller subunits Rpb3 and Rpb11, and the largest subunit Rpb1. The results of our domain-level co-evolutionary analysis for interactions between subunits Rpb8 (YOR224c) and Rpb3 (YIL021w), and subunits Rpb8 and Rpb1 (YDL140c) are shown in Figure 5(a) and (b), respectively. YOR224c was inferred to contain just one domain: RNA_pol_Rpb8 (PF03870, 4e-92). YIL021w was assigned with dimeri-sation domain (PF01193, 1e-19) and insert domain (PF01000, 7e-41), and YDL140c was assigned with seven domains: clamp domain (PF04997, 7e-178), active site domain (PF00623, 5e-188), pore domain (PF04983, 2e-69), funnel domain (PF05000, 2e-50), cleft domain (PF04998, 2e-170), and two mobile module domains (PF04992, 4e-97 and PF04990, 1e-78).

Figure 5.

Inferred domain–domain interactions in DNA-directed RNA polymerase complex. Protein sequences are shown using thick gray lines, and the domain annotations are shown using colored rectangular boxes (not drawn to scale). The names of the protein sequences are to the left of the domain architecture. The correlation scores of all possible domain pairs between the two proteins, sorted in descending order, are listed as a table. Inter-chain domain–domain interactions, which are known to be true from PDB crystal structures (as inferred in iPfam), are shown using double-arrow lines in the domain architecture, and Y in the table. Domain pairs that are known to interact have high correlation scores, exhibiting high degree of co-evolution. Cartoons of PDB crystal structures, supporting the interactions, are shown with domain colors consistent with the domain architecture. (a) Interaction between subunits 3 and 8 of the DNA-directed RNA polymerase (PDB: 1y1v). (b) Interaction between subunits 1 and 8 of the DNA-directed RNA polymerase (PDB : 1y1v). Since PF04998 contains nested domain PF04992, interaction between PF04998 and PF03870 is considered to be true (denoted by ¶).

The correlation results for the interaction between Rpb3 and Rpb8 subunits (using orthologs from a common set of 15 species), listed as a table in Figure 5(a), show that the interacting domain pair (PF01193, PF03870), shown in the cartoon of crystal structure (PDB: 1y1v), has a higher level of co-evolution when compared to the non-interacting domain pair (PF01000, PF03870). The correlation results are not that clear for the interaction between the Rpb1 and Rpb8 subunits (refer to the table in Figure 5(b)). While two out of the three interacting domain pairs have high correlation scores, the interaction between the funnel domain (PF05000) and RNA_pol_Rpb8 (PF03870) has the lowest correlation score among all possible domain pairs. An approach that picks four domain pairs out of the six possibilities at random (without replacement) will have a 0.086 probability (p-value) of getting three out its four picks correct (truly interacting domain pairs).

An interacting domain pair with a low correlation (false negative in some sense) could be explained using one or both of the following reasons. When assessing the degree of co-evolution between two domains, we tend to ignore the number of interacting partners a domain may have. Even though the co-evolutionary hypothesis for interacting domains assumes that the interacting domains undergo correlated mutations, more specifically, it is actually the binding surfaces that undergo correlated mutations. A domain having multiple interacting partners may use distinct patches on its surface to interact with each of its partners.^34,58 Each binding region of a domain is highly specific to its interacting partner. Thus, the surface patches used by a domain to interact with many interacting partners may undergo independent correlated mutations with their corresponding interacting partner. As a result, mutations at different surface patches of a domain need not be correlated (see Figure 6). Consequently, the degree of co-evolution between two interacting domains, one or both with multiple interacting partners, may actually be suppressed, resulting in a low correlation score. Thus, it may not always be the case that a pair of interacting domains, each of which has multiple interacting partners, has a high correlation score.

Figure 6.

Uncorrelated set of correlated mutations. Each rectangular box is a cartoon representation of a multiple sequence alignment of a family of orthologous proteins/domains. There are a total of six families, A, B, C, D, E, and F. The binding residues of interaction, referred to as binding surface, between family A and each of the other five families are highlighted using distinct colors. Under the co-evolutionary hypothesis, which states interacting domains undergo correlated mutations, mutations at each of A's five surface patches must be correlated with those at the binding surface in the corresponding interacting partners. However, mutations at A's five surface patches need not be correlated. As a result, for example, it may be unreasonable to expect A and E to have similar evolutionary histories even though the corresponding binding surfaces in A and E may have high correlation.

Mutations occurring in interacting domains may not be correlated due to many other biological constraints imposed on them. There may be cases in which the mutations at a binding surface in a domain may not be followed by compensatory mutations at the binding surface of its interacting partner. Since protein binding surfaces are relatively more conserved than the rest of the sequence,^59,60 domains with many interacting partners, and thus many surface patches, are likely to be relatively more conserved than those with few interacting partners.^61,62 For each interacting domain, from its multiple sequence alignment, we computed the sequence identity of each orthologous domain in reference to the yeast domain. The alignments for Rpb8 and Rpb1 had orthologs in a common set of 17 species, including yeast. The average sequence identities for the interacting domains, along with the number of known interacting partners are listed in Table 1. Interestingly, at least for this example, those domains with many interacting partners are relatively more conserved than those with few partners.

Table 1.

The average sequence identities of interacting domains between subunits Rpb1 (YDL140c) and Rpb8 (YOR224c) of DNA-directed RNA polymerase, along with the number of known interacting partners for each domain

YDL140c			YOR224c
Domain	Average sequence identity	No. interacting partners	Domain	Average sequence identity	No. interacting partners
PF04992	43.48	6	PF03870	43.21	5
PF04983	56.64	11	PF03870	43.21	5
PF05000	66.27	12	PF03870	43.21	5

There is a good correlation between the number of interacting partners and the average sequence identity, which suggests that those domains with many partners are relatively more conserved than those with few partners. The interacting domain pairs with low correlation are highlighted in black.

Exportin Cse1p complexed with its cargo

Nuclear pore complexes serve as a medium for exchange of macromolecules between the nucleus and the cytoplasm. Carrier proteins that shuttle between the nucleus and the cytoplasm enable active transport of large molecules through these pore complexes. Importin-alpha Srp1 (YNL189w), which acts as a carrier for many nuclear trafficking processes, binds cargo in the cytoplasm, moves through the nuclear pore and releases the cargo in the nucleus. The nuclear envelope protein Cse1p (YGL238w), a yeast homolog of mammalian CAS, recycles importin-alpha from the nucleus back to the cytoplasm, thereby allowing it to participate in multiple rounds of nuclear import.^63,64

To understand the degree of co-evolution between the interacting domains in this complex, we first assigned Pfam domains to the proteins. Cse1 (YGL238w) was assigned with importin-beta N-terminal domain (PF03810, 2e-22), Cse1 domain containing HEAT repeats (PF08506, 7e-275), and Cas/Cse C terminus domain (PF03378, 5e-77). Importin-alpha Srp1 (YNL189w) was assigned with importin beta binding domain (PF01749, 1e-45) and eight Armadillo repeats (PF00514, <5e-6). The domain architecture and the domain-level interactions in this complex are shown in Figure 7. The co-evolution scores for all domain pairs between these chains are listed as a table in Figure 7(b). Three out of the five interacting domain pairs have high correlation, implying high level of co-evolution. The remaining two interacting domain pairs do not have high correlation scores. An approach that picks five domain pairs out of the 29 possibilities at random (without replacement) will have a 0.019 probability (p-value) of getting two out its five picks correct (truly interacting domain pairs).

Figure 7.

Interaction between importin alpha Srp1 (YNL189w) and nuclear export receptor Cse1 (YGL238w). (a) Protein sequences are shown using thick gray lines, and Pfam domain annotations are shown using colored rectangular boxes (not drawn to scale). The names of the protein sequences are to the left of the domain architecture. Inter-chain domain–domain interactions, which are known to be true from PDB crystal structures (as inferred in iPfam), are shown using a double arrow line. (b) The correlation scores of all possible domain pairs between two proteins, sorted in descending order, are listed as a table. Two of the five domain pairs, which are known to interact (denoted with Y), have high correlation scores, exhibiting high degree of co-evolution. The reason for the other three known interacting domain pairs not having high correlation scores could be attributed to “uncorrelated set of correlated-mutations” illustrated in Figure 4. (c) A cartoon of the PDB crystal structure (PDB: 1wa5), supporting the interaction, is shown with domain colors consistent with the domain architecture. A subset of the interaction sites is shown using dotted spheres.

For each interacting domain, from its multiple sequence alignment, we computed the sequence identity of each orthologous domain in reference to the yeast domain. The average sequence identities for the interacting domains, along with the number of known interacting partners are listed in Table 2, which shows that those domains with many interacting partners are relatively more conserved than those with few partners, which is consistent with similar other findings suggesting that hubs (those proteins/domains with numerous interacting partners) are relatively more conserved.^59–62 If true, this could possibly explain why domains PF03378 and PF08506, with average sequence identities ~34% and ~46%, respectively, have low correlation with domain PF00514_8, which happens to have a relatively high average sequence identity at ~75%.

Table 2.

The average sequence identities of interacting domains between importin alpha Srp1 (YNL189w) and nuclear export receptor Cse1 (YGL238w), along with the number of known interacting partners for each domain

YGL238w			YNL189w
Domain	Average sequence identity	No. Interacting parnters	Domain	Average sequence identity	No. interacting parnters
PF08506	45.90	4	PF00514_7	70.16	16
PF08506	45.90	4	PF01749	47.30	5
PF03810	45.31	4	PF01749	47.30	5
PF08506	45.90	4	PF00514_8	75.31	16
PF03378	33.76l	3	F00514_8	75.31	16

There is a clear correlation between the number of interacting partners and the average sequence identity, which suggests that those domains with many partners are relatively more conserved than those with few partners. The interacting domain pairs with low correlation are highlighted in black.

Predicting large-scale domain–domain interactions from the yeast interactome

Motivated by our results that interacting domain pairs (in interacting proteins) have higher correlation compared to non-interacting domain pairs, we developed a method to test the generality of the observed trend, and to predict large-scale domain–domain (i.e. Pfam–Pfam) interactions using the yeast interactome. First, we assigned the interacting yeast protein sequences with Pfam domains (see Materials and Methods). We then considered only those interactions involving proteins with at least 50% of their sequence lengths assigned (SLA) with Pfam domain(s), which we refer to as “test set SLA ≥50%”. A cutoff of 50% was chosen as a compromise between being sufficiently small to provide enough interactions, and large enough for assigned domains to contain sufficient binding sites. In addition, we imposed a restriction that the interacting proteins have orthologs in at least a common set of ten species. This resulted in a set of 1180 interactions among 654 proteins.

For each protein–protein interaction, we computed the correlation scores of all possible domain pairs between the two proteins, and inferred the domain pair(s) with the highest correlation score to be the interacting pair that is most likely to mediate the protein–protein interaction. For our set of 1180 protein–protein interactions, we inferred a total of 1222 domain–domain interactions (Supplementary material S3), 960 of which are unique. In order to validate our predictions, we used the iPfam database,⁵⁰ which contains the list of known domain–domain interactions inferred from PDB crystal structures. We found that 206 out of our 1222 predictions (109 out of the 960 unique predictions ≈11.35%) are in iPfam.

Supplementary material S3.

RCDP prediction results for the test set 1, containing 1222 domain-domain interactions.

Format: <Protein1> <startResidue> <endResidue> <PfamDomain> <e-value> <Protein2> <startResidue> <endResidue> <PfamDomain> <e-value> <correlationCoefficient> <inPDBorNOT>

Protein1	startResidue	endResidue	PfamDomain	e-value	Protein2	startResidue	endResidue	PfamDomain	e-value	correlationCoefficient	inPDBorNOT
YAL012w	10	390	PF01053	8.30E-227	YMR101c	73	309	PF01255	7.80E-150	0.916145	0
YAL036c	294	368	PF02824	2.00E-38	YJL138c	46	211	PF00270	1.70E-62	0.816533	0
YAL038w	18	365	PF00224	2.10E-267	YNL307c	35	327	PF00069	2.40E-75	0.637991	0
YAL038w	379	499	PF02887	4.60E-74	YOR226c	26	153	PF01592	2.10E-78	0.871644	0
YAL054c	165	606	PF00501	9.50E-125	YNL189w	9	110	PF01749	1.10E-45	0.78557	0
YAL062w	40	170	PF02812	3.80E-74	YNL189w	9	110	PF01749	1.10E-45	0.9223	0
YBL002w	35	105	PF00125	2.60E-25	YKR001c	258	550	PF01031	6.60E-156	0.827532	0
YBL002w	35	105	PF00125	2.60E-25	YKR048c	93	366	PF00956	9.30E-158	0.881475	0
YBL002w	35	105	PF00125	2.60E-25	YNL262w	511	1194	PF00136	3.70E-08	0.874084	0
YBL002w	35	105	PF00125	2.60E-25	YOL006c	364	599	PF01028	6.10E-154	0.85893	0
YBL002w	35	105	PF00125	2.60E-25	YOR116c	10	368	PF04997	6.30E-106	0.833282	0
YBL002w	35	105	PF00125	2.60E-25	YOR207c	201	378	PF04561	3.40E-63	0.529505	0
YBL002w	35	105	PF00125	2.60E-25	YPR010c	486	552	PF04565	1.50E-30	0.827751	0
YBL003c	19	92	PF00125	2.00E-30	YDL188c	118	313	PF00149	6.90E-40	0.336094	0
YBL022c	181	478	PF02190	2.50E-166	YLR180w	115	237	PF02772	1.00E-94	0.911493	0
YBL026w	5	72	PF01423	1.40E-19	YDR378c	14	83	PF01423	2.20E-18	0.889358	1
YBL026w	5	72	PF01423	1.40E-19	YER146w	10	83	PF01423	2.20E-20	0.807144	1
YBL026w	5	72	PF01423	1.40E-19	YIL048w	223	476	PF00122	2.80E-05	0.865482	0
YBL026w	5	72	PF01423	1.40E-19	YLR264w	1	67	PF01200	3.20E-44	0.838633	0
YBL026w	5	72	PF01423	1.40E-19	YLR275w	32	106	PF01423	2.00E-15	0.813445	1
YBL026w	5	72	PF01423	1.40E-19	YLR438c-a	6	78	PF01423	3.30E-23	0.912768	1
YBL026w	5	72	PF01423	1.40E-19	YNL147w	20	96	PF01423	4.90E-22	0.887793	1
YBL026w	5	72	PF01423	1.40E-19	YNL287w	19	560	PF01602	1.90E-161	0.88403	0
YBL026w	5	72	PF01423	1.40E-19	YPL249c-a	2	100	PF01158	2.60E-68	0.899282	0
YBL030c	22	119	PF00153	4.40E-35	YEL020w-a	12	77	PF02953	3.50E-28	0.884107	0
YBL030c	22	119	PF00153	4.40E-35	YGL137w	325	794	PF04053	1.20E-254	0.795204	0
YBL039c	1	280	PF06418	2.50E-194	YJR103w	1	280	PF06418	5.70E-194	0.998837	0
YBL040c	1	209	PF00810	1.40E-157	YGR060w	47	265	PF01598	3.70E-106	0.876577	0
YBL040c	1	209	PF00810	1.40E-157	YOL020w	86	546	PF00324	2.90E-141	0.901858	0
YBL078c	13	116	PF02991	1.30E-79	YOR100c	140	226	PF00153	4.20E-26	0.749538	0
YBL091c	103	358	PF00557	1.80E-99	YNL290w	48	218	PF00004	4.60E-16	0.725567	0
YBL099w	421	525	PF00306	1.60E-37	YBR039w	34	310	PF00231	9.50E-131	0.934749	1
YBL099w	421	525	PF00306	1.60E-37	YDR298c	32	208	PF00213	1.20E-73	0.925202	0
YBL099w	185	409	PF00006	3.30E-122	YJR121w	169	388	PF00006	1.10E-96	0.95957	1
YBL099w	421	525	PF00306	1.60E-37	YPL078c	75	237	PF05405	2.70E-82	0.964984	0
YBR009c	25	94	PF00125	4.80E-17	YBR010w	58	132	PF00125	2.70E-36	0.698304	1
YBR009c	25	94	PF00125	4.80E-17	YDR224c	35	105	PF00125	1.00E-24	0.863566	1
YBR009c	25	94	PF00125	4.80E-17	YDR225w	19	92	PF00125	2.00E-30	0.81132	1
YBR009c	25	94	PF00125	4.80E-17	YKL067w	6	140	PF00334	4.60E-104	0.408179	0
YBR009c	25	94	PF00125	4.80E-17	YLR180w	115	237	PF02772	1.00E-94	0.596718	0
YBR009c	25	94	PF00125	4.80E-17	YLR340w	3	105	PF00466	2.60E-49	0.532261	0
YBR009c	25	94	PF00125	4.80E-17	YPR010c	652	693	PF04567	8.40E-08	0.543852	0
YBR009c	25	94	PF00125	4.80E-17	YPR110c	48	330	PF01193	8.90E-20	0.772446	0
YBR010w	58	132	PF00125	2.70E-36	YDR224c	35	105	PF00125	1.00E-24	0.776497	1
YBR010w	58	132	PF00125	2.70E-36	YDR225w	19	92	PF00125	2.00E-30	0.731597	1
YBR010w	58	132	PF00125	2.70E-36	YPL209c	104	355	PF00069	1.40E-82	0.535964	0
YBR011c	45	229	PF00719	2.00E-135	YGL120c	95	258	PF00270	0.00018	0.740863	0
YBR011c	45	229	PF00719	2.00E-135	YHR030c	23	318	PF00069	3.20E-85	0.753089	0
YBR011c	45	229	PF00719	2.00E-135	YMR267w	77	265	PF00719	1.40E-80	0.840552	1
YBR018c	194	366	PF02744	1.20E-104	YER081w	61	381	PF00389	1.40E-39	0.929025	0
YBR018c	4	192	PF01087	1.60E-115	YGL137w	325	794	PF04053	1.20E-254	0.926431	0
YBR018c	194	366	PF02744	1.20E-104	YHR030c	23	318	PF00069	3.20E-85	0.701962	0
YBR018c	4	192	PF01087	1.60E-115	YPR054w	38	337	PF00069	1.00E-72	0.695854	0
YBR021w	103	562	PF02133	1.00E-256	YHR042w	261	481	PF00667	5.70E-112	0.983251	0
YBR024w	84	267	PF02630	1.40E-122	YBR024w	84	267	PF02630	1.40E-122	1	1
YBR039w	34	310	PF00231	9.50E-131	YDL047w	46	242	PF00149	2.20E-40	0.663361	0
YBR039w	34	310	PF00231	9.50E-131	YDL145c	812	1200	PF06957	1.10E-30	0.970729	0
YBR039w	34	310	PF00231	9.50E-131	YJR068w	261	350	PF08542	5.80E-27	0.834343	0
YBR061c	21	209	PF01728	8.70E-97	YJL097w	54	209	PF04387	2.40E-81	0.937175	0
YBR068c	99	567	PF00324	1.00E-193	YDR046c	94	562	PF00324	1.00E-171	0.998889	0
YBR068c	99	567	PF00324	1.00E-193	YDR385w	723	811	PF00679	1.20E-36	0.65148	0
YBR069c	98	561	PF00324	6.30E-155	YLR343w	20	344	PF03198	9.60E-238	0.933159	0
YBR069c	98	561	PF00324	6.30E-155	YNL064c	228	350	PF01556	5.40E-15	0.937407	0
YBR085w	215	305	PF00153	9.10E-29	YHR002w	32	127	PF00153	6.20E-29	0.898158	1
YBR087w	38	243	PF00004	0.001	YNL088w	690	1171	PF00521	3.00E-123	0.967145	0
YBR088c	1	125	PF00705	1.10E-78	YBR087w	38	243	PF00004	0.001	0.921543	0
YBR088c	127	254	PF02747	2.30E-79	YJR068w	261	350	PF08542	5.80E-27	0.89377	0
YBR088c	1	125	PF00705	1.10E-78	YKL113c	144	235	PF00867	1.30E-52	0.864749	0
YBR088c	1	125	PF00705	1.10E-78	YNL290w	237	327	PF08542	4.10E-28	0.705218	0
YBR088c	1	125	PF00705	1.10E-78	YOL094c	229	316	PF08542	1.90E-33	0.919656	0
YBR088c	1	125	PF00705	1.10E-78	YOR116c	855	1386	PF04998	4.80E-158	0.905903	0
YBR089c-a	27	95	PF00505	1.60E-31	YJL026w	76	358	PF00268	7.00E-177	0.864707	0
YBR089c-a	27	95	PF00505	1.60E-31	YPL235w	70	412	PF00004	0.00044	0.888551	0
YBR109c	85	113	PF00036	2.70E-08	YBR011c	45	229	PF00719	2.00E-135	0.517943	0
YBR109c	85	113	PF00036	2.70E-08	YDR032c	6	135	PF00258	4.00E-23	0.54778	0
YBR109c	85	113	PF00036	2.70E-08	YDR155c	3	162	PF00160	1.20E-116	0.444661	1
YBR109c	85	113	PF00036	2.70E-08	YEL034w	84	151	PF01287	1.10E-38	0.479657	0
YBR109c	85	113	PF00036	2.70E-08	YFR014c	37	297	PF07714	6.40E-20	0.496099	0
YBR109c	85	113	PF00036	2.70E-08	YGR144w	67	296	PF01266	0.00021	0.573306	0
YBR109c	48	76	PF00036	3.80E-06	YHR028c	608	815	PF00326	2.30E-71	0.62772	0
YBR109c	85	113	PF00036	2.70E-08	YHR179w	16	368	PF00724	3.10E-200	0.576261	0
YBR109c	85	113	PF00036	2.70E-08	YIL021w	49	171	PF01000	7.10E-41	0.584261	0
YBR109c	85	113	PF00036	2.70E-08	YJR073c	10	205	PF04191	4.70E-162	0.527914	0
YBR109c	85	113	PF00036	2.70E-08	YJR104c	1	154	PF00080	1.30E-101	0.331116	0
YBR109c	85	113	PF00036	2.70E-08	YKL067w	6	140	PF00334	4.60E-104	0.615271	0
YBR109c	85	113	PF00036	2.70E-08	YKL129c	758	960	PF06017	1.10E-76	0.58845	0
YBR109c	85	113	PF00036	2.70E-08	YLL050c	10	137	PF00241	2.10E-66	0.480575	0
YBR109c	85	113	PF00036	2.70E-08	YMR105c	450	558	PF00408	4.70E-45	0.556348	0
YBR109c	85	113	PF00036	2.70E-08	YMR109w	759	961	PF06017	1.00E-77	0.582283	0
YBR109c	85	113	PF00036	2.70E-08	YMR250w	63	412	PF00282	1.70E-42	0.541872	0
YBR109c	85	113	PF00036	2.70E-08	YNL202w	28	198	PF00106	3.20E-14	0.474418	0
YBR109c	85	113	PF00036	2.70E-08	YOL016c	47	307	PF07714	3.30E-26	0.557703	0
YBR117c	7	339	PF00456	5.70E-239	YLR447c	12	343	PF01992	2.50E-169	0.968223	0
YBR118w	258	325	PF03144	3.50E-24	YKL081w	250	356	PF00647	2.50E-82	0.914141	0
YBR121c	53	383	PF00587	1.00E-82	YNL244c	20	101	PF01253	6.80E-42	0.939489	0
YBR126c	16	482	PF00982	5.90E-294	YOR089c	9	173	PF00071	5.60E-94	0.821956	0
YBR127c	397	500	PF00306	1.80E-24	YKL080w	8	392	PF03223	3.50E-84	0.95271	0
YBR127c	397	500	PF00306	1.80E-24	YLR447c	12	343	PF01992	2.50E-169	0.828209	0
YBR132c	92	565	PF00324	7.50E-192	YHR042w	261	481	PF00667	5.70E-112	0.962516	0
YBR154c	1	101	PF03871	6.20E-65	YDL140c	510	669	PF04983	1.50E-69	0.964818	0
YBR154c	1	101	PF03871	6.20E-65	YDR404c	1	79	PF03876	1.20E-38	0.967535	0
YBR154c	142	215	PF01191	7.60E-49	YER125w	505	809	PF00632	5.90E-182	0.687592	0
YBR154c	1	101	PF03871	6.20E-65	YKL144c	1	77	PF03876	9.60E-41	0.913435	0
YBR154c	1	101	PF03871	6.20E-65	YOR116c	742	848	PF05000	6.20E-45	0.900691	0
YBR154c	142	215	PF01191	7.60E-49	YPR110c	48	330	PF01193	8.90E-20	0.866512	0
YBR159w	63	242	PF00106	2.50E-08	YMR279c	76	487	PF07690	2.00E-27	0.942033	0
YBR160w	8	295	PF00069	4.30E-98	YBR038w	267	862	PF03142	3.00E-05	0.76017	0
YBR160w	8	295	PF00069	4.30E-98	YDR097c	435	606	PF05188	1.30E-05	0.970653	0
YBR160w	8	295	PF00069	4.30E-98	YDR212w	36	549	PF00118	8.70E-163	0.771758	0
YBR160w	8	295	PF00069	4.30E-98	YHL035c	981	1274	PF00664	3.20E-24	0.666369	0
YBR160w	8	295	PF00069	4.30E-98	YKL129c	758	960	PF06017	1.10E-76	0.902716	0
YBR160w	8	295	PF00069	4.30E-98	YLR086w	155	1406	PF02463	1.10E-140	0.703017	0
YBR160w	8	295	PF00069	4.30E-98	YNL102w	792	1248	PF00136	1.20E-165	0.665905	0
YBR160w	8	295	PF00069	4.30E-98	YPL209c	104	355	PF00069	1.40E-82	0.857856	1
YBR170c	259	577	PF05021	2.20E-223	YER081w	61	381	PF00389	1.40E-39	0.937835	0
YBR170c	259	577	PF05021	2.20E-223	YGR048w	13	199	PF03152	1.30E-132	0.943442	0
YBR170c	259	577	PF05021	2.20E-223	YLR044c	387	538	PF02775	1.50E-08	0.946819	0
YBR176w	24	291	PF02548	7.50E-184	YBR176w	24	291	PF02548	7.50E-184	1	1
YBR176w	24	291	PF02548	7.50E-184	YNL189w	204	244	PF00514	2.00E-09	0.920074	0
YBR192w	51	168	PF00153	7.70E-33	YER078c	65	202	PF05195	2.60E-66	0.960707	0
YBR205w	17	357	PF01793	9.10E-230	YFL038c	1	169	PF00025	4.70E-06	0.548945	0
YBR218c	852	1060	PF02436	5.90E-131	YPR110c	48	330	PF01193	8.90E-20	0.958684	0
YBR221c	39	215	PF02779	7.20E-73	YER081w	61	381	PF00389	1.40E-39	0.923027	0
YBR247c	143	476	PF05291	1.30E-267	YHR148w	2	108	PF00163	2.20E-37	0.879993	0
YBR247c	143	476	PF05291	1.30E-267	YLR180w	239	376	PF02773	2.70E-91	0.893719	0
YBR247c	143	476	PF05291	1.30E-267	YNL075w	89	262	PF04427	3.80E-71	0.942471	0
YBR247c	143	476	PF05291	1.30E-267	YNL244c	20	101	PF01253	6.80E-42	0.933727	0
YBR247c	143	476	PF05291	1.30E-267	YOL010w	5	341	PF01137	1.90E-91	0.981926	0
YBR249c	40	355	PF00793	5.20E-182	YER081w	61	381	PF00389	1.40E-39	0.900106	0
YBR249c	40	355	PF00793	5.20E-182	YPR110c	48	330	PF01193	8.90E-20	0.941637	0
YBR252w	16	146	PF00692	1.60E-58	YNL189w	9	110	PF01749	1.10E-45	0.822352	0
YBR291c	213	299	PF00153	5.60E-27	YHR096c	89	549	PF00083	9.80E-241	0.942393	0
YBR296c	24	554	PF01384	3.80E-226	YLL028w	152	544	PF07690	9.70E-42	0.881424	0
YBR298c	102	561	PF00083	8.60E-144	YBR159w	63	242	PF00106	2.50E-08	0.892175	0
YBR298c	108	518	PF07690	0.00069	YLR372w	10	321	PF01151	3.70E-232	0.907995	0
YBR298c	102	561	PF00083	8.60E-144	YMR279c	76	487	PF07690	2.00E-27	0.948604	0
YCL025c	124	591	PF00324	3.50E-163	YBR159w	63	242	PF00106	2.50E-08	0.935941	0
YCL025c	124	591	PF00324	3.50E-163	YCR034w	10	313	PF01151	7.70E-229	0.967504	0
YCL025c	124	591	PF00324	3.50E-163	YER026c	117	267	PF01066	4.00E-33	0.982644	0
YCL025c	124	591	PF00324	3.50E-163	YFL041w	367	517	PF07731	5.70E-49	0.967713	0
YCL025c	124	591	PF00324	3.50E-163	YGR060w	47	265	PF01598	3.70E-106	0.947132	0
YCL025c	124	591	PF00324	3.50E-163	YHL003c	109	169	PF08390	1.40E-30	0.98006	0
YCL025c	124	591	PF00324	3.50E-163	YJR095w	9	104	PF00153	1.40E-33	0.965331	0
YCL025c	124	591	PF00324	3.50E-163	YKL008c	109	169	PF08390	3.80E-32	0.966544	0
YCL025c	124	591	PF00324	3.50E-163	YLR343w	20	344	PF03198	9.60E-238	0.934175	0
YCL025c	124	591	PF00324	3.50E-163	YLR372w	10	321	PF01151	3.70E-232	0.965267	0
YCL025c	124	591	PF00324	3.50E-163	YPL227c	76	263	PF00535	2.10E-27	0.95611	0
YCL025c	124	591	PF00324	3.50E-163	YPL234c	96	161	PF00137	5.40E-24	0.8139	0
YCL025c	124	591	PF00324	3.50E-163	YPL265w	90	561	PF00324	1.90E-142	0.851473	0
YCL030c	370	789	PF00815	2.80E-287	YLR044c	387	538	PF02775	1.50E-08	0.968048	0
YCL030c	165	240	PF01502	8.60E-48	YLR180w	115	237	PF02772	1.00E-94	0.938759	0
YCL030c	370	789	PF00815	2.80E-287	YML124c	249	394	PF03953	9.30E-73	0.959513	0
YCL040w	12	230	PF00349	2.60E-134	YCL040w	12	230	PF00349	2.60E-134	1	1
YCL040w	243	500	PF03727	8.50E-148	YCL040w	243	500	PF03727	8.50E-148	1	1
YCL040w	243	500	PF03727	8.50E-148	YNL189w	9	110	PF01749	1.10E-45	0.907044	0
YCR002c	29	309	PF00735	9.20E-183	YFL018c	380	489	PF02852	3.30E-66	0.899385	0
YCR002c	33	182	PF01926	0.00011	YHR107c	31	321	PF00735	1.30E-188	0.761177	0
YCR002c	29	309	PF00735	9.20E-183	YJR076c	23	174	PF01926	1.60E-06	0.765931	0
YCR002c	29	309	PF00735	9.20E-183	YLR314c	116	418	PF00735	1.90E-180	0.690069	0
YCR005c	64	441	PF00285	1.60E-205	YCR005c	64	441	PF00285	1.60E-205	1	1
YCR005c	64	441	PF00285	1.60E-205	YKL085w	165	331	PF02866	3.50E-83	0.922119	0
YCR009c	6	232	PF03114	3.00E-80	YGL137w	325	794	PF04053	1.20E-254	0.926542	0
YCR010c	71	281	PF01184	7.60E-167	YEL063c	92	557	PF00324	8.30E-189	0.979797	0
YCR012w	3	412	PF00162	1.40E-292	YGL137w	325	794	PF04053	1.20E-254	0.85069	0
YCR028c	41	424	PF07690	1.10E-18	YLR372w	10	321	PF01151	3.70E-232	0.97881	0
YCR034w	10	313	PF01151	7.70E-229	YBR069c	98	561	PF00324	6.30E-155	0.950659	0
YCR034w	10	313	PF01151	7.70E-229	YGL055w	411	487	PF00173	2.00E-20	0.973438	0
YCR034w	10	313	PF01151	7.70E-229	YHR094c	72	488	PF07690	4.20E-29	0.951123	0
YCR034w	10	313	PF01151	7.70E-229	YJL219w	68	486	PF07690	1.70E-26	0.952833	0
YCR034w	10	313	PF01151	7.70E-229	YLL028w	152	544	PF07690	9.70E-42	0.887122	0
YCR034w	10	313	PF01151	7.70E-229	YLL061w	77	540	PF00324	8.50E-124	0.884575	0
YCR034w	10	313	PF01151	7.70E-229	YMR058w	29	147	PF07731	0.00048	0.971213	0
YCR034w	10	313	PF01151	7.70E-229	YOL020w	86	546	PF00324	2.90E-141	0.951499	0
YCR034w	10	313	PF01151	7.70E-229	YOL030w	14	331	PF03198	4.30E-233	0.942134	0
YCR034w	10	313	PF01151	7.70E-229	YPL274w	81	544	PF00324	2.50E-132	0.89473	0
YCR034w	10	313	PF01151	7.70E-229	YPR156c	188	616	PF00083	0.00011	0.823463	0
YDL004w	31	114	PF02823	2.10E-10	YBL099w	421	525	PF00306	1.60E-37	0.944759	0
YDL004w	31	114	PF02823	2.10E-10	YJR121w	401	508	PF00306	2.30E-48	0.921629	0
YDL047w	46	242	PF00149	2.20E-40	YJR072c	8	258	PF03029	4.50E-116	0.679757	0
YDL047w	46	242	PF00149	2.20E-40	YNL101w	295	711	PF01490	8.70E-157	0.668677	0
YDL055c	2	236	PF00483	8.30E-75	YNL189w	9	110	PF01749	1.10E-45	0.842224	0
YDL064w	8	152	PF00179	2.00E-69	YDL064w	8	152	PF00179	2.00E-69	1	1
YDL081c	20	105	PF00428	6.50E-35	YPR086w	133	203	PF00382	1.30E-35	0.905273	0
YDL100c	18	336	PF02374	4.70E-196	YDR304c	35	196	PF00160	1.60E-113	0.891698	0
YDL100c	18	336	PF02374	4.70E-196	YHR057c	37	199	PF00160	1.50E-110	0.758264	0
YDL100c	18	336	PF02374	4.70E-196	YJL153c	66	515	PF07994	1.80E-199	0.926979	0
YDL100c	18	336	PF02374	4.70E-196	YNL055c	2	276	PF01459	9.70E-121	0.950579	0
YDL100c	18	336	PF02374	4.70E-196	YOL126c	225	416	PF02866	7.10E-78	0.909399	0
YDL108w	7	290	PF00069	2.80E-111	YDL140c	873	1056	PF04992	4.00E-97	0.940923	0
YDL108w	7	290	PF00069	2.80E-111	YOR151c	1126	1219	PF04560	5.80E-50	0.655472	0
YDL126c	32	118	PF02359	6.20E-36	YBR170c	259	577	PF05021	2.20E-223	0.886013	0
YDL126c	32	118	PF02359	6.20E-36	YDR037w	225	578	PF00152	2.40E-115	0.712262	0
YDL126c	32	118	PF02359	6.20E-36	YGR048w	13	199	PF03152	1.30E-132	0.736641	0
YDL126c	32	118	PF02359	6.20E-36	YGR078c	48	179	PF02996	3.90E-36	0.551838	0
YDL126c	523	710	PF00004	2.60E-94	YLL039c	82	150	PF00240	5.60E-38	0.589708	0
YDL134c	110	305	PF00149	7.10E-40	YDL188c	118	313	PF00149	6.90E-40	0.996699	1
YDL134c	110	305	PF00149	7.10E-40	YIL021w	16	260	PF01193	1.30E-19	0.436547	0
YDL134c	110	305	PF00149	7.10E-40	YPR110c	48	330	PF01193	8.90E-20	0.58532	0
YDL135c	1	202	PF02115	7.30E-27	YPR165w	12	185	PF00071	6.20E-87	0.662604	1
YDL137w	4	177	PF00025	2.90E-125	YPR110c	48	330	PF01193	8.90E-20	0.725142	0
YDL140c	342	507	PF00623	4.50E-118	YER125w	505	809	PF00632	5.90E-182	0.782564	0
YDL143w	31	527	PF00118	3.00E-167	YKR026c	12	294	PF01008	5.40E-118	0.947321	0
YDL145c	343	787	PF04053	8.00E-253	YCR012w	3	412	PF00162	1.40E-292	0.872514	0
YDL145c	343	787	PF04053	8.00E-253	YDR238c	682	961	PF07718	5.60E-155	0.983597	0
YDL145c	812	1200	PF06957	1.10E-30	YGL137w	325	794	PF04053	1.20E-254	0.973047	0
YDL145c	343	787	PF04053	8.00E-253	YNL287w	19	560	PF01602	1.90E-161	0.969671	0
YDL145c	812	1200	PF06957	1.10E-30	YPL010w	8	159	PF01217	8.20E-09	0.978099	0
YDL164c	146	325	PF04675	1.10E-97	YBR088c	1	125	PF00705	1.10E-78	0.922852	0
YDL164c	393	598	PF01068	2.50E-98	YEL030w	27	407	PF06723	1.30E-05	0.896409	0
YDL164c	393	598	PF01068	2.50E-98	YLR276c	292	418	PF00271	2.70E-05	0.950277	0
YDL171c	512	808	PF04898	2.20E-193	YBL087c	16	137	PF00238	2.50E-53	0.884576	0
YDL171c	512	808	PF04898	2.20E-193	YDL047w	46	242	PF00149	2.20E-40	0.678082	0
YDL171c	1784	2097	PF07992	2.20E-11	YPR086w	133	203	PF00382	1.30E-35	0.938101	0
YDL188c	118	313	PF00149	6.90E-40	YBL041w	25	226	PF00227	5.10E-40	0.60293	0
YDL188c	118	313	PF00149	6.90E-40	YDR190c	126	449	PF06068	4.80E-235	0.584553	0
YDL188c	118	313	PF00149	6.90E-40	YER012w	1	184	PF00227	3.20E-57	0.575037	0
YDL188c	118	313	PF00149	6.90E-40	YER094c	7	190	PF00227	5.60E-52	0.62046	0
YDL188c	118	313	PF00149	6.90E-40	YFR050c	38	233	PF00227	2.20E-21	0.532796	0
YDL188c	118	313	PF00149	6.90E-40	YGL011c	40	228	PF00227	7.10E-48	0.690056	0
YDL188c	118	313	PF00149	6.90E-40	YGR135w	29	216	PF00227	1.60E-73	0.499583	0
YDL188c	118	313	PF00149	6.90E-40	YJR009c	2	150	PF00044	8.20E-98	0.453549	0
YDL188c	118	313	PF00149	6.90E-40	YML092c	28	214	PF00227	1.90E-72	0.498166	0
YDL188c	118	313	PF00149	6.90E-40	YMR314w	29	216	PF00227	9.70E-52	0.61285	0
YDL188c	118	313	PF00149	6.90E-40	YOL005c	29	103	PF01193	7.80E-20	0.513926	0
YDL188c	118	313	PF00149	6.90E-40	YOL038w	27	215	PF00227	5.80E-70	0.481441	0
YDL188c	118	313	PF00149	6.90E-40	YOR157c	26	207	PF00227	8.90E-68	0.577107	0
YDL188c	118	313	PF00149	6.90E-40	YPR010c	698	1065	PF00562	1.60E-179	0.51444	0
YDL188c	118	313	PF00149	6.90E-40	YPR103w	72	255	PF00227	1.50E-66	0.485511	0
YDL192w	4	177	PF00025	4.30E-126	YDL137w	4	177	PF00025	2.90E-125	0.999971	1
YDL192w	4	177	PF00025	4.30E-126	YNL287w	19	560	PF01602	1.90E-161	0.36637	0
YDL192w	4	177	PF00025	4.30E-126	YPR110c	48	330	PF01193	8.90E-20	0.727796	0
YDL192w	4	177	PF00025	4.30E-126	YPR176c	206	249	PF00432	5.90E-15	0.542683	0
YDL219w	28	148	PF02580	1.50E-71	YDL047w	46	242	PF00149	2.20E-40	0.879672	0
YDL229w	7	391	PF06723	0.00065	YNL064c	228	350	PF01556	5.40E-15	0.629497	0
YDL236w	24	276	PF00702	6.40E-20	YNL189w	9	110	PF01749	1.10E-45	0.958621	0
YDL245c	79	484	PF07690	1.70E-24	YHR096c	93	509	PF07690	1.20E-31	0.985558	0
YDL245c	79	484	PF07690	1.70E-24	YJR160c	104	517	PF07690	0.0005	0.934402	0
YDL246c	30	141	PF08240	2.50E-42	YDL246c	30	141	PF08240	2.50E-42	1	1
YDL246c	170	316	PF00107	2.40E-40	YDL246c	170	316	PF00107	2.40E-40	1	1
YDR012w	18	261	PF00573	5.20E-142	YER081w	61	381	PF00389	1.40E-39	0.906418	0
YDR021w	47	216	PF00270	4.00E-60	YJR007w	125	237	PF07541	1.40E-67	0.737761	0
YDR023w	1	112	PF02403	7.10E-36	YBL036c	21	250	PF01168	3.80E-08	0.931749	0
YDR032c	6	135	PF00258	4.00E-23	YCR004c	6	137	PF00258	4.80E-23	0.977849	1
YDR032c	6	135	PF00258	4.00E-23	YDR032c	6	135	PF00258	4.00E-23	1	1
YDR044w	9	327	PF01218	9.00E-161	YNL189w	9	110	PF01749	1.10E-45	0.880468	0
YDR045c	2	55	PF02150	1.20E-25	YOR116c	10	368	PF04997	6.30E-106	0.938008	0
YDR046c	94	562	PF00324	1.00E-171	YBR159w	63	242	PF00106	2.50E-08	0.91098	0
YDR046c	94	562	PF00324	1.00E-171	YGR060w	47	265	PF01598	3.70E-106	0.915126	0
YDR046c	94	562	PF00324	1.00E-171	YLR372w	10	321	PF01151	3.70E-232	0.94653	0
YDR062w	155	515	PF00155	1.90E-95	YDR502c	117	239	PF02772	2.20E-90	0.942314	0
YDR062w	155	515	PF00155	1.90E-95	YIL094c	25	367	PF00180	9.70E-178	0.836665	0
YDR062w	155	515	PF00155	1.90E-95	YJR077c	16	105	PF00153	1.50E-28	0.877843	0
YDR062w	155	515	PF00155	1.90E-95	YLR180w	115	237	PF02772	1.00E-94	0.943842	0
YDR075w	44	239	PF00149	1.10E-40	YDR212w	36	549	PF00118	8.70E-163	0.692696	0
YDR091c	103	297	PF00005	6.80E-18	YPR041w	1	129	PF01873	2.90E-80	0.944208	0
YDR097c	923	1169	PF00488	1.10E-89	YKR001c	613	704	PF02212	5.70E-41	0.972403	0
YDR097c	312	427	PF01624	7.10E-54	YPL235w	122	433	PF06068	1.90E-220	0.964055	0
YDR099w	5	241	PF00244	2.30E-151	YBR001c	192	750	PF01204	8.20E-278	0.891849	0
YDR099w	5	241	PF00244	2.30E-151	YDR062w	155	515	PF00155	1.90E-95	0.751933	0
YDR099w	5	241	PF00244	2.30E-151	YDR099w	5	241	PF00244	2.30E-151	1	1
YDR099w	5	241	PF00244	2.30E-151	YGR123c	120	234	PF08321	5.80E-07	0.734496	0
YDR127w	1311	1393	PF08501	1.80E-32	YJL008c	38	549	PF00118	9.90E-164	0.979215	0
YDR127w	17	367	PF01761	1.10E-144	YOR136w	38	365	PF00180	1.70E-159	0.95761	0
YDR127w	897	1064	PF01202	1.70E-55	YPL235w	122	433	PF06068	1.90E-220	0.947078	0
YDR129c	412	521	PF00307	7.90E-29	YDR353w	5	294	PF07992	2.40E-46	0.909962	0
YDR139c	6	74	PF00240	4.80E-25	YDR328c	4	99	PF03931	1.90E-07	0.570641	0
YDR139c	6	74	PF00240	4.80E-25	YLR306w	31	172	PF00179	6.10E-51	0.640541	0
YDR148c	74	147	PF00364	1.00E-15	YDR148c	74	147	PF00364	1.00E-15	1	0
YDR148c	232	462	PF00198	6.70E-131	YDR148c	232	462	PF00198	6.70E-131	1	1
YDR148c	232	462	PF00198	6.70E-131	YDR510w	27	96	PF00240	2.40E-13	0.908532	0
YDR148c	74	147	PF00364	1.00E-15	YFL018c	206	305	PF00070	4.30E-34	0.939291	0
YDR148c	74	147	PF00364	1.00E-15	YLR180w	115	237	PF02772	1.00E-94	0.953613	0
YDR148c	232	462	PF00198	6.70E-131	YNL189w	9	110	PF01749	1.10E-45	0.949315	0
YDR155c	3	162	PF00160	1.20E-116	YBR009c	25	94	PF00125	4.80E-17	0.364117	0
YDR155c	3	162	PF00160	1.20E-116	YDR510w	27	96	PF00240	2.40E-13	0.800491	0
YDR155c	3	162	PF00160	1.20E-116	YER081w	164	349	PF02826	3.10E-72	0.907935	0
YDR155c	3	162	PF00160	1.20E-116	YGL194c	27	340	PF00850	1.20E-183	0.712938	0
YDR155c	3	162	PF00160	1.20E-116	YKL103c	59	501	PF02127	3.80E-263	0.744427	0
YDR155c	3	162	PF00160	1.20E-116	YNL244c	20	101	PF01253	6.80E-42	0.792188	0
YDR155c	3	162	PF00160	1.20E-116	YPL235w	122	433	PF06068	1.90E-220	0.563227	0
YDR172w	258	483	PF00009	7.40E-92	YBR143c	277	413	PF03465	2.50E-61	0.933384	0
YDR172w	258	483	PF00009	7.40E-92	YDR172w	258	483	PF00009	7.40E-92	1	1
YDR172w	502	570	PF03144	4.90E-11	YDR172w	502	570	PF03144	4.90E-11	1	1
YDR172w	576	684	PF03143	2.30E-39	YDR172w	576	684	PF03143	2.30E-39	1	1
YDR188w	29	538	PF00118	4.60E-158	YDL047w	46	242	PF00149	2.20E-40	0.707284	0
YDR188w	29	538	PF00118	4.60E-158	YGL137w	325	794	PF04053	1.20E-254	0.942909	0
YDR190c	126	449	PF06068	4.80E-235	YPL235w	70	412	PF00004	0.00044	0.545168	0
YDR212w	36	549	PF00118	8.70E-163	YJL164c	87	328	PF07714	5.80E-19	0.837855	0
YDR224c	35	105	PF00125	1.00E-24	YGL058w	8	145	PF00179	1.90E-77	0.505188	0
YDR224c	35	105	PF00125	1.00E-24	YKL103c	59	501	PF02127	3.80E-263	0.87709	0
YDR224c	35	105	PF00125	1.00E-24	YPR041w	318	403	PF02020	1.60E-36	0.929819	0
YDR225w	19	92	PF00125	2.00E-30	YDR224c	35	105	PF00125	1.00E-24	0.78745	1
YDR225w	19	92	PF00125	2.00E-30	YGR103w	4	285	PF06732	1.20E-197	0.41604	0
YDR225w	19	92	PF00125	2.00E-30	YHL001w	54	130	PF01929	1.80E-45	0.514412	0
YDR225w	19	92	PF00125	2.00E-30	YKR048c	93	366	PF00956	9.30E-158	0.313155	0
YDR225w	19	92	PF00125	2.00E-30	YOR116c	742	848	PF05000	6.20E-45	0.482787	0
YDR225w	19	92	PF00125	2.00E-30	YOR207c	1058	1144	PF04560	5.20E-47	0.430723	0
YDR226w	11	198	PF00406	2.10E-97	YBL036c	21	250	PF01168	3.80E-08	0.856139	0
YDR226w	11	198	PF00406	2.10E-97	YDR177w	6	145	PF00179	1.20E-64	0.866088	0
YDR226w	11	198	PF00406	2.10E-97	YOR176w	38	357	PF00762	5.50E-174	0.93667	0
YDR226w	11	198	PF00406	2.10E-97	YPL031c	7	258	PF07714	3.50E-18	0.813632	0
YDR238c	682	961	PF07718	5.60E-155	YGL137w	325	794	PF04053	1.20E-254	0.975054	0
YDR256c	23	410	PF00199	1.00E-277	YMR314w	29	216	PF00227	9.70E-52	0.833534	0
YDR256c	23	410	PF00199	1.00E-277	YNL189w	9	110	PF01749	1.10E-45	0.735524	0
YDR280w	32	165	PF01138	4.60E-48	YNL189w	9	110	PF01749	1.10E-45	0.931665	0
YDR297w	49	277	PF01598	4.10E-89	YBR159w	63	242	PF00106	2.50E-08	0.948462	0
YDR297w	49	277	PF01598	4.10E-89	YLL028w	152	544	PF07690	9.70E-42	0.948984	0
YDR297w	49	277	PF01598	4.10E-89	YLR372w	10	321	PF01151	3.70E-232	0.941187	0
YDR328c	4	99	PF03931	1.90E-07	YBR127c	397	500	PF00306	1.80E-24	0.911862	0
YDR328c	116	193	PF01466	1.20E-51	YEL051w	13	211	PF01813	5.90E-98	0.878649	0
YDR342c	72	488	PF07690	3.70E-29	YBL036c	21	250	PF01168	3.80E-08	0.956096	0
YDR342c	72	488	PF07690	3.70E-29	YLR340w	3	105	PF00466	2.60E-49	0.951126	0
YDR342c	72	488	PF07690	3.70E-29	YNL323w	93	407	PF03381	1.20E-201	0.939934	0
YDR343c	72	488	PF07690	3.70E-29	YBL036c	21	250	PF01168	3.80E-08	0.956096	0
YDR343c	72	488	PF07690	3.70E-29	YER081w	61	381	PF00389	1.40E-39	0.964545	0
YDR343c	72	488	PF07690	3.70E-29	YER125w	505	809	PF00632	5.90E-182	0.925851	0
YDR343c	72	488	PF07690	3.70E-29	YGR040w	13	313	PF00069	3.30E-95	0.685304	0
YDR353w	156	249	PF00070	2.80E-29	YOL128c	41	329	PF00069	2.10E-62	0.756139	0
YDR378c	14	83	PF01423	2.20E-18	YLR275w	32	106	PF01423	2.00E-15	0.866245	1
YDR378c	14	83	PF01423	2.20E-18	YNL147w	20	96	PF01423	4.90E-22	0.804147	1
YDR382w	17	109	PF00428	1.30E-36	YBR006w	27	488	PF00171	2.00E-205	0.791924	0
YDR385w	723	811	PF00679	1.20E-36	YDR328c	4	99	PF03931	1.90E-07	0.690041	0
YDR404c	1	79	PF03876	1.20E-38	YDL140c	510	669	PF04983	1.50E-69	0.971808	0
YDR404c	1	79	PF03876	1.20E-38	YGR063c	2	99	PF06093	1.60E-66	0.925248	0
YDR404c	1	79	PF03876	1.20E-38	YOR224c	7	146	PF03870	3.90E-92	0.961401	0
YDR430c	479	723	PF08367	1.80E-122	YBR221c	231	355	PF02780	8.40E-56	0.949602	0
YDR430c	221	407	PF05193	1.60E-28	YER178w	86	382	PF00676	3.30E-184	0.890631	0
YDR430c	221	407	PF05193	1.60E-28	YFL018c	28	321	PF01134	0.00073	0.967531	0
YDR430c	221	407	PF05193	1.60E-28	YNL071w	248	482	PF00198	4.30E-108	0.935623	0
YDR487c	5	208	PF00926	5.80E-135	YNL189w	9	110	PF01749	1.10E-45	0.919764	0
YDR497c	93	505	PF07690	1.80E-27	YLL028w	152	544	PF07690	9.70E-42	0.914656	0
YDR508c	153	621	PF00324	5.70E-166	YBR159w	63	242	PF00106	2.50E-08	0.939103	0
YDR508c	153	621	PF00324	5.70E-166	YMR279c	76	487	PF07690	2.00E-27	0.953023	0
YDR510w	27	96	PF00240	2.40E-13	YDL064w	8	152	PF00179	2.00E-69	0.646759	0
YDR510w	27	96	PF00240	2.40E-13	YDR510w	27	96	PF00240	2.40E-13	1	1
YDR510w	27	96	PF00240	2.40E-13	YNL088w	55	204	PF02518	1.40E-15	0.848632	0
YDR510w	27	96	PF00240	2.40E-13	YNL189w	9	110	PF01749	1.10E-45	0.755373	0
YDR516c	243	500	PF03727	1.10E-124	YCL040w	243	500	PF03727	8.50E-148	0.999243	1
YDR529c	15	119	PF02271	1.10E-68	YBR082c	6	143	PF00179	3.90E-80	0.50018	0
YEL011w	209	589	PF00128	1.30E-07	YPR086w	133	203	PF00382	1.30E-35	0.861304	0
YEL021w	30	251	PF00215	1.30E-89	YEL021w	30	251	PF00215	1.30E-89	1	1
YEL027w	12	77	PF00137	8.70E-21	YBR298c	102	561	PF00083	8.60E-144	0.699544	0
YEL027w	12	77	PF00137	8.70E-21	YLL028w	152	544	PF07690	9.70E-42	0.541017	0
YEL027w	12	77	PF00137	8.70E-21	YLR034c	31	408	PF01566	2.00E-226	0.770609	0
YEL034w	84	151	PF01287	1.10E-38	YLR340w	222	311	PF00428	2.60E-30	0.837336	0
YEL046c	16	303	PF01212	5.50E-135	YEL046c	16	303	PF01212	5.50E-135	1	1
YEL046c	16	303	PF01212	5.50E-135	YNL189w	9	110	PF01749	1.10E-45	0.970587	0
YEL054c	75	143	PF00298	5.60E-29	YDL081c	20	105	PF00428	6.50E-35	0.867395	0
YEL054c	75	143	PF00298	5.60E-29	YDR382w	17	109	PF00428	1.30E-36	0.850745	0
YEL054c	75	143	PF00298	5.60E-29	YOL039w	16	105	PF00428	6.80E-32	0.856575	0
YEL063c	92	557	PF00324	8.30E-189	YBL040c	1	209	PF00810	1.40E-157	0.905131	0
YEL063c	92	557	PF00324	8.30E-189	YBR159w	63	242	PF00106	2.50E-08	0.921873	0
YEL063c	92	557	PF00324	8.30E-189	YCR034w	10	313	PF01151	7.70E-229	0.925666	0
YEL063c	92	557	PF00324	8.30E-189	YFL041w	26	150	PF07732	1.80E-52	0.965524	0
YEL063c	92	557	PF00324	8.30E-189	YJL196c	7	309	PF01151	1.70E-227	0.914412	0
YEL063c	92	557	PF00324	8.30E-189	YLR343w	20	344	PF03198	9.60E-238	0.918178	0
YEL063c	92	557	PF00324	8.30E-189	YLR372w	10	321	PF01151	3.70E-232	0.910386	0
YEL063c	92	557	PF00324	8.30E-189	YOR161c	187	539	PF04515	2.30E-152	0.971086	0
YEL063c	92	557	PF00324	8.30E-189	YPL234c	96	161	PF00137	5.40E-24	0.907556	0
YEL069c	76	481	PF07690	6.20E-27	YPR110c	48	330	PF01193	8.90E-20	0.975212	0
YEL071w	243	495	PF02913	1.40E-81	YPR165w	12	185	PF00071	6.20E-87	0.633138	0
YER009w	8	121	PF02136	1.20E-46	YNL189w	9	110	PF01749	1.10E-45	0.839762	0
YER012w	1	184	PF00227	3.20E-57	YBL041w	25	226	PF00227	5.10E-40	0.982626	1
YER012w	1	184	PF00227	3.20E-57	YER094c	7	190	PF00227	5.60E-52	0.960061	1
YER012w	1	184	PF00227	3.20E-57	YFR050c	38	233	PF00227	2.20E-21	0.962879	1
YER012w	1	184	PF00227	3.20E-57	YGL011c	40	228	PF00227	7.10E-48	0.944294	1
YER012w	1	184	PF00227	3.20E-57	YGR135w	29	216	PF00227	1.60E-73	0.814694	1
YER012w	1	184	PF00227	3.20E-57	YJL001w	16	197	PF00227	3.70E-65	0.957508	1
YER012w	1	184	PF00227	3.20E-57	YML092c	28	214	PF00227	1.90E-72	0.798269	1
YER012w	1	184	PF00227	3.20E-57	YMR314w	29	216	PF00227	9.70E-52	0.967412	1
YER012w	1	184	PF00227	3.20E-57	YOL038w	27	215	PF00227	5.80E-70	0.706616	1
YER012w	1	184	PF00227	3.20E-57	YPR103w	72	255	PF00227	1.50E-66	0.911584	1
YER017c	146	297	PF06480	1.70E-36	YBR247c	143	476	PF05291	1.30E-267	0.879296	0
YER017c	524	728	PF01434	4.20E-125	YFL018c	28	352	PF07992	6.20E-63	0.87481	0
YER017c	146	297	PF06480	1.70E-36	YMR089c	204	357	PF06480	8.80E-40	0.766966	0
YER020w	108	399	PF00025	0.00018	YGL245w	509	681	PF03950	9.60E-73	0.922865	0
YER020w	108	399	PF00025	0.00018	YNL037c	30	353	PF00180	7.50E-87	0.789057	0
YER020w	108	399	PF00025	0.00018	YPL036w	86	174	PF00690	3.40E-25	0.846122	0
YER025w	98	314	PF00009	2.30E-40	YBL026w	5	72	PF01423	1.40E-19	0.908041	0
YER025w	98	314	PF00009	2.30E-40	YER146w	10	83	PF01423	2.20E-20	0.656155	0
YER025w	98	314	PF00009	2.30E-40	YJR007w	125	237	PF07541	1.40E-67	0.930557	0
YER025w	98	314	PF00009	2.30E-40	YKR026c	12	294	PF01008	5.40E-118	0.934297	0
YER025w	98	314	PF00009	2.30E-40	YPR110c	48	330	PF01193	8.90E-20	0.921472	0
YER026c	117	267	PF01066	4.00E-33	YDR297w	49	277	PF01598	4.10E-89	0.971909	0
YER026c	117	267	PF01066	4.00E-33	YGR060w	47	265	PF01598	3.70E-106	0.967345	0
YER026c	117	267	PF01066	4.00E-33	YMR058w	29	147	PF07731	0.00048	0.983146	0
YER036c	107	299	PF00005	2.30E-49	YNL142w	33	444	PF00909	8.20E-198	0.838445	0
YER043c	6	448	PF05221	2.50E-221	YKL161c	23	318	PF00069	7.70E-71	0.552925	0
YER057c	10	127	PF01042	6.50E-63	YNL189w	9	110	PF01749	1.10E-45	0.796174	0
YER073w	52	511	PF00171	9.60E-257	YPR086w	133	203	PF00382	1.30E-35	0.907022	0
YER081w	61	381	PF00389	1.40E-39	YBR143c	277	413	PF03465	2.50E-61	0.936825	0
YER081w	61	381	PF00389	1.40E-39	YCR072c	134	172	PF00400	5.90E-07	0.952353	0
YER081w	61	381	PF00389	1.40E-39	YDL168w	196	342	PF00107	5.00E-32	0.911998	0
YER081w	61	381	PF00389	1.40E-39	YDR105c	17	467	PF03348	6.40E-293	0.943076	0
YER081w	61	381	PF00389	1.40E-39	YER078c	251	482	PF00557	3.20E-107	0.927867	0
YER081w	61	381	PF00389	1.40E-39	YER081w	61	381	PF00389	1.40E-39	1	1
YER081w	164	349	PF02826	3.10E-72	YER081w	164	349	PF02826	3.10E-72	1	1
YER081w	61	381	PF00389	1.40E-39	YFL037w	246	383	PF03953	2.00E-72	0.913189	0
YER081w	61	381	PF00389	1.40E-39	YGR020c	8	111	PF01990	2.70E-35	0.869884	0
YER081w	164	349	PF02826	3.10E-72	YPL234c	96	161	PF00137	5.40E-24	0.877085	0
YER081w	61	381	PF00389	1.40E-39	YPR016c	3	204	PF01912	2.40E-136	0.94692	0
YER086w	72	371	PF00291	5.90E-96	YER086w	72	371	PF00291	5.90E-96	1	1
YER086w	383	481	PF00585	3.10E-07	YER086w	383	481	PF00585	3.10E-07	1	1
YER086w	485	574	PF00585	3.40E-45	YER086w	485	574	PF00585	3.40E-45	1	1
YER086w	72	371	PF00291	5.90E-96	YKL081w	104	196	PF00043	7.30E-17	0.957656	0
YER094c	7	190	PF00227	5.60E-52	YGL011c	40	228	PF00227	7.10E-48	0.937577	1
YER126c	1	238	PF01201	6.30E-95	YCR072c	311	387	PF00400	5.30E-05	0.942113	0
YER126c	1	238	PF01201	6.30E-95	YKR081c	31	238	PF04427	1.90E-56	0.971053	0
YER126c	1	238	PF01201	6.30E-95	YPR016c	3	204	PF01912	2.40E-136	0.856728	0
YER133w	56	251	PF00149	4.00E-43	YGR103w	4	285	PF06732	1.20E-197	0.706601	0
YER133w	56	251	PF00149	4.00E-43	YJR007w	13	88	PF00575	7.50E-16	0.723954	0
YER133w	56	251	PF00149	4.00E-43	YKL085w	18	163	PF00056	7.70E-70	0.626668	0
YER133w	56	251	PF00149	4.00E-43	YKR002w	4	352	PF04928	1.50E-173	0.354063	0
YER133w	56	251	PF00149	4.00E-43	YLR134w	200	348	PF00205	2.70E-49	0.409457	0
YER146w	10	83	PF01423	2.20E-20	YCR024c	133	487	PF00152	4.00E-72	0.883096	0
YER146w	10	83	PF01423	2.20E-20	YDR378c	14	83	PF01423	2.20E-18	0.979358	1
YER146w	10	83	PF01423	2.20E-20	YER131w	1	113	PF01283	1.30E-82	0.634338	0
YER146w	10	83	PF01423	2.20E-20	YER146w	10	83	PF01423	2.20E-20	1	1
YER146w	10	83	PF01423	2.20E-20	YIL048w	497	903	PF00702	0.00092	0.758921	0
YER146w	10	83	PF01423	2.20E-20	YLR058c	40	357	PF00282	0.00014	0.479739	0
YER146w	10	83	PF01423	2.20E-20	YLR275w	32	106	PF01423	2.00E-15	0.873926	1
YER146w	10	83	PF01423	2.20E-20	YNL147w	20	96	PF01423	4.90E-22	0.864287	1
YER146w	10	83	PF01423	2.20E-20	YPL090c	1	127	PF01092	8.70E-85	0.731559	0
YER146w	10	83	PF01423	2.20E-20	YPL152w	2	305	PF03095	2.40E-193	0.751133	0
YER146w	10	83	PF01423	2.20E-20	YPR010c	652	693	PF04567	8.40E-08	0.530435	0
YER148w	152	238	PF00352	4.10E-44	YKL058w	5	53	PF02268	1.50E-34	0.733664	0
YER148w	62	147	PF00352	5.20E-38	YKR001c	613	704	PF02212	5.70E-41	0.888555	0
YER148w	152	238	PF00352	4.10E-44	YPR086w	22	66	PF08271	2.50E-17	0.863106	0
YER156c	11	338	PF03690	2.40E-245	YFL038c	1	169	PF00025	4.70E-06	0.515765	0
YER170w	19	209	PF00406	1.10E-52	YKL002w	20	191	PF03357	1.30E-35	0.772321	0
YER177w	5	241	PF00244	2.40E-151	YDR062w	155	515	PF00155	1.90E-95	0.744732	0
YER177w	5	241	PF00244	2.40E-151	YDR099w	5	241	PF00244	2.30E-151	0.999704	1
YER177w	5	241	PF00244	2.40E-151	YGL115w	193	318	PF00571	3.90E-21	0.69678	0
YER177w	5	241	PF00244	2.40E-151	YNL189w	9	110	PF01749	1.10E-45	0.75834	0
YER178w	86	382	PF00676	3.30E-184	YBR221c	39	215	PF02779	7.20E-73	0.931449	1
YER178w	86	382	PF00676	3.30E-184	YGL137w	325	794	PF04053	1.20E-254	0.8614	0
YFL005w	21	136	PF08477	3.00E-21	YFL038c	10	171	PF00071	4.70E-102	0.770305	0
YFL016c	61	122	PF00226	2.60E-33	YFL016c	61	122	PF00226	2.60E-33	1	0
YFL016c	218	300	PF00684	2.50E-14	YFL016c	218	300	PF00684	2.50E-14	1	0
YFL016c	313	445	PF01556	7.60E-12	YFL016c	313	445	PF01556	7.60E-12	1	0
YFL016c	61	122	PF00226	2.60E-33	YJR045c	30	413	PF06723	0.00044	0.922875	0
YFL017c	67	149	PF00583	2.30E-21	YBL072c	1	184	PF01201	1.40E-101	0.93731	0
YFL017c	67	149	PF00583	2.30E-21	YNL189w	9	110	PF01749	1.10E-45	0.943761	0
YFL017c	67	149	PF00583	2.30E-21	YOL059w	84	259	PF01210	4.50E-83	0.948813	0
YFL018c	28	352	PF07992	6.20E-63	YBR221c	231	355	PF02780	8.40E-56	0.807822	0
YFL022c	212	492	PF01409	1.80E-154	YKR026c	12	294	PF01008	5.40E-118	0.92219	0
YFL028c	34	225	PF00005	7.40E-25	YFL028c	34	225	PF00005	7.40E-25	1	1
YFL041w	156	305	PF00394	1.00E-53	YLL028w	152	544	PF07690	9.70E-42	0.970641	0
YFL041w	26	150	PF07732	1.80E-52	YML123c	81	507	PF07690	2.50E-21	0.948258	0
YFL041w	156	305	PF00394	1.00E-53	YPR156c	188	616	PF00083	0.00011	0.888811	0
YFL045c	35	254	PF03332	1.20E-179	YLR343w	20	344	PF03198	9.60E-238	0.960419	0
YFL045c	16	251	PF08282	0.00089	YNL189w	9	110	PF01749	1.10E-45	0.835653	0
YFL059w	4	211	PF01680	1.50E-122	YFL059w	4	211	PF01680	1.50E-122	1	0
YFL059w	4	211	PF01680	1.50E-122	YNL189w	9	110	PF01749	1.10E-45	0.940193	0
YFL060c	7	217	PF01174	6.30E-163	YFL059w	4	211	PF01680	1.50E-122	0.970731	0
YFL060c	7	217	PF01174	6.30E-163	YMR096w	6	212	PF01680	6.30E-130	0.977839	0
YFR009w	225	440	PF00005	5.00E-35	YLR058c	40	357	PF00282	0.00014	0.878337	0
YFR047c	26	117	PF02749	2.80E-35	YFR047c	26	117	PF02749	2.80E-35	1	0
YFR047c	119	292	PF01729	1.50E-100	YFR047c	119	292	PF01729	1.50E-100	1	1
YFR047c	26	117	PF02749	2.80E-35	YNL189w	372	412	PF00514	4.70E-13	0.855561	0
YFR050c	38	233	PF00227	2.20E-21	YGL011c	40	228	PF00227	7.10E-48	0.945335	1
YFR050c	38	233	PF00227	2.20E-21	YML092c	28	214	PF00227	1.90E-72	0.67814	1
YFR053c	21	223	PF00349	1.20E-137	YER081w	61	381	PF00389	1.40E-39	0.959708	0
YGL006w	960	1123	PF00689	7.50E-07	YDR339c	87	185	PF04900	3.80E-68	0.834338	0
YGL008c	61	145	PF00690	2.40E-27	YHR030c	23	318	PF00069	3.20E-85	0.726859	0
YGL019w	26	233	PF01214	4.10E-170	YBR009c	25	94	PF00125	4.80E-17	0.402127	0
YGL019w	26	233	PF01214	4.10E-170	YGL019w	26	233	PF01214	4.10E-170	1	1
YGL019w	26	233	PF01214	4.10E-170	YGL115w	193	318	PF00571	3.90E-21	0.863774	0
YGL019w	26	233	PF01214	4.10E-170	YIL118w	18	212	PF00071	3.70E-88	0.781529	0
YGL019w	26	233	PF01214	4.10E-170	YNL088w	250	418	PF00204	1.80E-49	0.903665	0
YGL019w	26	233	PF01214	4.10E-170	YOR039w	38	213	PF01214	8.20E-140	0.943245	1
YGL040c	13	338	PF00490	3.00E-224	YGL040c	13	338	PF00490	3.00E-224	1	1
YGL040c	13	338	PF00490	3.00E-224	YNL189w	9	110	PF01749	1.10E-45	0.858525	0
YGL054c	2	125	PF03311	1.10E-77	YLR372w	10	321	PF01151	3.70E-232	0.90263	0
YGL055w	138	358	PF00487	1.20E-78	YBR159w	63	242	PF00106	2.50E-08	0.929447	0
YGL062w	851	1059	PF02436	4.20E-133	YPR110c	48	330	PF01193	8.90E-20	0.95907	0
YGL087c	9	130	PF00179	2.10E-06	YDR092w	7	144	PF00179	1.70E-73	0.51427	1
YGL087c	9	130	PF00179	2.10E-06	YER125w	505	809	PF00632	5.90E-182	0.700707	1
YGL120c	621	725	PF07717	2.20E-31	YPR182w	17	83	PF01423	2.20E-21	0.753756	0
YGL130w	28	249	PF01068	0.00054	YBR221c	39	215	PF02779	7.20E-73	0.966166	0
YGL130w	252	399	PF03919	1.70E-26	YDL140c	873	1056	PF04992	4.00E-97	0.963014	0
YGL130w	252	399	PF03919	1.70E-26	YGL120c	621	725	PF07717	2.20E-31	0.796543	0
YGL135w	1	213	PF00687	3.40E-46	YER081w	61	381	PF00389	1.40E-39	0.957864	0
YGL137w	325	794	PF04053	1.20E-254	YBR187w	42	117	PF01169	2.20E-39	0.97608	0
YGL137w	325	794	PF04053	1.20E-254	YDR212w	36	549	PF00118	8.70E-163	0.919297	0
YGL137w	325	794	PF04053	1.20E-254	YKL081w	104	196	PF00043	7.30E-17	0.934844	0
YGL137w	325	794	PF04053	1.20E-254	YKL166c	88	342	PF00069	2.50E-100	0.864496	0
YGL156w	670	1080	PF07748	1.20E-129	YPR110c	48	330	PF01193	8.90E-20	0.970122	0
YGL206c	1134	1275	PF00637	2.10E-44	YBR169c	4	644	PF00012	1.40E-214	0.911455	0
YGL206c	839	978	PF00637	3.30E-42	YIL094c	25	367	PF00180	9.70E-178	0.903823	0
YGL206c	1134	1275	PF00637	2.10E-44	YKR026c	12	294	PF01008	5.40E-118	0.886649	0
YGL206c	1134	1275	PF00637	2.10E-44	YPL106c	4	644	PF00012	1.50E-248	0.890959	0
YGL221c	17	280	PF01784	2.30E-83	YGL221c	17	280	PF01784	2.30E-83	1	1
YGL221c	17	280	PF01784	2.30E-83	YNL189w	9	110	PF01749	1.10E-45	0.898897	0
YGL234w	624	794	PF02769	8.60E-53	YBL026w	5	72	PF01423	1.40E-19	0.895423	0
YGL234w	345	440	PF02843	1.30E-54	YJR068w	261	350	PF08542	5.80E-27	0.917835	0
YGL234w	448	612	PF00586	1.10E-66	YKL166c	88	329	PF07714	4.50E-19	0.940607	0
YGL234w	345	440	PF02843	1.30E-54	YOL094c	229	316	PF08542	1.90E-33	0.94671	0
YGL238w	23	96	PF03810	1.80E-22	YLR293c	14	172	PF00071	1.20E-72	0.866688	1
YGL238w	23	96	PF03810	1.80E-22	YNL189w	372	412	PF00514	4.70E-13	0.814625	0
YGL253w	21	223	PF00349	1.10E-139	YGL253w	21	223	PF00349	1.10E-139	1	1
YGL253w	225	473	PF03727	5.10E-163	YGL253w	225	473	PF03727	5.10E-163	1	1
YGR020c	8	111	PF01990	2.70E-35	YEL051w	13	211	PF01813	5.90E-98	0.923643	0
YGR024c	1	237	PF04446	2.30E-184	YGR024c	1	237	PF04446	2.30E-184	1	0
YGR040w	13	313	PF00069	3.30E-95	YBL022c	181	478	PF02190	2.50E-166	0.839005	0
YGR040w	13	313	PF00069	3.30E-95	YDR190c	126	449	PF06068	4.80E-235	0.681459	0
YGR040w	13	313	PF00069	3.30E-95	YGL008c	146	368	PF00122	1.60E-86	0.730719	0
YGR040w	13	313	PF00069	3.30E-95	YGL062w	851	1059	PF02436	4.20E-133	0.826408	0
YGR040w	13	313	PF00069	3.30E-95	YGL245w	509	681	PF03950	9.60E-73	0.779298	0
YGR040w	13	313	PF00069	3.30E-95	YJR072c	8	258	PF03029	4.50E-116	0.884108	0
YGR040w	13	313	PF00069	3.30E-95	YKR048c	93	366	PF00956	9.30E-158	0.910912	0
YGR040w	13	313	PF00069	3.30E-95	YLL039c	234	302	PF00240	5.60E-38	0.778215	0
YGR040w	13	313	PF00069	3.30E-95	YML123c	81	507	PF07690	2.50E-21	0.820486	0
YGR040w	13	313	PF00069	3.30E-95	YOL033w	44	365	PF00749	6.40E-181	0.785583	0
YGR040w	13	313	PF00069	3.30E-95	YPR010c	40	468	PF04563	2.30E-84	0.788234	0
YGR048w	13	199	PF03152	1.30E-132	YHR039c-a	1	106	PF03179	4.50E-55	0.898668	0
YGR060w	47	265	PF01598	3.70E-106	YBR159w	63	242	PF00106	2.50E-08	0.943083	0
YGR060w	47	265	PF01598	3.70E-106	YDR343c	72	488	PF07690	3.70E-29	0.982852	0
YGR060w	47	265	PF01598	3.70E-106	YGL001c	6	316	PF04321	0.00066	0.957315	0
YGR060w	47	265	PF01598	3.70E-106	YKL008c	191	400	PF03798	3.30E-106	0.946872	0
YGR060w	47	265	PF01598	3.70E-106	YLL028w	152	544	PF07690	9.70E-42	0.954898	0
YGR060w	47	265	PF01598	3.70E-106	YLR343w	20	344	PF03198	9.60E-238	0.956457	0
YGR060w	47	265	PF01598	3.70E-106	YLR372w	10	321	PF01151	3.70E-232	0.930471	0
YGR060w	47	265	PF01598	3.70E-106	YPR028w	44	148	PF03134	1.80E-53	0.961452	0
YGR078c	48	179	PF02996	3.90E-36	YLR200w	2	107	PF01920	1.70E-33	0.976695	1
YGR078c	48	179	PF02996	3.90E-36	YLR212c	48	246	PF00091	8.00E-70	0.760238	0
YGR087c	387	538	PF02775	1.70E-08	YHR030c	23	318	PF00069	3.20E-85	0.672516	0
YGR088w	16	421	PF00199	4.80E-176	YNL189w	9	110	PF01749	1.10E-45	0.767461	0
YGR103w	4	285	PF06732	1.20E-197	YFR031c-a	96	231	PF03947	6.10E-64	0.968202	0
YGR103w	4	285	PF06732	1.20E-197	YHR066w	26	343	PF04427	2.30E-78	0.984108	0
YGR103w	4	285	PF06732	1.20E-197	YKR081c	31	238	PF04427	1.90E-56	0.977216	0
YGR103w	4	285	PF06732	1.20E-197	YNL189w	9	110	PF01749	1.10E-45	0.875065	0
YGR103w	4	285	PF06732	1.20E-197	YPR016c	3	204	PF01912	2.40E-136	0.892034	0
YGR103w	4	285	PF06732	1.20E-197	YPR041w	1	129	PF01873	2.90E-80	0.967087	0
YGR133w	21	174	PF00179	7.70E-55	YGR133w	21	174	PF00179	7.70E-55	1	1
YGR135w	29	216	PF00227	1.60E-73	YGL011c	40	228	PF00227	7.10E-48	0.93446	1
YGR135w	29	216	PF00227	1.60E-73	YNL244c	20	101	PF01253	6.80E-42	0.837348	0
YGR144w	39	306	PF01946	5.30E-180	YGR144w	39	306	PF01946	5.30E-180	1	0
YGR144w	67	296	PF01266	0.00021	YGR144w	67	296	PF01266	0.00021	1	1
YGR155w	14	320	PF00291	6.70E-114	YBR088c	1	125	PF00705	1.10E-78	0.919288	0
YGR155w	14	320	PF00291	6.70E-114	YGR040w	13	313	PF00069	3.30E-95	0.841094	0
YGR155w	14	320	PF00291	6.70E-114	YJR045c	30	413	PF06723	0.00044	0.776951	0
YGR155w	371	507	PF00571	6.40E-20	YNL189w	9	110	PF01749	1.10E-45	0.853289	0
YHR005c-a	17	83	PF02953	4.00E-30	YBL030c	22	119	PF00153	4.40E-35	0.849774	0
YHR005c-a	17	83	PF02953	4.00E-30	YEL020w-a	12	77	PF02953	3.50E-28	0.939869	0
YHR007c	57	521	PF00067	7.10E-134	YPL274w	81	544	PF00324	2.50E-132	0.90946	0
YHR008c	121	228	PF02777	1.30E-65	YBR061c	21	209	PF01728	8.70E-97	0.908862	0
YHR018c	11	307	PF00206	1.90E-132	YGL137w	325	794	PF04053	1.20E-254	0.788015	0
YHR018c	11	307	PF00206	1.90E-132	YNL189w	9	110	PF01749	1.10E-45	0.817592	0
YHR018c	11	307	PF00206	1.90E-132	YNL244c	20	101	PF01253	6.80E-42	0.866013	0
YHR019c	230	550	PF00152	7.60E-92	YNL244c	20	101	PF01253	6.80E-42	0.947982	0
YHR030c	23	318	PF00069	3.20E-85	YJL138c	46	211	PF00270	1.70E-62	0.563858	0
YHR030c	23	318	PF00069	3.20E-85	YLR262c	1	173	PF00025	1.00E-05	0.44307	0
YHR030c	23	318	PF00069	3.20E-85	YPR054w	38	337	PF00069	1.00E-72	0.602694	1
YHR039c-a	1	106	PF03179	4.50E-55	YBR127c	397	500	PF00306	1.80E-24	0.858839	0
YHR039c-a	1	106	PF03179	4.50E-55	YGR020c	8	111	PF01990	2.70E-35	0.900294	0
YHR042w	261	481	PF00667	5.70E-112	YAL067c	143	522	PF07690	1.20E-14	0.956379	0
YHR068w	45	377	PF01916	1.40E-230	YNL189w	9	110	PF01749	1.10E-45	0.875549	0
YHR074w	6	201	PF00795	1.60E-31	YHR074w	6	201	PF00795	1.60E-31	1	1
YHR074w	343	659	PF02540	3.70E-08	YHR074w	343	659	PF02540	3.70E-08	1	1
YHR075c	144	375	PF00561	9.10E-29	YDL134c	110	305	PF00149	7.10E-40	0.5094	0
YHR075c	144	375	PF00561	9.10E-29	YDL188c	118	313	PF00149	6.90E-40	0.510698	0
YHR088w	96	271	PF04427	5.80E-62	YPR016c	3	204	PF01912	2.40E-136	0.932876	0
YHR094c	72	488	PF07690	4.20E-29	YLR372w	10	321	PF01151	3.70E-232	0.940889	0
YHR096c	93	509	PF07690	1.20E-31	YDL047w	46	242	PF00149	2.20E-40	0.723271	0
YHR096c	93	509	PF07690	1.20E-31	YDL095w	343	520	PF02815	1.10E-93	0.94809	0
YHR107c	31	321	PF00735	1.30E-188	YER091c	439	760	PF01717	1.20E-217	0.703598	0
YHR107c	31	321	PF00735	1.30E-188	YFL045c	16	251	PF08282	0.00089	0.788113	0
YHR107c	31	321	PF00735	1.30E-188	YGL062w	851	1059	PF02436	4.20E-133	0.904636	0
YHR107c	31	321	PF00735	1.30E-188	YGL245w	509	681	PF03950	9.60E-73	0.712344	0
YHR107c	31	321	PF00735	1.30E-188	YHR107c	31	321	PF00735	1.30E-188	1	0
YHR107c	35	182	PF01926	0.00015	YHR107c	35	182	PF01926	0.00015	1	1
YHR107c	31	321	PF00735	1.30E-188	YKL056c	1	164	PF00838	2.70E-114	0.74968	0
YHR107c	31	321	PF00735	1.30E-188	YLR314c	116	418	PF00735	1.90E-180	0.826543	0
YHR107c	31	321	PF00735	1.30E-188	YML056c	36	513	PF00478	2.50E-233	0.834836	0
YHR111w	66	200	PF00899	7.00E-65	YHR111w	66	200	PF00899	7.00E-65	1	1
YHR111w	204	293	PF05237	1.10E-38	YHR111w	204	293	PF05237	1.10E-38	1	0
YHR111w	330	432	PF00581	2.60E-23	YHR111w	330	432	PF00581	2.60E-23	1	1
YHR113w	25	478	PF02127	9.20E-301	YHR113w	25	478	PF02127	9.20E-301	1	0
YHR169w	26	198	PF00270	2.60E-59	YDR238c	20	560	PF01602	2.40E-162	0.88146	0
YHR169w	273	349	PF00271	1.80E-34	YHR179w	16	368	PF00724	3.10E-200	0.885446	0
YHR169w	273	349	PF00271	1.80E-34	YIL125w	250	577	PF00676	9.10E-49	0.89093	0
YHR169w	273	349	PF00271	1.80E-34	YJL026w	76	358	PF00268	7.00E-177	0.887988	0
YHR169w	26	198	PF00270	2.60E-59	YJL138c	46	211	PF00270	1.70E-62	0.799852	1
YHR169w	26	198	PF00270	2.60E-59	YMR105c	307	429	PF02880	5.30E-46	0.922697	0
YHR174w	144	435	PF00113	1.00E-201	YIL091c	292	720	PF06862	1.30E-293	0.985879	0
YHR179w	16	368	PF00724	3.10E-200	YHR030c	23	318	PF00069	3.20E-85	0.679523	0
YHR179w	16	368	PF00724	3.10E-200	YOL128c	41	329	PF00069	2.10E-62	0.710313	0
YHR183w	178	476	PF00393	2.00E-210	YHR030c	23	318	PF00069	3.20E-85	0.69318	0
YHR183w	178	476	PF00393	2.00E-210	YKL085w	18	163	PF00056	7.70E-70	0.787604	0
YHR183w	178	476	PF00393	2.00E-210	YPR110c	48	330	PF01193	8.90E-20	0.913366	0
YHR193c	135	174	PF00627	8.70E-05	YHR030c	23	318	PF00069	3.20E-85	0.580086	0
YHR208w	68	373	PF01063	3.10E-164	YJR148w	51	356	PF01063	2.30E-166	0.999337	1
YHR216w	35	512	PF00478	6.90E-230	YNL189w	9	110	PF01749	1.10E-45	0.866763	0
YIL021w	16	260	PF01193	1.30E-19	YBR154c	142	215	PF01191	7.60E-49	0.926415	0
YIL021w	16	260	PF01193	1.30E-19	YDR404c	1	79	PF03876	1.20E-38	0.943482	0
YIL021w	16	260	PF01193	1.30E-19	YER125w	505	809	PF00632	5.90E-182	0.752594	0
YIL021w	16	260	PF01193	1.30E-19	YOR224c	7	146	PF03870	3.90E-92	0.958503	1
YIL033c	202	287	PF00027	1.90E-25	YER133w	56	251	PF00149	4.00E-43	0.798642	0
YIL033c	202	287	PF00027	1.90E-25	YIL035c	40	363	PF00069	3.20E-69	0.800801	0
YIL033c	202	287	PF00027	1.90E-25	YJL164c	87	341	PF00069	6.20E-95	0.936897	0
YIL033c	202	287	PF00027	1.90E-25	YJR017c	64	170	PF00639	2.00E-61	0.889322	0
YIL033c	320	406	PF00027	2.30E-21	YKL166c	88	342	PF00069	2.50E-100	0.91261	0
YIL033c	7	45	PF02197	1.40E-15	YMR022w	8	159	PF00179	7.50E-85	0.791301	0
YIL033c	202	287	PF00027	1.90E-25	YNL093w	3	179	PF00025	1.20E-06	0.881397	0
YIL033c	320	406	PF00027	2.30E-21	YNL189w	9	110	PF01749	1.10E-45	0.940618	0
YIL033c	202	287	PF00027	1.90E-25	YPL203w	70	324	PF00069	6.10E-95	0.933534	0
YIL033c	320	406	PF00027	2.30E-21	YPR086w	133	203	PF00382	1.30E-35	0.928221	0
YIL034c	1	287	PF01115	6.20E-231	YBR264c	1	167	PF00025	0.00042	0.891858	0
YIL034c	1	287	PF01115	6.20E-231	YBR291c	107	204	PF00153	3.50E-21	0.887304	0
YIL034c	1	287	PF01115	6.20E-231	YCL035c	19	85	PF00462	1.60E-18	0.881234	0
YIL035c	40	363	PF00069	3.20E-69	YBL002w	35	105	PF00125	2.60E-25	0.824542	0
YIL035c	40	363	PF00069	3.20E-69	YBR009c	25	94	PF00125	4.80E-17	0.791705	0
YIL035c	40	363	PF00069	3.20E-69	YBR010w	58	132	PF00125	2.70E-36	0.646254	0
YIL035c	40	363	PF00069	3.20E-69	YDR225w	19	92	PF00125	2.00E-30	0.632192	0
YIL035c	40	363	PF00069	3.20E-69	YGL019w	26	233	PF01214	4.10E-170	0.833282	1
YIL035c	40	363	PF00069	3.20E-69	YGL115w	193	318	PF00571	3.90E-21	0.844288	0
YIL035c	40	363	PF00069	3.20E-69	YGR103w	355	436	PF00533	1.90E-11	0.878524	0
YIL035c	40	363	PF00069	3.20E-69	YHL035c	1350	1548	PF00005	4.70E-42	0.900998	0
YIL035c	40	363	PF00069	3.20E-69	YIL118w	18	212	PF00071	3.70E-88	0.780596	0
YIL035c	40	363	PF00069	3.20E-69	YJL087c	565	827	PF08302	1.50E-153	0.927698	0
YIL035c	40	363	PF00069	3.20E-69	YLR197w	173	225	PF08060	8.70E-34	0.557238	0
YIL035c	40	363	PF00069	3.20E-69	YML069w	252	468	PF03531	1.20E-139	0.891409	0
YIL035c	40	363	PF00069	3.20E-69	YNL262w	1527	1920	PF08490	7.60E-243	0.832952	0
YIL035c	40	363	PF00069	3.20E-69	YNL330c	20	331	PF00850	2.40E-183	0.753009	0
YIL035c	40	363	PF00069	3.20E-69	YOR039w	38	213	PF01214	8.20E-140	0.918092	1
YIL035c	40	363	PF00069	3.20E-69	YOR061w	50	334	PF00069	6.50E-66	0.988947	1
YIL035c	40	363	PF00069	3.20E-69	YPR016c	3	204	PF01912	2.40E-136	0.710527	0
YIL074c	164	349	PF02826	3.80E-72	YER081w	164	349	PF02826	3.10E-72	0.99993	1
YIL074c	61	381	PF00389	8.00E-38	YIL074c	61	381	PF00389	8.00E-38	1	1
YIL074c	164	349	PF02826	3.80E-72	YIL074c	164	349	PF02826	3.80E-72	1	1
YIL094c	25	367	PF00180	9.70E-178	YBL039c	1	280	PF06418	2.50E-194	0.800427	0
YIL094c	25	367	PF00180	9.70E-178	YHR030c	23	318	PF00069	3.20E-85	0.637136	0
YIL094c	25	367	PF00180	9.70E-178	YKR048c	93	366	PF00956	9.30E-158	0.83179	0
YIL109c	301	551	PF04811	1.40E-124	YLR026c	50	161	PF00804	1.30E-16	0.971262	0
YIL118w	18	212	PF00071	3.70E-88	YEL020c	3	171	PF02776	4.00E-80	0.784339	0
YIL125w	250	577	PF00676	9.10E-49	YDR148c	232	462	PF00198	6.70E-131	0.964047	0
YIL125w	646	857	PF02779	2.00E-69	YFL018c	28	352	PF07992	6.20E-63	0.942852	0
YIL125w	250	577	PF00676	9.10E-49	YIL125w	250	577	PF00676	9.10E-49	1	1
YIL125w	646	857	PF02779	2.00E-69	YIL125w	646	857	PF02779	2.00E-69	1	1
YIL142w	29	519	PF00118	3.20E-166	YDL047w	46	242	PF00149	2.20E-40	0.737716	0
YIL142w	29	519	PF00118	3.20E-166	YDL080c	15	191	PF02776	6.90E-56	0.957956	0
YIL142w	29	519	PF00118	3.20E-166	YDR075w	44	239	PF00149	1.10E-40	0.720542	0
YIL142w	29	519	PF00118	3.20E-166	YDR212w	36	549	PF00118	8.70E-163	0.972817	1
YIL142w	29	519	PF00118	3.20E-166	YGL137w	325	794	PF04053	1.20E-254	0.91363	0
YIL142w	29	519	PF00118	3.20E-166	YGR040w	13	313	PF00069	3.30E-95	0.864403	0
YIL145c	1	309	PF02569	1.10E-223	YLR447c	12	343	PF01992	2.50E-169	0.954206	0
YIR034c	175	323	PF01262	1.40E-20	YLR354c	25	329	PF00923	1.10E-199	0.929727	0
YJL001w	16	197	PF00227	3.70E-65	YGL011c	40	228	PF00227	7.10E-48	0.930749	1
YJL001w	16	197	PF00227	3.70E-65	YOR157c	26	207	PF00227	8.90E-68	0.896018	1
YJL001w	16	197	PF00227	3.70E-65	YPR054w	38	337	PF00069	1.00E-72	0.656586	0
YJL014w	31	531	PF00118	1.30E-162	YDR075w	44	239	PF00149	1.10E-40	0.673712	0
YJL026w	76	358	PF00268	7.00E-177	YDL047w	46	242	PF00149	2.20E-40	0.605826	0
YJL026w	76	358	PF00268	7.00E-177	YGL137w	325	794	PF04053	1.20E-254	0.906824	0
YJL026w	76	358	PF00268	7.00E-177	YJL026w	76	358	PF00268	7.00E-177	1	1
YJL026w	76	358	PF00268	7.00E-177	YPR054w	38	337	PF00069	1.00E-72	0.709372	0
YJL034w	50	430	PF06723	0.00096	YJL034w	50	430	PF06723	0.00096	1	0
YJL034w	50	430	PF06723	0.00096	YMR214w	253	374	PF01556	3.80E-05	0.808186	0
YJL034w	50	430	PF06723	0.00096	YMR297w	116	528	PF00450	7.60E-184	0.926555	0
YJL053w	5	364	PF03643	1.10E-258	YDR372c	59	340	PF05719	5.80E-206	0.910236	0
YJL060w	54	437	PF00155	3.00E-111	YBR160w	8	295	PF00069	4.30E-98	0.650912	0
YJL060w	54	437	PF00155	3.00E-111	YLR314c	116	418	PF00735	1.90E-180	0.816639	0
YJL087c	565	827	PF08302	1.50E-153	YLR447c	12	343	PF01992	2.50E-169	0.926738	0
YJL138c	46	211	PF00270	1.70E-62	YBL039c	1	280	PF06418	2.50E-194	0.881474	0
YJL138c	46	211	PF00270	1.70E-62	YBR126c	16	482	PF00982	5.90E-294	0.877405	0
YJL153c	66	515	PF07994	1.80E-199	YJL190c	5	130	PF00410	2.10E-56	0.822388	0
YJL164c	87	341	PF00069	6.20E-95	YJL164c	87	341	PF00069	6.20E-95	1	1
YJL164c	87	328	PF07714	5.80E-19	YJL164c	87	328	PF07714	5.80E-19	1	1
YJL164c	87	328	PF07714	5.80E-19	YKL166c	88	342	PF00069	2.50E-100	0.882032	0
YJL164c	87	328	PF07714	5.80E-19	YNL093w	3	179	PF00025	1.20E-06	0.646918	0
YJL164c	87	328	PF07714	5.80E-19	YPL203w	70	311	PF07714	2.20E-19	0.969601	1
YJL167w	39	313	PF00348	3.50E-135	YJL167w	39	313	PF00348	3.50E-135	1	1
YJL167w	39	313	PF00348	3.50E-135	YNL244c	20	101	PF01253	6.80E-42	0.835558	0
YJL196c	7	309	PF01151	1.70E-227	YBR159w	63	242	PF00106	2.50E-08	0.953177	0
YJL196c	7	309	PF01151	1.70E-227	YCR034w	10	313	PF01151	7.70E-229	0.957972	0
YJL196c	7	309	PF01151	1.70E-227	YDR297w	49	277	PF01598	4.10E-89	0.961418	0
YJL196c	7	309	PF01151	1.70E-227	YIL048w	497	903	PF00702	0.00092	0.981609	0
YJL196c	7	309	PF01151	1.70E-227	YLR372w	10	321	PF01151	3.70E-232	0.964207	0
YJL196c	7	309	PF01151	1.70E-227	YMR058w	29	148	PF07732	1.70E-53	0.956411	0
YJL196c	7	309	PF01151	1.70E-227	YNL101w	295	711	PF01490	8.70E-157	0.940725	0
YJL214w	73	490	PF07690	8.10E-24	YBR159w	63	242	PF00106	2.50E-08	0.941157	0
YJL214w	73	490	PF07690	8.10E-24	YLR372w	10	321	PF01151	3.70E-232	0.943671	0
YJL219w	68	486	PF07690	1.70E-26	YBR159w	63	242	PF00106	2.50E-08	0.944265	0
YJL219w	68	486	PF07690	1.70E-26	YLR447c	12	343	PF01992	2.50E-169	0.909469	0
YJR007w	125	237	PF07541	1.40E-67	YCR053w	90	402	PF00291	1.40E-38	0.937947	0
YJR007w	125	237	PF07541	1.40E-67	YJL138c	46	211	PF00270	1.70E-62	0.82404	0
YJR017c	64	170	PF00639	2.00E-61	YDL140c	873	1056	PF04992	4.00E-97	0.900094	0
YJR017c	64	170	PF00639	2.00E-61	YDR343c	72	488	PF07690	3.70E-29	0.906018	0
YJR017c	64	170	PF00639	2.00E-61	YIL021w	16	260	PF01193	1.30E-19	0.913003	0
YJR017c	64	170	PF00639	2.00E-61	YPR086w	239	309	PF00382	5.70E-16	0.886966	0
YJR024c	18	235	PF00596	1.00E-71	YJR024c	18	235	PF00596	1.00E-71	1	1
YJR045c	30	413	PF06723	0.00044	YJL143w	3	132	PF02466	1.80E-55	0.725473	0
YJR045c	30	413	PF06723	0.00044	YJR045c	30	413	PF06723	0.00044	1	0
YJR063w	7	59	PF02150	7.80E-21	YBR154c	142	215	PF01191	7.60E-49	0.872278	0
YJR063w	7	59	PF02150	7.80E-21	YDR196c	2	188	PF01121	5.10E-117	0.961175	0
YJR063w	7	59	PF02150	7.80E-21	YOR224c	7	146	PF03870	3.90E-92	0.972726	0
YJR063w	7	59	PF02150	7.80E-21	YPR010c	1067	1138	PF04560	1.50E-12	0.961913	0
YJR063w	7	59	PF02150	7.80E-21	YPR110c	48	330	PF01193	8.90E-20	0.96172	0
YJR068w	261	350	PF08542	5.80E-27	YBR087w	38	243	PF00004	0.001	0.86917	1
YJR068w	261	350	PF08542	5.80E-27	YEL013w	281	321	PF00514	2.40E-07	0.826553	0
YJR068w	60	243	PF00004	1.10E-08	YNL189w	9	110	PF01749	1.10E-45	0.812293	0
YJR068w	261	350	PF08542	5.80E-27	YNL290w	237	327	PF08542	4.10E-28	0.705802	1
YJR068w	60	243	PF00004	1.10E-08	YOL094c	229	316	PF08542	1.90E-33	0.865888	1
YJR072c	8	258	PF03029	4.50E-116	YLR243w	8	255	PF03029	1.30E-124	0.963954	0
YJR076c	23	174	PF01926	1.60E-06	YDL064w	8	152	PF00179	2.00E-69	0.68195	0
YJR076c	19	305	PF00735	6.10E-175	YHR107c	31	321	PF00735	1.30E-188	0.92304	0
YJR076c	19	305	PF00735	6.10E-175	YLR314c	116	418	PF00735	1.90E-180	0.868918	0
YJR076c	19	305	PF00735	6.10E-175	YNL088w	690	1171	PF00521	3.00E-123	0.899555	0
YJR077c	213	302	PF00153	1.10E-09	YBR069c	98	561	PF00324	6.30E-155	0.788569	0
YJR103w	1	280	PF06418	5.70E-194	YJR103w	1	280	PF06418	5.70E-194	1	0
YJR103w	314	557	PF00117	2.40E-76	YJR103w	314	557	PF00117	2.40E-76	1	1
YJR105w	21	336	PF00294	2.20E-82	YDL047w	46	242	PF00149	2.20E-40	0.706886	0
YJR109c	436	567	PF02787	3.10E-74	YBL039c	314	555	PF00117	3.20E-71	0.917023	0
YJR109c	436	567	PF02787	3.10E-74	YHR169w	26	198	PF00270	2.60E-59	0.922594	0
YJR109c	436	567	PF02787	3.10E-74	YJR068w	261	350	PF08542	5.80E-27	0.760857	0
YJR121w	401	508	PF00306	2.30E-48	YBR039w	34	310	PF00231	9.50E-131	0.913245	1
YJR121w	46	113	PF02874	1.40E-27	YDR298c	32	208	PF00213	1.20E-73	0.872075	0
YJR121w	46	113	PF02874	1.40E-27	YJR121w	46	113	PF02874	1.40E-27	1	1
YJR121w	169	388	PF00006	1.10E-96	YJR121w	169	388	PF00006	1.10E-96	1	1
YJR121w	401	508	PF00306	2.30E-48	YJR121w	401	508	PF00306	2.30E-48	1	1
YJR121w	46	113	PF02874	1.40E-27	YPL078c	75	237	PF05405	2.70E-82	0.944338	0
YJR159w	170	316	PF00107	2.40E-40	YDL246c	170	316	PF00107	2.40E-40	1	1
YJR159w	170	316	PF00107	2.40E-40	YLR447c	12	343	PF01992	2.50E-169	0.894915	0
YJR159w	170	316	PF00107	2.40E-40	YNL189w	9	110	PF01749	1.10E-45	0.858407	0
YJR160c	104	517	PF07690	0.0005	YLR372w	10	321	PF01151	3.70E-232	0.919537	0
YKL002w	20	191	PF03357	1.30E-35	YER031c	5	174	PF00025	3.10E-05	0.51176	0
YKL002w	20	191	PF03357	1.30E-35	YER044c	15	131	PF03694	1.00E-83	0.929385	0
YKL002w	20	191	PF03357	1.30E-35	YGR020c	8	111	PF01990	2.70E-35	0.943624	0
YKL008c	191	400	PF03798	3.30E-106	YBR159w	63	242	PF00106	2.50E-08	0.96737	0
YKL008c	109	169	PF08390	3.80E-32	YHL003c	109	169	PF08390	1.40E-30	1	0
YKL008c	109	169	PF08390	3.80E-32	YLR372w	10	321	PF01151	3.70E-232	0.951642	0
YKL013c	1	169	PF05856	9.20E-112	YKL129c	758	960	PF06017	1.10E-76	0.935634	0
YKL013c	1	169	PF05856	9.20E-112	YMR109w	759	961	PF06017	1.00E-77	0.945236	0
YKL013c	1	169	PF05856	9.20E-112	YNR035c	55	318	PF04045	2.50E-198	0.949778	0
YKL029c	355	609	PF03949	2.50E-103	YDL047w	46	242	PF00149	2.20E-40	0.712863	0
YKL029c	165	353	PF00390	7.80E-87	YGL137w	325	794	PF04053	1.20E-254	0.909148	0
YKL029c	165	353	PF00390	7.80E-87	YLR447c	12	343	PF01992	2.50E-169	0.925243	0
YKL029c	165	353	PF00390	7.80E-87	YPR054w	38	337	PF00069	1.00E-72	0.748181	0
YKL060c	16	359	PF01116	1.50E-218	YOR116c	10	368	PF04997	6.30E-106	0.813904	0
YKL067w	6	140	PF00334	4.60E-104	YKL067w	6	140	PF00334	4.60E-104	1	1
YKL078w	84	247	PF00270	1.30E-05	YGL137w	325	794	PF04053	1.20E-254	0.674687	0
YKL080w	8	392	PF03223	3.50E-84	YEL051w	13	211	PF01813	5.90E-98	0.938925	0
YKL081w	250	356	PF00647	2.50E-82	YBR025c	307	390	PF06071	3.40E-50	0.893585	0
YKL081w	250	356	PF00647	2.50E-82	YGL245w	509	681	PF03950	9.60E-73	0.954814	0
YKL085w	165	331	PF02866	3.50E-83	YDR129c	412	521	PF00307	7.90E-29	0.916605	0
YKL085w	165	331	PF02866	3.50E-83	YOL128c	41	329	PF00069	2.10E-62	0.672584	0
YKL085w	165	331	PF02866	3.50E-83	YPR110c	48	330	PF01193	8.90E-20	0.949242	0
YKL103c	59	501	PF02127	3.80E-263	YKL103c	59	501	PF02127	3.80E-263	1	0
YKL103c	59	501	PF02127	3.80E-263	YNL189w	9	110	PF01749	1.10E-45	0.916494	0
YKL104c	563	703	PF01380	7.50E-37	YBL087c	16	137	PF00238	2.50E-53	0.78019	0
YKL104c	2	215	PF00310	8.80E-58	YDR062w	155	515	PF00155	1.90E-95	0.964169	0
YKL104c	391	525	PF01380	2.10E-38	YGR040w	13	313	PF00069	3.30E-95	0.799428	0
YKL104c	2	215	PF00310	8.80E-58	YKL081w	104	196	PF00043	7.30E-17	0.938522	0
YKL104c	2	215	PF00310	8.80E-58	YKL161c	23	318	PF00069	7.70E-71	0.729318	0
YKL104c	563	703	PF01380	7.50E-37	YLR058c	40	357	PF00282	0.00014	0.833701	0
YKL104c	2	215	PF00310	8.80E-58	YPR110c	48	330	PF01193	8.90E-20	0.961773	0
YKL106w	44	441	PF00155	1.60E-119	YLR447c	12	343	PF01992	2.50E-169	0.831604	0
YKL113c	144	235	PF00867	1.30E-52	YLR447c	12	343	PF01992	2.50E-169	0.878378	0
YKL129c	38	701	PF00063	2.90E-271	YMR109w	38	702	PF00063	1.10E-285	0.989135	1
YKL135c	24	553	PF01602	6.40E-182	YGL206c	1429	1588	PF00637	8.00E-36	0.92728	0
YKL135c	24	553	PF01602	6.40E-182	YHR068w	45	377	PF01916	1.40E-230	0.778163	0
YKL135c	24	553	PF01602	6.40E-182	YLR170c	3	146	PF01217	3.10E-96	0.80364	1
YKL135c	24	553	PF01602	6.40E-182	YNL189w	119	160	PF00514	1.20E-12	0.930017	0
YKL135c	24	553	PF01602	6.40E-182	YPL259c	1	142	PF01217	3.10E-05	0.705831	1
YKL135c	24	553	PF01602	6.40E-182	YPR010c	1067	1138	PF04560	1.50E-12	0.779472	0
YKL144c	79	211	PF08292	5.80E-89	YOR116c	855	1386	PF04998	4.80E-158	0.955007	0
YKL144c	79	211	PF08292	5.80E-89	YPR110c	48	330	PF01193	8.90E-20	0.953026	0
YKL152c	3	189	PF00300	6.30E-43	YDL090c	278	322	PF00432	1.90E-11	0.921642	0
YKL152c	3	189	PF00300	6.30E-43	YKL129c	38	701	PF00063	2.90E-271	0.960496	0
YKL152c	3	189	PF00300	6.30E-43	YMR109w	38	702	PF00063	1.10E-285	0.963435	0
YKL165c	442	874	PF04987	3.30E-227	YLR372w	10	321	PF01151	3.70E-232	0.952886	0
YKL165c	49	451	PF01663	0.00017	YPR028w	44	148	PF03134	1.80E-53	0.987176	0
YKL166c	88	342	PF00069	2.50E-100	YKL166c	88	342	PF00069	2.50E-100	1	1
YKL166c	88	329	PF07714	4.50E-19	YKL166c	88	329	PF07714	4.50E-19	1	1
YKL166c	88	329	PF07714	4.50E-19	YML001w	10	178	PF00071	1.10E-88	0.639014	0
YKL166c	88	329	PF07714	4.50E-19	YNL093w	3	179	PF00025	1.20E-06	0.629213	0
YKL180w	17	152	PF00237	1.50E-78	YGR118w	10	144	PF00164	1.00E-74	0.9128	0
YKR002w	4	352	PF04928	1.50E-173	YGR048w	13	199	PF03152	1.30E-132	0.965014	0
YKR002w	353	532	PF04926	9.20E-103	YNL189w	9	110	PF01749	1.10E-45	0.938503	0
YKR002w	353	532	PF04926	9.20E-103	YNL222w	7	206	PF04722	2.60E-164	0.955812	0
YKR014c	5	195	PF00071	2.50E-88	YNL093w	14	181	PF00071	9.60E-87	0.826077	1
YKR026c	12	294	PF01008	5.40E-118	YBL030c	22	119	PF00153	4.40E-35	0.872628	0
YKR026c	12	294	PF01008	5.40E-118	YEL051w	13	211	PF01813	5.90E-98	0.891922	0
YKR026c	12	294	PF01008	5.40E-118	YER146w	10	83	PF01423	2.20E-20	0.704063	0
YKR026c	12	294	PF01008	5.40E-118	YHL032c	396	656	PF02782	8.10E-45	0.937952	0
YKR026c	12	294	PF01008	5.40E-118	YJR007w	125	237	PF07541	1.40E-67	0.951222	0
YKR026c	12	294	PF01008	5.40E-118	YJR072c	8	258	PF03029	4.50E-116	0.924422	0
YKR026c	12	294	PF01008	5.40E-118	YKR026c	12	294	PF01008	5.40E-118	1	1
YKR026c	12	294	PF01008	5.40E-118	YLR289w	447	537	PF00679	2.10E-30	0.954038	0
YKR026c	12	294	PF01008	5.40E-118	YLR432w	35	512	PF00478	1.50E-235	0.895836	0
YKR026c	12	294	PF01008	5.40E-118	YMR145c	114	430	PF07992	1.30E-06	0.879942	0
YKR026c	12	294	PF01008	5.40E-118	YMR267w	77	265	PF00719	1.40E-80	0.818859	0
YKR030w	35	273	PF05216	9.60E-167	YER031c	5	174	PF00025	3.10E-05	0.804818	0
YKR039w	94	560	PF00324	8.10E-217	YBR159w	63	242	PF00106	2.50E-08	0.96903	0
YKR048c	93	366	PF00956	9.30E-158	YDR002w	75	197	PF00638	1.40E-86	0.948193	0
YKR048c	93	366	PF00956	9.30E-158	YJR045c	30	413	PF06723	0.00044	0.650978	0
YKR048c	93	366	PF00956	9.30E-158	YMR139w	39	322	PF00069	1.70E-78	0.589763	0
YKR081c	31	238	PF04427	1.90E-56	YPR016c	3	204	PF01912	2.40E-136	0.896065	0
YLL001w	31	246	PF00350	1.20E-88	YLL001w	31	246	PF00350	1.20E-88	1	0
YLL001w	255	549	PF01031	7.10E-164	YLL001w	255	549	PF01031	7.10E-164	1	0
YLL001w	665	756	PF02212	1.60E-43	YLL001w	665	756	PF02212	1.60E-43	1	0
YLL028w	152	544	PF07690	9.70E-42	YBR159w	63	242	PF00106	2.50E-08	0.92763	0
YLL057c	114	393	PF02668	2.60E-122	YLL057c	114	393	PF02668	2.60E-122	1	1
YLL061w	77	540	PF00324	8.50E-124	YBR159w	63	242	PF00106	2.50E-08	0.924502	0
YLL061w	77	540	PF00324	8.50E-124	YLR372w	10	321	PF01151	3.70E-232	0.931111	0
YLR005w	72	325	PF04056	1.00E-186	YLR005w	72	325	PF04056	1.00E-186	1	0
YLR005w	402	456	PF07975	5.80E-31	YLR005w	402	456	PF07975	5.80E-31	1	0
YLR026c	50	161	PF00804	1.30E-16	YDR189w	53	653	PF00995	6.90E-269	0.981682	1
YLR026c	50	161	PF00804	1.30E-16	YNL049c	234	507	PF04811	7.30E-89	0.971474	0
YLR027c	30	405	PF00155	5.60E-99	YLR027c	30	405	PF00155	5.60E-99	1	1
YLR027c	30	405	PF00155	5.60E-99	YLR314c	116	418	PF00735	1.90E-180	0.803291	0
YLR027c	30	405	PF00155	5.60E-99	YNL244c	20	101	PF01253	6.80E-42	0.862034	0
YLR038c	5	79	PF02297	5.00E-65	YML125c	74	172	PF00970	1.60E-38	0.798019	0
YLR044c	387	538	PF02775	1.50E-08	YBR069c	98	561	PF00324	6.30E-155	0.930534	0
YLR056w	85	295	PF01598	1.60E-80	YBR159w	63	242	PF00106	2.50E-08	0.962311	0
YLR056w	85	295	PF01598	1.60E-80	YIL074c	61	381	PF00389	8.00E-38	0.957463	0
YLR056w	85	295	PF01598	1.60E-80	YLL028w	152	544	PF07690	9.70E-42	0.945186	0
YLR058c	40	357	PF00282	0.00014	YNL189w	9	110	PF01749	1.10E-45	0.800147	0
YLR070c	31	142	PF08240	6.20E-37	YLR070c	31	142	PF08240	6.20E-37	1	1
YLR070c	171	315	PF00107	3.70E-41	YLR070c	171	315	PF00107	3.70E-41	1	1
YLR109w	4	176	PF08534	1.10E-48	YLR109w	4	176	PF08534	1.10E-48	1	1
YLR109w	4	176	PF08534	1.10E-48	YLR340w	222	311	PF00428	2.60E-30	0.882435	0
YLR109w	4	176	PF08534	1.10E-48	YMR022w	8	159	PF00179	7.50E-85	0.843329	0
YLR134w	387	538	PF02775	1.50E-09	YLR447c	12	343	PF01992	2.50E-169	0.956648	0
YLR134w	4	180	PF02776	1.40E-81	YNL244c	20	101	PF01253	6.80E-42	0.945861	0
YLR153c	124	563	PF00501	1.90E-123	YNL244c	20	101	PF01253	6.80E-42	0.84354	0
YLR153c	124	563	PF00501	1.90E-123	YPR165w	12	185	PF00071	6.20E-87	0.5578	0
YLR163c	189	380	PF05193	3.10E-52	YHR024c	181	374	PF05193	6.60E-47	0.967983	1
YLR163c	189	380	PF05193	3.10E-52	YLR086w	155	1406	PF02463	1.10E-140	0.951332	0
YLR172c	1	209	PF00590	8.40E-63	YOR159c	19	92	PF01423	2.30E-19	0.861404	0
YLR175w	267	340	PF01472	3.20E-25	YBR247c	143	476	PF05291	1.30E-267	0.794545	0
YLR175w	80	217	PF01509	3.00E-65	YDL208w	41	135	PF01248	9.20E-30	0.931877	0
YLR175w	18	76	PF08068	1.30E-40	YHR072w-a	3	53	PF04135	2.40E-21	0.871543	0
YLR175w	18	76	PF08068	1.30E-40	YLR134w	200	348	PF00205	2.70E-49	0.935183	0
YLR175w	80	217	PF01509	3.00E-65	YLR197w	173	225	PF08060	8.70E-34	0.796764	0
YLR175w	267	340	PF01472	3.20E-25	YMR205c	588	881	PF00365	1.10E-15	0.875604	0
YLR175w	80	217	PF01509	3.00E-65	YNL189w	417	457	PF00514	5.30E-06	0.857792	0
YLR175w	80	217	PF01509	3.00E-65	YNL307c	35	327	PF00069	2.40E-75	0.598145	0
YLR180w	115	237	PF02772	1.00E-94	YBL039c	314	555	PF00117	3.20E-71	0.914165	0
YLR180w	115	237	PF02772	1.00E-94	YER090w	31	174	PF04715	1.10E-43	0.93249	0
YLR186w	81	247	PF03587	8.10E-95	YBR247c	143	476	PF05291	1.30E-267	0.831031	0
YLR186w	81	247	PF03587	8.10E-95	YHR179w	16	368	PF00724	3.10E-200	0.679832	0
YLR197w	5	72	PF08156	5.50E-34	YNL088w	55	204	PF02518	1.40E-15	0.794955	0
YLR209c	37	311	PF00896	1.10E-148	YNL189w	119	160	PF00514	1.20E-12	0.858639	0
YLR212c	48	246	PF00091	8.00E-70	YLR200w	2	107	PF01920	1.70E-33	0.776821	0
YLR215c	27	330	PF07065	5.00E-174	YER025w	98	314	PF00009	2.30E-40	0.89687	0
YLR215c	27	330	PF07065	5.00E-174	YLR447c	12	343	PF01992	2.50E-169	0.979042	0
YLR216c	308	341	PF00515	3.40E-07	YDR353w	5	294	PF07992	2.40E-46	0.925808	0
YLR216c	308	341	PF00515	3.40E-07	YGL137w	325	794	PF04053	1.20E-254	0.910353	0
YLR216c	308	341	PF00515	3.40E-07	YHR030c	23	318	PF00069	3.20E-85	0.656721	0
YLR216c	5	175	PF00160	3.70E-98	YHR039c-a	1	106	PF03179	4.50E-55	0.915524	0
YLR216c	308	341	PF00515	3.40E-07	YHR074w	343	659	PF02540	3.70E-08	0.898668	0
YLR216c	5	175	PF00160	3.70E-98	YIR037w	4	111	PF00255	1.70E-76	0.738518	0
YLR216c	308	341	PF00515	3.40E-07	YJR017c	64	170	PF00639	2.00E-61	0.920296	0
YLR216c	308	341	PF00515	3.40E-07	YKL166c	88	342	PF00069	2.50E-100	0.818207	0
YLR216c	308	341	PF00515	3.40E-07	YNL330c	20	331	PF00850	2.40E-183	0.776085	0
YLR216c	308	341	PF00515	3.40E-07	YNR032w	43	251	PF00149	6.20E-38	0.664348	0
YLR229c	5	178	PF00071	5.90E-81	YDL135c	1	202	PF02115	7.30E-27	0.526573	1
YLR245c	8	115	PF00383	4.90E-37	YLR245c	8	115	PF00383	4.90E-37	1	1
YLR245c	8	115	PF00383	4.90E-37	YNL189w	9	110	PF01749	1.10E-45	0.838523	0
YLR264w	1	67	PF01200	3.20E-44	YLR264w	1	67	PF01200	3.20E-44	1	0
YLR270w	1	331	PF05652	1.70E-33	YLR081w	74	534	PF00083	2.90E-242	0.973452	0
YLR275w	32	106	PF01423	2.00E-15	YFL017w-a	5	73	PF01423	2.00E-16	0.819601	1
YLR275w	32	106	PF01423	2.00E-15	YOR159c	19	92	PF01423	2.30E-19	0.866488	1
YLR275w	32	106	PF01423	2.00E-15	YPR182w	17	83	PF01423	2.20E-21	0.881897	1
YLR276c	292	418	PF00271	2.70E-05	YKR081c	31	238	PF04427	1.90E-56	0.957983	0
YLR293c	13	127	PF08477	9.20E-16	YDR002w	75	197	PF00638	1.40E-86	0.947417	0
YLR293c	13	127	PF08477	9.20E-16	YER009w	8	121	PF02136	1.20E-46	0.748787	0
YLR293c	13	127	PF08477	9.20E-16	YNL189w	9	110	PF01749	1.10E-45	0.752039	0
YLR293c	14	172	PF00071	1.20E-72	YOR185c	15	173	PF00071	1.20E-72	0.999787	1
YLR300w	98	369	PF00150	2.40E-05	YOL126c	225	416	PF02866	7.10E-78	0.906125	0
YLR303w	6	436	PF01053	2.00E-250	YNL189w	9	110	PF01749	1.10E-45	0.970749	0
YLR304c	60	500	PF00330	2.70E-279	YGR040w	13	313	PF00069	3.30E-95	0.628094	0
YLR304c	60	500	PF00330	2.70E-279	YLR262c	1	173	PF00025	1.00E-05	0.44928	0
YLR304c	60	500	PF00330	2.70E-279	YOL006c	364	599	PF01028	6.10E-154	0.966303	0
YLR304c	60	500	PF00330	2.70E-279	YOL094c	44	215	PF00004	9.10E-07	0.81084	0
YLR314c	116	418	PF00735	1.90E-180	YCR053w	90	402	PF00291	1.40E-38	0.802238	0
YLR314c	116	418	PF00735	1.90E-180	YDR158w	165	346	PF02774	7.70E-79	0.808971	0
YLR340w	3	105	PF00466	2.60E-49	YDL081c	20	105	PF00428	6.50E-35	0.902215	0
YLR340w	3	105	PF00466	2.60E-49	YDR382w	17	109	PF00428	1.30E-36	0.881181	0
YLR340w	222	311	PF00428	2.60E-30	YPR016c	3	204	PF01912	2.40E-136	0.841555	0
YLR354c	25	329	PF00923	1.10E-199	YJL068c	13	291	PF00756	1.70E-109	0.775248	0
YLR355c	74	244	PF07991	9.10E-54	YHR030c	23	318	PF00069	3.20E-85	0.662459	0
YLR370c	1	178	PF04062	3.40E-137	YKL013c	1	169	PF05856	9.20E-112	0.948468	0
YLR370c	1	178	PF04062	3.40E-137	YNR035c	55	318	PF04045	2.50E-198	0.903244	0
YLR372w	10	321	PF01151	3.70E-232	YBR069c	98	561	PF00324	6.30E-155	0.95887	0
YLR372w	10	321	PF01151	3.70E-232	YLL028w	152	544	PF07690	9.70E-42	0.902903	0
YLR372w	10	321	PF01151	3.70E-232	YLR241w	370	781	PF02714	3.10E-193	0.904648	0
YLR372w	10	321	PF01151	3.70E-232	YNL101w	295	711	PF01490	8.70E-157	0.942701	0
YLR372w	10	321	PF01151	3.70E-232	YPR156c	188	616	PF00083	0.00011	0.811786	0
YLR377c	21	347	PF00316	1.80E-218	YLR377c	21	347	PF00316	1.80E-218	1	1
YLR377c	21	347	PF00316	1.80E-218	YML121w	99	310	PF04670	8.40E-123	0.859526	0
YLR377c	21	347	PF00316	1.80E-218	YNL189w	9	110	PF01749	1.10E-45	0.832446	0
YLR378c	76	461	PF00344	1.10E-08	YBR159w	63	242	PF00106	2.50E-08	0.861859	0
YLR378c	76	461	PF00344	1.10E-08	YDR086c	24	80	PF00584	1.70E-22	0.932924	0
YLR378c	76	461	PF00344	1.10E-08	YLR372w	10	321	PF01151	3.70E-232	0.931047	0
YLR438c-a	6	78	PF01423	3.30E-23	YER146w	10	83	PF01423	2.20E-20	0.940084	1
YLR438c-a	6	78	PF01423	3.30E-23	YLR438c-a	6	78	PF01423	3.30E-23	1	1
YLR438c-a	6	78	PF01423	3.30E-23	YMR142c	7	173	PF01294	1.20E-120	0.819584	0
YLR438c-a	6	78	PF01423	3.30E-23	YNL147w	20	96	PF01423	4.90E-22	0.846871	1
YLR438c-a	6	78	PF01423	3.30E-23	YOR096w	4	190	PF01251	2.80E-134	0.740254	0
YLR438w	29	367	PF00202	1.20E-148	YHR169w	273	349	PF00271	1.80E-34	0.883835	0
YLR438w	29	367	PF00202	1.20E-148	YJR017c	64	170	PF00639	2.00E-61	0.886034	0
YLR438w	29	367	PF00202	1.20E-148	YLR186w	81	247	PF03587	8.10E-95	0.865484	0
YLR438w	29	367	PF00202	1.20E-148	YNL244c	20	101	PF01253	6.80E-42	0.905105	0
YLR438w	29	367	PF00202	1.20E-148	YPR165w	12	185	PF00071	6.20E-87	0.673595	0
YLR447c	12	343	PF01992	2.50E-169	YBR028c	468	518	PF00433	1.80E-07	0.987372	0
YLR447c	12	343	PF01992	2.50E-169	YGR020c	8	111	PF01990	2.70E-35	0.891512	0
YLR447c	12	343	PF01992	2.50E-169	YIR035c	3	169	PF00106	2.90E-17	0.935663	0
YML008c	61	320	PF02353	9.10E-06	YPR113w	46	201	PF01066	1.00E-30	0.97656	0
YML022w	29	169	PF00156	3.00E-47	YDR441c	30	170	PF00156	4.00E-39	0.982245	1
YML022w	29	169	PF00156	3.00E-47	YLR447c	12	343	PF01992	2.50E-169	0.813727	0
YML042w	73	658	PF00755	5.70E-305	YML042w	73	658	PF00755	5.70E-305	1	1
YML042w	73	658	PF00755	5.70E-305	YNL189w	330	370	PF00514	2.30E-14	0.932793	0
YML056c	36	513	PF00478	2.50E-233	YBR088c	1	125	PF00705	1.10E-78	0.793389	0
YML056c	36	513	PF00478	2.50E-233	YER117w	16	137	PF00238	2.50E-53	0.747241	0
YML060w	127	292	PF00730	2.00E-22	YOL010w	183	286	PF05189	2.70E-45	0.920471	0
YML085c	50	247	PF00091	5.60E-99	YFL037w	246	383	PF03953	2.00E-72	0.2298	1
YML092c	28	214	PF00227	1.90E-72	YER094c	7	190	PF00227	5.60E-52	0.809669	1
YML092c	28	214	PF00227	1.90E-72	YGL011c	40	228	PF00227	7.10E-48	0.717951	1
YML092c	28	214	PF00227	1.90E-72	YGR135w	29	216	PF00227	1.60E-73	0.638342	1
YML092c	28	214	PF00227	1.90E-72	YOR157c	26	207	PF00227	8.90E-68	0.798032	1
YML094w	23	143	PF02996	1.10E-36	YGR078c	48	179	PF02996	3.90E-36	0.979125	0
YML094w	23	143	PF02996	1.10E-36	YLR200w	2	107	PF01920	1.70E-33	0.987844	1
YML094w	23	143	PF02996	1.10E-36	YLR212c	48	246	PF00091	8.00E-70	0.798947	0
YML110c	116	225	PF08241	5.30E-06	YGL115w	193	318	PF00571	3.90E-21	0.962894	0
YML121w	7	129	PF01926	0.00014	YML121w	7	129	PF01926	0.00014	1	1
YML121w	99	310	PF04670	8.40E-123	YML121w	99	310	PF04670	8.40E-123	1	0
YML123c	81	507	PF07690	2.50E-21	YBR159w	63	242	PF00106	2.50E-08	0.9387	0
YML123c	65	557	PF00083	7.10E-28	YDL198c	209	295	PF00153	1.20E-11	0.899502	0
YML123c	81	507	PF07690	2.50E-21	YER125w	505	809	PF00632	5.90E-182	0.943206	0
YML123c	81	507	PF07690	2.50E-21	YLR372w	10	321	PF01151	3.70E-232	0.94182	0
YML126c	217	490	PF08540	3.40E-184	YDL188c	118	313	PF00149	6.90E-40	0.483846	0
YML126c	217	490	PF08540	3.40E-184	YIL094c	25	367	PF00180	9.70E-178	0.787469	0
YML126c	217	490	PF08540	3.40E-184	YLR180w	115	237	PF02772	1.00E-94	0.871644	0
YMR022w	8	159	PF00179	7.50E-85	YLL039c	6	74	PF00240	5.60E-38	0.496123	0
YMR022w	8	159	PF00179	7.50E-85	YLL039c	82	150	PF00240	5.60E-38	0.496123	0
YMR058w	154	302	PF00394	2.70E-47	YBR159w	63	242	PF00106	2.50E-08	0.964958	0
YMR058w	29	147	PF07731	0.00048	YGL084c	170	510	PF03062	8.50E-82	0.964542	0
YMR058w	29	147	PF07731	0.00048	YKL008c	191	400	PF03798	3.30E-106	0.957176	0
YMR058w	29	147	PF07731	0.00048	YLR372w	10	321	PF01151	3.70E-232	0.954047	0
YMR058w	29	148	PF07732	1.70E-53	YOR161c	187	539	PF04515	2.30E-152	0.978746	0
YMR058w	154	302	PF00394	2.70E-47	YPL234c	96	161	PF00137	5.40E-24	0.908847	0
YMR058w	362	504	PF07731	1.90E-54	YPL274w	81	544	PF00324	2.50E-132	0.905259	0
YMR095c	52	211	PF07685	5.90E-05	YFL059w	4	211	PF01680	1.50E-122	0.97057	0
YMR095c	52	211	PF07685	5.90E-05	YMR096w	6	212	PF01680	6.30E-130	0.975253	0
YMR095c	52	211	PF07685	5.90E-05	YNL333w	4	211	PF01680	1.50E-122	0.97057	0
YMR096w	6	212	PF01680	6.30E-130	YFL059w	4	211	PF01680	1.50E-122	0.99527	0
YMR096w	6	212	PF01680	6.30E-130	YNL333w	4	211	PF01680	1.50E-122	0.99527	0
YMR105c	450	558	PF00408	4.70E-45	YJR068w	261	350	PF08542	5.80E-27	0.863716	0
YMR109w	38	702	PF00063	1.10E-285	YMR109w	38	702	PF00063	1.10E-285	1	1
YMR109w	759	961	PF06017	1.00E-77	YMR109w	759	961	PF06017	1.00E-77	1	0
YMR109w	1088	1145	PF00018	1.90E-18	YMR109w	1088	1145	PF00018	1.90E-18	1	1
YMR109w	1089	1145	PF07653	0.0006	YMR109w	1089	1145	PF07653	0.0006	1	0
YMR116c	8	46	PF00400	2.90E-07	YGL120c	95	258	PF00270	0.00018	0.902184	0
YMR116c	8	46	PF00400	2.90E-07	YLR197w	173	225	PF08060	8.70E-34	0.69807	0
YMR116c	8	46	PF00400	2.90E-07	YOR116c	10	368	PF04997	6.30E-106	0.836063	0
YMR116c	8	46	PF00400	2.90E-07	YPL106c	4	644	PF00012	1.50E-248	0.830562	0
YMR145c	114	430	PF07992	1.30E-06	YDL047w	46	242	PF00149	2.20E-40	0.712252	0
YMR205c	197	509	PF00365	5.80E-201	YDL047w	46	242	PF00149	2.20E-40	0.70035	0
YMR205c	588	881	PF00365	1.10E-15	YER148w	152	238	PF00352	4.10E-44	0.803422	0
YMR205c	588	881	PF00365	1.10E-15	YJL138c	46	211	PF00270	1.70E-62	0.774547	0
YMR224c	9	245	PF00149	9.70E-21	YMR224c	9	245	PF00149	9.70E-21	1	1
YMR224c	246	474	PF04152	2.00E-137	YMR224c	246	474	PF04152	2.00E-137	1	0
YMR246w	101	582	PF00501	2.30E-74	YDL047w	46	242	PF00149	2.20E-40	0.774053	0
YMR246w	101	582	PF00501	2.30E-74	YDR129c	412	521	PF00307	7.90E-29	0.871732	0
YMR246w	101	582	PF00501	2.30E-74	YNL088w	690	1171	PF00521	3.00E-123	0.986326	0
YMR246w	101	582	PF00501	2.30E-74	YOL126c	225	416	PF02866	7.10E-78	0.853946	0
YMR296c	145	545	PF00155	1.40E-80	YDR062w	155	515	PF00155	1.90E-95	0.962316	1
YMR297w	1	108	PF05388	1.30E-67	YLR378c	76	461	PF00344	1.10E-08	0.882639	0
YMR300c	2	214	PF00310	5.30E-54	YAL012w	10	390	PF01053	8.30E-227	0.861221	0
YMR303c	170	311	PF00107	8.00E-40	YLR216c	5	175	PF00160	3.70E-98	0.92726	0
YMR303c	170	311	PF00107	8.00E-40	YLR229c	5	178	PF00071	5.90E-81	0.441083	0
YMR303c	31	140	PF08240	3.70E-41	YOL094c	229	316	PF08542	1.90E-33	0.799824	0
YMR303c	170	311	PF00107	8.00E-40	YPR110c	48	330	PF01193	8.90E-20	0.972261	0
YMR314w	29	216	PF00227	9.70E-52	YDL084w	325	401	PF00271	1.10E-27	0.535313	0
YMR314w	29	216	PF00227	9.70E-52	YGL011c	40	228	PF00227	7.10E-48	0.95673	1
YMR314w	29	216	PF00227	9.70E-52	YML092c	28	214	PF00227	1.90E-72	0.68245	1
YNL007c	229	352	PF01556	7.20E-13	YHR030c	23	318	PF00069	3.20E-85	0.705342	0
YNL037c	30	353	PF00180	7.50E-87	YGL137w	325	794	PF04053	1.20E-254	0.796528	0
YNL037c	30	353	PF00180	7.50E-87	YHR030c	23	318	PF00069	3.20E-85	0.691958	0
YNL037c	30	353	PF00180	7.50E-87	YOR136w	38	365	PF00180	1.70E-159	0.673997	1
YNL055c	2	276	PF01459	9.70E-121	YCR009c	6	232	PF03114	3.00E-80	0.942858	0
YNL055c	2	276	PF01459	9.70E-121	YNL090w	9	179	PF00071	8.20E-80	0.811261	0
YNL055c	2	276	PF01459	9.70E-121	YNL093w	3	179	PF00025	1.20E-06	0.931602	0
YNL071w	248	482	PF00198	4.30E-108	YBR221c	231	355	PF02780	8.40E-56	0.898646	0
YNL088w	250	418	PF00204	1.80E-49	YBR025c	21	158	PF01926	7.00E-25	0.928812	0
YNL088w	55	204	PF02518	1.40E-15	YNL088w	55	204	PF02518	1.40E-15	1	1
YNL088w	250	418	PF00204	1.80E-49	YNL088w	250	418	PF00204	1.80E-49	1	1
YNL088w	690	1171	PF00521	3.00E-123	YNL088w	690	1171	PF00521	3.00E-123	1	0
YNL090w	9	179	PF00071	8.20E-80	YOR089c	1	171	PF00025	7.50E-07	0.472051	0
YNL096c	4	190	PF01251	4.60E-125	YMR243c	7	378	PF01545	2.20E-69	0.881045	0
YNL096c	4	190	PF01251	4.60E-125	YPR086w	133	203	PF00382	1.30E-35	0.94529	0
YNL102w	375	719	PF03104	3.70E-99	YIR008c	18	339	PF01896	8.40E-151	0.982243	0
YNL102w	375	719	PF03104	3.70E-99	YNL262w	121	442	PF03104	1.20E-128	0.985461	1
YNL135c	17	111	PF00254	2.50E-53	YDR037w	124	209	PF01336	1.30E-13	0.855263	0
YNL135c	17	111	PF00254	2.50E-53	YDR129c	412	521	PF00307	7.90E-29	0.824252	0
YNL135c	17	111	PF00254	2.50E-53	YDR341c	489	607	PF05746	5.90E-42	0.81679	0
YNL135c	17	111	PF00254	2.50E-53	YIL078w	629	723	PF03129	6.90E-30	0.815144	0
YNL135c	17	111	PF00254	2.50E-53	YJR104c	1	154	PF00080	1.30E-101	0.82163	0
YNL135c	17	111	PF00254	2.50E-53	YLR005w	72	325	PF04056	1.00E-186	0.817639	0
YNL135c	17	111	PF00254	2.50E-53	YMR205c	197	509	PF00365	5.80E-201	0.816927	0
YNL147w	20	96	PF01423	4.90E-22	YLR275w	32	106	PF01423	2.00E-15	0.823916	1
YNL153c	19	124	PF01920	2.20E-28	YGR078c	48	179	PF02996	3.90E-36	0.979334	1
YNL153c	19	124	PF01920	2.20E-28	YLR212c	48	246	PF00091	8.00E-70	0.718396	0
YNL169c	183	493	PF02666	5.70E-20	YLR447c	12	343	PF01992	2.50E-169	0.973761	0
YNL189w	9	110	PF01749	1.10E-45	YDL246c	170	316	PF00107	2.40E-40	0.858407	0
YNL189w	9	110	PF01749	1.10E-45	YDR353w	5	294	PF07992	2.40E-46	0.95007	0
YNL189w	9	110	PF01749	1.10E-45	YDR453c	5	182	PF00578	1.60E-101	0.77382	0
YNL189w	372	412	PF00514	4.70E-13	YGR024c	1	237	PF04446	2.30E-184	0.799248	0
YNL189w	330	370	PF00514	2.30E-14	YGR144w	39	306	PF01946	5.30E-180	0.904475	0
YNL189w	9	110	PF01749	1.10E-45	YHR112c	5	372	PF01053	6.20E-27	0.906409	0
YNL189w	9	110	PF01749	1.10E-45	YJL052w	2	150	PF00044	4.20E-97	0.812677	0
YNL189w	9	110	PF01749	1.10E-45	YJR009c	2	150	PF00044	8.20E-98	0.77617	0
YNL189w	9	110	PF01749	1.10E-45	YKL067w	6	140	PF00334	4.60E-104	0.799804	0
YNL189w	9	110	PF01749	1.10E-45	YML028w	5	182	PF00578	1.70E-113	0.769988	0
YNL189w	9	110	PF01749	1.10E-45	YMR226c	14	187	PF00106	6.50E-21	0.946164	0
YNL189w	9	110	PF01749	1.10E-45	YPL088w	10	336	PF00248	1.20E-90	0.923047	0
YNL220w	2	429	PF00709	1.70E-265	YEL046c	16	303	PF01212	5.50E-135	0.949393	0
YNL244c	20	101	PF01253	6.80E-42	YCR053w	90	402	PF00291	1.40E-38	0.914914	0
YNL244c	20	101	PF01253	6.80E-42	YDL124w	10	289	PF00248	2.50E-58	0.866411	0
YNL244c	20	101	PF01253	6.80E-42	YDR353w	5	294	PF07992	2.40E-46	0.913173	0
YNL244c	20	101	PF01253	6.80E-42	YPR041w	318	403	PF02020	1.60E-36	0.916537	0
YNL262w	1527	1920	PF08490	7.60E-243	YIR008c	18	339	PF01896	8.40E-151	0.98259	0
YNL262w	121	442	PF03104	1.20E-128	YKL045w	59	445	PF04104	6.10E-157	0.978626	0
YNL262w	121	442	PF03104	1.20E-128	YNL262w	121	442	PF03104	1.20E-128	1	1
YNL262w	511	1194	PF00136	3.70E-08	YNL262w	511	1194	PF00136	3.70E-08	1	1
YNL262w	1527	1920	PF08490	7.60E-243	YNL262w	1527	1920	PF08490	7.60E-243	1	0
YNL287w	19	560	PF01602	1.90E-161	YGL137w	325	794	PF04053	1.20E-254	0.980494	0
YNL290w	237	327	PF08542	4.10E-28	YBR087w	38	243	PF00004	0.001	0.706377	1
YNL290w	48	218	PF00004	4.60E-16	YLR058c	40	357	PF00282	0.00014	0.737453	0
YNL290w	237	327	PF08542	4.10E-28	YMR226c	14	187	PF00106	6.50E-21	0.827905	0
YNL290w	48	218	PF00004	4.60E-16	YOL094c	229	316	PF08542	1.90E-33	0.718085	1
YNL323w	93	407	PF03381	1.20E-201	YDR212w	36	549	PF00118	8.70E-163	0.923391	0
YNL323w	93	407	PF03381	1.20E-201	YLR447c	12	343	PF01992	2.50E-169	0.965593	0
YNL330c	20	331	PF00850	2.40E-183	YKR001c	613	704	PF02212	5.70E-41	0.864416	0
YNL330c	20	331	PF00850	2.40E-183	YOL006c	364	599	PF01028	6.10E-154	0.797304	0
YNL333w	4	211	PF01680	1.50E-122	YFL059w	4	211	PF01680	1.50E-122	1	0
YNL333w	4	211	PF01680	1.50E-122	YNL189w	9	110	PF01749	1.10E-45	0.940193	0
YNL333w	4	211	PF01680	1.50E-122	YNL333w	4	211	PF01680	1.50E-122	1	0
YNR001c	83	460	PF00285	1.60E-222	YKL085w	165	331	PF02866	3.50E-83	0.921078	0
YNR001c	83	460	PF00285	1.60E-222	YLR447c	12	343	PF01992	2.50E-169	0.902531	0
YNR032w	43	251	PF00149	6.20E-38	YBR187w	193	268	PF01169	3.10E-43	0.818216	0
YNR032w	43	251	PF00149	6.20E-38	YGR123c	242	438	PF00149	2.00E-34	0.7845	1
YNR035c	55	318	PF04045	2.50E-198	YBR109c	85	113	PF00036	2.70E-08	0.661531	0
YNR053c	41	171	PF08153	1.10E-93	YER126c	1	238	PF01201	6.30E-95	0.966092	0
YNR053c	316	435	PF01926	2.90E-19	YPR016c	3	204	PF01912	2.40E-136	0.938302	0
YNR070w	591	747	PF06422	2.10E-72	YBR159w	63	242	PF00106	2.50E-08	0.915138	0
YOL005c	29	103	PF01193	7.80E-20	YDL140c	807	1398	PF04998	2.30E-170	0.972271	0
YOL005c	29	103	PF01193	7.80E-20	YDR404c	80	161	PF00575	2.40E-10	0.956917	0
YOL005c	29	103	PF01193	7.80E-20	YIL021w	16	260	PF01193	1.30E-19	0.932452	1
YOL012c	25	99	PF00125	2.50E-24	YKR048c	93	366	PF00956	9.30E-158	0.724922	0
YOL038w	27	215	PF00227	5.80E-70	YGL011c	40	228	PF00227	7.10E-48	0.850827	1
YOL038w	27	215	PF00227	5.80E-70	YML092c	28	214	PF00227	1.90E-72	0.543852	1
YOL058w	7	410	PF00764	2.20E-254	YBR160w	8	295	PF00069	4.30E-98	0.712523	0
YOL058w	7	410	PF00764	2.20E-254	YNL189w	9	110	PF01749	1.10E-45	0.848415	0
YOL062c	198	491	PF00928	9.90E-130	YFL045c	35	254	PF03332	1.20E-179	0.729137	0
YOL062c	198	491	PF00928	9.90E-130	YJR058c	2	147	PF01217	1.80E-95	0.947699	1
YOL077c	34	227	PF04427	2.30E-64	YKR081c	31	238	PF04427	1.90E-56	0.956625	1
YOL086c	170	311	PF00107	7.90E-40	YGL009c	11	471	PF00330	5.00E-298	0.957946	0
YOL086c	170	311	PF00107	7.90E-40	YML085c	249	394	PF03953	1.20E-73	0.919317	0
YOL090w	491	587	PF05190	1.10E-28	YBR025c	21	158	PF01926	7.00E-25	0.893929	0
YOL090w	17	128	PF01624	6.20E-07	YJL138c	46	211	PF00270	1.70E-62	0.826301	0
YOL094c	229	316	PF08542	1.90E-33	YBR087w	38	243	PF00004	0.001	0.903437	1
YOL094c	229	316	PF08542	1.90E-33	YGL245w	509	681	PF03950	9.60E-73	0.838537	0
YOL126c	225	416	PF02866	7.10E-78	YJR068w	261	350	PF08542	5.80E-27	0.861494	0
YOL139c	4	213	PF01652	2.80E-118	YDL087c	8	261	PF03194	5.30E-137	0.979278	0
YOL139c	4	213	PF01652	2.80E-118	YER165w	221	291	PF00076	2.50E-26	0.926134	0
YOL139c	4	213	PF01652	2.80E-118	YGL115w	193	318	PF00571	3.90E-21	0.926015	0
YOL139c	4	213	PF01652	2.80E-118	YJL138c	46	211	PF00270	1.70E-62	0.807544	0
YOL139c	4	213	PF01652	2.80E-118	YJR007w	125	237	PF07541	1.40E-67	0.97077	0
YOL139c	4	213	PF01652	2.80E-118	YMR246w	101	582	PF00501	2.30E-74	0.914149	0
YOL139c	4	213	PF01652	2.80E-118	YNL093w	3	179	PF00025	1.20E-06	0.682102	0
YOL139c	4	213	PF01652	2.80E-118	YNL147w	20	96	PF01423	4.90E-22	0.938654	0
YOL139c	4	213	PF01652	2.80E-118	YNL262w	1527	1920	PF08490	7.60E-243	0.978093	0
YOL156w	68	486	PF07690	4.30E-27	YBR159w	63	242	PF00106	2.50E-08	0.94283	0
YOL156w	68	486	PF07690	4.30E-27	YLR372w	10	321	PF01151	3.70E-232	0.945331	0
YOR020c	10	103	PF00166	4.70E-37	YLR259c	44	550	PF00118	6.20E-174	0.835726	1
YOR020c	10	103	PF00166	4.70E-37	YML092c	28	214	PF00227	1.90E-72	0.811924	0
YOR020c	10	103	PF00166	4.70E-37	YNL189w	9	110	PF01749	1.10E-45	0.934904	0
YOR020c	10	103	PF00166	4.70E-37	YOR020c	10	103	PF00166	4.70E-37	1	1
YOR039w	38	213	PF01214	8.20E-140	YGR103w	4	285	PF06732	1.20E-197	0.915066	0
YOR039w	38	213	PF01214	8.20E-140	YNL330c	20	331	PF00850	2.40E-183	0.834549	0
YOR039w	38	213	PF01214	8.20E-140	YOR039w	38	213	PF01214	8.20E-140	1	1
YOR039w	38	213	PF01214	8.20E-140	YPL235w	122	433	PF06068	1.90E-220	0.613262	0
YOR061w	50	334	PF00069	6.50E-66	YBR094w	1	231	PF01975	1.20E-08	0.949798	0
YOR061w	50	334	PF00069	6.50E-66	YGL019w	26	233	PF01214	4.10E-170	0.8275	1
YOR061w	50	334	PF00069	6.50E-66	YGR103w	355	436	PF00533	1.90E-11	0.845508	0
YOR061w	50	334	PF00069	6.50E-66	YIL118w	18	212	PF00071	3.70E-88	0.727959	0
YOR061w	50	334	PF00069	6.50E-66	YNL088w	55	204	PF02518	1.40E-15	0.83936	0
YOR061w	50	334	PF00069	6.50E-66	YOR039w	38	213	PF01214	8.20E-140	0.899784	1
YOR074c	8	304	PF00303	1.10E-225	YPR086w	22	66	PF08271	2.50E-17	0.882695	0
YOR089c	1	171	PF00025	7.50E-07	YKR014c	1	193	PF00025	0.00042	0.81967	1
YOR089c	9	173	PF00071	5.60E-94	YNL093w	14	181	PF00071	9.60E-87	0.858055	1
YOR125c	135	226	PF03232	1.50E-42	YJL068c	13	291	PF00756	1.70E-109	0.954706	0
YOR128c	105	285	PF02222	2.80E-99	YBR021w	103	562	PF02133	1.00E-256	0.912431	0
YOR128c	105	285	PF02222	2.80E-99	YCR012w	3	412	PF00162	1.40E-292	0.830825	0
YOR128c	105	299	PF07478	0.001	YKR026c	12	294	PF01008	5.40E-118	0.98372	0
YOR128c	105	285	PF02222	2.80E-99	YMR323w	2	134	PF03952	3.30E-77	0.883423	0
YOR128c	105	285	PF02222	2.80E-99	YOR128c	105	285	PF02222	2.80E-99	1	1
YOR128c	105	299	PF07478	0.001	YOR128c	105	299	PF07478	0.001	1	1
YOR128c	403	559	PF00731	1.40E-106	YOR128c	403	559	PF00731	1.40E-106	1	1
YOR128c	105	285	PF02222	2.80E-99	YPR054w	38	337	PF00069	1.00E-72	0.675525	0
YOR128c	105	285	PF02222	2.80E-99	YPR088c	108	304	PF00448	1.50E-124	0.890333	0
YOR136w	38	365	PF00180	1.70E-159	YBL022c	181	478	PF02190	2.50E-166	0.934259	0
YOR136w	38	365	PF00180	1.70E-159	YNL189w	9	110	PF01749	1.10E-45	0.738094	0
YOR136w	38	365	PF00180	1.70E-159	YPR110c	48	330	PF01193	8.90E-20	0.914313	0
YOR150w	16	145	PF00572	8.00E-32	YDR172w	576	684	PF03143	2.30E-39	0.975668	0
YOR150w	16	145	PF00572	8.00E-32	YER081w	61	381	PF00389	1.40E-39	0.956863	0
YOR151c	1126	1219	PF04560	5.80E-50	YBL039c	314	555	PF00117	3.20E-71	0.733248	0
YOR151c	1126	1219	PF04560	5.80E-50	YBR154c	142	215	PF01191	7.60E-49	0.763685	0
YOR151c	42	464	PF04563	6.30E-120	YDL140c	807	1398	PF04998	2.30E-170	0.814773	1
YOR151c	42	464	PF04563	6.30E-120	YDR404c	1	79	PF03876	1.20E-38	0.848309	0
YOR151c	681	745	PF04567	6.50E-26	YIL021w	49	171	PF01000	7.10E-41	0.873951	0
YOR157c	26	207	PF00227	8.90E-68	YER094c	7	190	PF00227	5.60E-52	0.906405	1
YOR159c	19	92	PF01423	2.30E-19	YPR182w	17	83	PF01423	2.20E-21	0.927989	1
YOR176w	38	357	PF00762	5.50E-174	YDL134c	110	305	PF00149	7.10E-40	0.503145	0
YOR176w	38	357	PF00762	5.50E-174	YGR123c	242	438	PF00149	2.00E-34	0.937623	0
YOR185c	14	128	PF08477	9.20E-16	YER009w	8	121	PF02136	1.20E-46	0.728111	0
YOR185c	14	128	PF08477	9.20E-16	YOL128c	41	329	PF00069	2.10E-62	0.458893	0
YOR190w	92	418	PF00150	7.50E-05	YLR447c	12	343	PF01992	2.50E-169	0.965142	0
YOR202w	57	201	PF00475	6.40E-110	YOR202w	57	201	PF00475	6.40E-110	1	1
YOR202w	57	201	PF00475	6.40E-110	YPR016c	3	204	PF01912	2.40E-136	0.952954	0
YOR207c	555	617	PF04566	2.10E-37	YDR045c	2	55	PF02150	1.20E-25	0.858902	1
YOR207c	555	617	PF04566	2.10E-37	YKL144c	79	211	PF08292	5.80E-89	0.914178	0
YOR207c	1058	1144	PF04560	5.20E-47	YNL113w	57	133	PF01193	2.00E-20	0.8153	0
YOR207c	555	617	PF04566	2.10E-37	YOR116c	370	537	PF00623	6.40E-117	0.833982	0
YOR207c	555	617	PF04566	2.10E-37	YPR110c	48	330	PF01193	8.90E-20	0.847708	0
YOR210w	1	61	PF01194	8.40E-41	YDL140c	1141	1274	PF04990	9.50E-79	0.954371	0
YOR210w	1	61	PF01194	8.40E-41	YOR151c	42	464	PF04563	6.30E-120	0.885226	1
YOR210w	1	61	PF01194	8.40E-41	YPR110c	48	330	PF01193	8.90E-20	0.878128	1
YOR224c	7	146	PF03870	3.90E-92	YDL140c	873	1056	PF04992	4.00E-97	0.975406	1
YOR224c	7	146	PF03870	3.90E-92	YKL144c	79	211	PF08292	5.80E-89	0.981323	0
YOR224c	7	146	PF03870	3.90E-92	YOR116c	855	1386	PF04998	4.80E-158	0.974056	0
YOR224c	7	146	PF03870	3.90E-92	YPR110c	48	330	PF01193	8.90E-20	0.971116	1
YOR232w	51	224	PF01025	3.20E-82	YJR045c	30	413	PF06723	0.00044	0.796176	0
YOR232w	51	224	PF01025	3.20E-82	YOR232w	51	224	PF01025	3.20E-82	1	1
YPL002c	85	233	PF04157	2.00E-29	YPR086w	239	309	PF00382	5.70E-16	0.934952	0
YPL010w	8	159	PF01217	8.20E-09	YGL137w	325	794	PF04053	1.20E-254	0.975472	0
YPL028w	2	267	PF00108	7.20E-159	YNL244c	20	101	PF01253	6.80E-42	0.769668	0
YPL028w	2	267	PF00108	7.20E-159	YPR165w	12	185	PF00071	6.20E-87	0.492694	0
YPL031c	7	297	PF00069	9.90E-95	YDL246c	170	316	PF00107	2.40E-40	0.846015	0
YPL031c	7	297	PF00069	9.90E-95	YFL030w	8	370	PF00266	3.00E-08	0.810633	0
YPL031c	7	297	PF00069	9.90E-95	YJR104c	1	154	PF00080	1.30E-101	0.811332	0
YPL031c	7	297	PF00069	9.90E-95	YJR159w	170	316	PF00107	2.40E-40	0.846015	0
YPL046c	4	66	PF03931	4.30E-21	YPL046c	4	66	PF03931	4.30E-21	1	1
YPL048w	253	359	PF00647	9.20E-84	YBR118w	258	325	PF03144	3.50E-24	0.91696	0
YPL050c	50	392	PF03452	1.10E-257	YLR447c	12	343	PF01992	2.50E-169	0.827343	0
YPL051w	3	186	PF00025	1.40E-42	YER044c	15	131	PF03694	1.00E-83	0.847211	0
YPL051w	19	188	PF00071	1.90E-06	YKR030w	35	273	PF05216	9.60E-167	0.725219	0
YPL051w	3	186	PF00025	1.40E-42	YPR086w	133	203	PF00382	1.30E-35	0.772631	0
YPL088w	10	336	PF00248	1.20E-90	YPL088w	10	336	PF00248	1.20E-90	1	1
YPL091w	25	339	PF07992	1.80E-62	YPL091w	25	339	PF07992	1.80E-62	1	1
YPL091w	199	294	PF00070	1.10E-28	YPL091w	199	294	PF00070	1.10E-28	1	1
YPL091w	372	483	PF02852	1.30E-52	YPL091w	372	483	PF02852	1.30E-52	1	1
YPL106c	4	644	PF00012	1.50E-248	YML028w	5	182	PF00578	1.70E-113	0.882539	0
YPL111w	11	332	PF00491	3.10E-177	YBR011c	45	229	PF00719	2.00E-135	0.757407	0
YPL111w	11	332	PF00491	3.10E-177	YEL034w	84	151	PF01287	1.10E-38	0.853004	0
YPL111w	11	332	PF00491	3.10E-177	YKL085w	18	163	PF00056	7.70E-70	0.930723	0
YPL111w	11	332	PF00491	3.10E-177	YKL104c	2	215	PF00310	8.80E-58	0.92477	0
YPL111w	11	332	PF00491	3.10E-177	YNL189w	9	110	PF01749	1.10E-45	0.847276	0
YPL111w	11	332	PF00491	3.10E-177	YPL111w	11	332	PF00491	3.10E-177	1	1
YPL111w	11	332	PF00491	3.10E-177	YPL160w	22	769	PF00133	7.10E-07	0.918923	0
YPL135w	34	161	PF01592	2.50E-84	YCL017c	100	462	PF00266	2.10E-158	0.950268	0
YPL152w	2	305	PF03095	2.40E-193	YLR447c	12	343	PF01992	2.50E-169	0.955334	0
YPL160w	806	951	PF08264	8.80E-09	YNL244c	20	101	PF01253	6.80E-42	0.926062	0
YPL160w	806	951	PF08264	8.80E-09	YPR110c	48	330	PF01193	8.90E-20	0.971631	0
YPL189w	202	559	PF03062	2.80E-90	YBR159w	63	242	PF00106	2.50E-08	0.93334	0
YPL203w	70	311	PF07714	2.20E-19	YKL166c	88	342	PF00069	2.50E-100	0.906159	0
YPL211w	1	175	PF03657	1.10E-06	YKR081c	31	238	PF04427	1.90E-56	0.962781	0
YPL227c	76	263	PF00535	2.10E-27	YEL063c	92	557	PF00324	8.30E-189	0.92283	0
YPL227c	76	263	PF00535	2.10E-27	YGR060w	47	265	PF01598	3.70E-106	0.929256	0
YPL227c	76	263	PF00535	2.10E-27	YJL026w	76	358	PF00268	7.00E-177	0.950882	0
YPL227c	76	263	PF00535	2.10E-27	YJL196c	7	309	PF01151	1.70E-227	0.962066	0
YPL227c	76	263	PF00535	2.10E-27	YPL274w	81	544	PF00324	2.50E-132	0.909445	0
YPL234c	96	161	PF00137	5.40E-24	YLL028w	152	544	PF07690	9.70E-42	0.771844	0
YPL259c	1	142	PF01217	3.10E-05	YBR221c	231	355	PF02780	8.40E-56	0.604028	0
YPL259c	1	142	PF01217	3.10E-05	YER165w	490	563	PF00658	4.60E-46	0.836505	0
YPL259c	1	142	PF01217	3.10E-05	YLR170c	3	146	PF01217	3.10E-96	0.81461	0
YPL259c	1	142	PF01217	3.10E-05	YOL010w	183	286	PF05189	2.70E-45	0.757546	0
YPL259c	1	142	PF01217	3.10E-05	YOL077c	34	227	PF04427	2.30E-64	0.741135	0
YPL259c	1	142	PF01217	3.10E-05	YOR187w	263	333	PF03144	4.00E-28	0.753804	0
YPL259c	1	142	PF01217	3.10E-05	YPR016c	3	204	PF01912	2.40E-136	0.721576	0
YPL262w	36	367	PF00206	9.80E-188	YPR165w	12	185	PF00071	6.20E-87	0.716682	0
YPL274w	81	544	PF00324	2.50E-132	YBR159w	63	242	PF00106	2.50E-08	0.906301	0
YPR006c	46	575	PF00463	6.40E-189	YLR447c	12	343	PF01992	2.50E-169	0.93307	0
YPR010c	652	693	PF04567	8.40E-08	YBR143c	277	413	PF03465	2.50E-61	0.850019	0
YPR010c	698	1065	PF00562	1.60E-179	YKL067w	6	140	PF00334	4.60E-104	0.892338	0
YPR010c	652	693	PF04567	8.40E-08	YOR210w	1	61	PF01194	8.40E-41	0.77082	0
YPR010c	698	1065	PF00562	1.60E-179	YPR016c	3	204	PF01912	2.40E-136	0.89537	0
YPR010c	1067	1138	PF04560	1.50E-12	YPR110c	48	330	PF01193	8.90E-20	0.94912	0
YPR035w	107	356	PF00120	1.10E-90	YBR126c	16	482	PF00982	5.90E-294	0.886741	0
YPR069c	13	256	PF01564	3.40E-152	YLR146c	13	263	PF01564	6.60E-142	0.88449	1
YPR074c	356	533	PF02779	4.70E-69	YBR117c	356	533	PF02779	1.50E-70	0.998733	1
YPR082c	5	137	PF02966	1.70E-102	YFL017w-a	5	73	PF01423	2.00E-16	0.892593	0
YPR082c	5	137	PF02966	1.70E-102	YNL147w	20	96	PF01423	4.90E-22	0.453444	0
YPR082c	5	137	PF02966	1.70E-102	YPR182w	17	83	PF01423	2.20E-21	0.537515	0
YPR086w	239	309	PF00382	5.70E-16	YDL086w	18	255	PF01738	9.30E-09	0.965065	0
YPR086w	239	309	PF00382	5.70E-16	YFL038c	1	169	PF00025	4.70E-06	0.473706	0
YPR086w	133	203	PF00382	1.30E-35	YKL058w	5	53	PF02268	1.50E-34	0.957305	0
YPR086w	133	203	PF00382	1.30E-35	YPR041w	1	129	PF01873	2.90E-80	0.945379	0
YPR086w	239	309	PF00382	5.70E-16	YPR066w	1	143	PF00899	9.90E-48	0.89968	0
YPR103w	72	255	PF00227	1.50E-66	YER094c	7	190	PF00227	5.60E-52	0.954401	1
YPR103w	72	255	PF00227	1.50E-66	YFR050c	38	233	PF00227	2.20E-21	0.865412	1
YPR103w	72	255	PF00227	1.50E-66	YGL011c	40	228	PF00227	7.10E-48	0.868728	1
YPR103w	72	255	PF00227	1.50E-66	YJL001w	16	197	PF00227	3.70E-65	0.928531	1
YPR103w	72	255	PF00227	1.50E-66	YNL244c	20	101	PF01253	6.80E-42	0.879222	0
YPR110c	48	330	PF01193	8.90E-20	YDR453c	5	182	PF00578	1.60E-101	0.905926	0
YPR110c	48	330	PF01193	8.90E-20	YGL026c	9	272	PF00290	9.30E-161	0.977752	0
YPR110c	48	330	PF01193	8.90E-20	YGL137w	325	794	PF04053	1.20E-254	0.893756	0
YPR110c	48	330	PF01193	8.90E-20	YGL245w	509	681	PF03950	9.60E-73	0.967892	0
YPR110c	48	330	PF01193	8.90E-20	YHR112c	5	372	PF01053	6.20E-27	0.958103	0
YPR110c	83	220	PF01000	4.50E-61	YKL218c	16	306	PF00291	1.00E-95	0.980264	0
YPR110c	48	330	PF01193	8.90E-20	YLR086w	155	1406	PF02463	1.10E-140	0.957635	0
YPR110c	48	330	PF01193	8.90E-20	YOR116c	10	368	PF04997	6.30E-106	0.937882	0
YPR145w	2	162	PF00310	6.20E-12	YHR113w	25	478	PF02127	9.20E-301	0.835055	0
YPR156c	188	616	PF00083	0.00011	YBR159w	63	242	PF00106	2.50E-08	0.813766	0
YPR165w	12	185	PF00071	6.20E-87	YFR044c	98	474	PF01546	7.50E-29	0.66954	0
YPR181c	399	512	PF08033	3.00E-43	YIL109c	301	551	PF04811	1.40E-124	0.962764	1
YPR181c	399	512	PF08033	3.00E-43	YLR026c	50	161	PF00804	1.30E-16	0.984641	0
YPR181c	119	391	PF04811	1.00E-135	YNL049c	234	507	PF04811	7.30E-89	0.963574	1
YPR182w	17	83	PF01423	2.20E-21	YNL189w	9	110	PF01749	1.10E-45	0.676128	0

If we restricted our set to only those interactions involving proteins with at least 75% (instead of 50% before) of their sequence lengths assigned with Pfam domain(s), the percentage of predictions in iPfam jumps by 52%. Our restricted set, referred to as “test set SLA ≥75%”, contained a total of 374 protein–protein interactions among 298 proteins. For this set, we inferred a total of 392 domain–domain interactions (Supplementary material S5), 336 of which are unique. 58 out of the 336 unique predictions (≈17.26%) are in iPfam. The increase in the prediction accuracy from 11.35% (for the test set SLA ≥50%) to 17.26% (for the test set SLA ≥75%) indicates that the higher the SLA, the better the prediction accuracy. This is understandable considering the fact that the binding region in an interacting protein needs to be contained in one of that protein's domains in order to have any possibility of it being identified.

Supplementary material S5.

RCDP prediction results for the test set 2, containing 394 domain-domain interactions.

Format: <Protein1> <startResidue> <endResidue> <PfamDomain> <e-value> <Protein2> <startResidue> <endResidue> <PfamDomain> <e-value> <correlationCoefficient> <inPDBorNOT>

Protein1	startResidue	endResidue	PfamDomain	e-value	Protein2	startResidue	endResidue	PfamDomain	e-value	correlationCoefficient	inPDBorNOT
YAL038w	18	365	PF00224	2.10E-267	YNL307c	35	327	PF00069	2.40E-75	0.637991	0
YAL038w	379	499	PF02887	4.60E-74	YOR226c	26	153	PF01592	2.10E-78	0.871644	0
YAL062w	40	170	PF02812	3.80E-74	YNL189w	9	110	PF01749	1.10E-45	0.9223	0
YBL039c	1	280	PF06418	2.50E-194	YJR103w	1	280	PF06418	5.70E-194	0.998837	0
YBL040c	1	209	PF00810	1.40E-157	YOL020w	86	546	PF00324	2.90E-141	0.901858	0
YBL078c	13	116	PF02991	1.30E-79	YOR100c	140	226	PF00153	4.20E-26	0.749538	0
YBR018c	4	192	PF01087	1.60E-115	YPR054w	38	337	PF00069	1.00E-72	0.695854	0
YBR039w	34	310	PF00231	9.50E-131	YDL145c	812	1200	PF06957	1.10E-30	0.970729	0
YBR039w	34	310	PF00231	9.50E-131	YJR068w	261	350	PF08542	5.80E-27	0.834343	0
YBR068c	99	567	PF00324	1.00E-193	YDR046c	94	562	PF00324	1.00E-171	0.998889	0
YBR085w	215	305	PF00153	9.10E-29	YHR002w	32	127	PF00153	6.20E-29	0.898158	1
YBR088c	127	254	PF02747	2.30E-79	YJR068w	261	350	PF08542	5.80E-27	0.89377	0
YBR088c	1	125	PF00705	1.10E-78	YNL290w	237	327	PF08542	4.10E-28	0.705218	0
YBR088c	1	125	PF00705	1.10E-78	YOL094c	229	316	PF08542	1.90E-33	0.919656	0
YBR088c	1	125	PF00705	1.10E-78	YOR116c	855	1386	PF04998	4.80E-158	0.905903	0
YBR117c	7	339	PF00456	5.70E-239	YLR447c	12	343	PF01992	2.50E-169	0.968223	0
YBR126c	16	482	PF00982	5.90E-294	YOR089c	9	173	PF00071	5.60E-94	0.821956	0
YBR127c	397	500	PF00306	1.80E-24	YKL080w	8	392	PF03223	3.50E-84	0.95271	0
YBR127c	397	500	PF00306	1.80E-24	YLR447c	12	343	PF01992	2.50E-169	0.828209	0
YBR154c	1	101	PF03871	6.20E-65	YDL140c	510	669	PF04983	1.50E-69	0.964818	0
YBR154c	1	101	PF03871	6.20E-65	YDR404c	1	79	PF03876	1.20E-38	0.967535	0
YBR154c	1	101	PF03871	6.20E-65	YKL144c	1	77	PF03876	9.60E-41	0.913435	0
YBR154c	1	101	PF03871	6.20E-65	YOR116c	742	848	PF05000	6.20E-45	0.900691	0
YBR154c	142	215	PF01191	7.60E-49	YPR110c	48	330	PF01193	8.90E-20	0.866512	0
YBR160w	8	295	PF00069	4.30E-98	YDR212w	36	549	PF00118	8.70E-163	0.771758	0
YBR160w	8	295	PF00069	4.30E-98	YLR086w	155	1406	PF02463	1.10E-140	0.703017	0
YBR170c	259	577	PF05021	2.20E-223	YLR044c	387	538	PF02775	1.50E-08	0.946819	0
YBR176w	24	291	PF02548	7.50E-184	YBR176w	24	291	PF02548	7.50E-184	1	1
YBR176w	24	291	PF02548	7.50E-184	YNL189w	204	244	PF00514	2.00E-09	0.920074	0
YBR205w	17	357	PF01793	9.10E-230	YFL038c	1	169	PF00025	4.70E-06	0.548945	0
YBR218c	852	1060	PF02436	5.90E-131	YPR110c	48	330	PF01193	8.90E-20	0.958684	0
YBR249c	40	355	PF00793	5.20E-182	YPR110c	48	330	PF01193	8.90E-20	0.941637	0
YBR252w	16	146	PF00692	1.60E-58	YNL189w	9	110	PF01749	1.10E-45	0.822352	0
YBR291c	213	299	PF00153	5.60E-27	YHR096c	89	549	PF00083	9.80E-241	0.942393	0
YCL040w	12	230	PF00349	2.60E-134	YCL040w	12	230	PF00349	2.60E-134	1	1
YCL040w	243	500	PF03727	8.50E-148	YCL040w	243	500	PF03727	8.50E-148	1	1
YCL040w	243	500	PF03727	8.50E-148	YNL189w	9	110	PF01749	1.10E-45	0.907044	0
YCR002c	29	309	PF00735	9.20E-183	YFL018c	380	489	PF02852	3.30E-66	0.899385	0
YCR005c	64	441	PF00285	1.60E-205	YCR005c	64	441	PF00285	1.60E-205	1	1
YCR005c	64	441	PF00285	1.60E-205	YKL085w	165	331	PF02866	3.50E-83	0.922119	0
YCR034w	10	313	PF01151	7.70E-229	YHR094c	72	488	PF07690	4.20E-29	0.951123	0
YCR034w	10	313	PF01151	7.70E-229	YJL219w	68	486	PF07690	1.70E-26	0.952833	0
YCR034w	10	313	PF01151	7.70E-229	YLL061w	77	540	PF00324	8.50E-124	0.884575	0
YCR034w	10	313	PF01151	7.70E-229	YOL020w	86	546	PF00324	2.90E-141	0.951499	0
YCR034w	10	313	PF01151	7.70E-229	YPL274w	81	544	PF00324	2.50E-132	0.89473	0
YDL064w	8	152	PF00179	2.00E-69	YDL064w	8	152	PF00179	2.00E-69	1	1
YDL100c	18	336	PF02374	4.70E-196	YHR057c	37	199	PF00160	1.50E-110	0.758264	0
YDL100c	18	336	PF02374	4.70E-196	YJL153c	66	515	PF07994	1.80E-199	0.926979	0
YDL100c	18	336	PF02374	4.70E-196	YNL055c	2	276	PF01459	9.70E-121	0.950579	0
YDL100c	18	336	PF02374	4.70E-196	YOL126c	225	416	PF02866	7.10E-78	0.909399	0
YDL108w	7	290	PF00069	2.80E-111	YDL140c	873	1056	PF04992	4.00E-97	0.940923	0
YDL108w	7	290	PF00069	2.80E-111	YOR151c	1126	1219	PF04560	5.80E-50	0.655472	0
YDL135c	1	202	PF02115	7.30E-27	YPR165w	12	185	PF00071	6.20E-87	0.662604	1
YDL137w	4	177	PF00025	2.90E-125	YPR110c	48	330	PF01193	8.90E-20	0.725142	0
YDL143w	31	527	PF00118	3.00E-167	YKR026c	12	294	PF01008	5.40E-118	0.947321	0
YDL145c	343	787	PF04053	8.00E-253	YCR012w	3	412	PF00162	1.40E-292	0.872514	0
YDL145c	343	787	PF04053	8.00E-253	YDR238c	682	961	PF07718	5.60E-155	0.983597	0
YDL145c	812	1200	PF06957	1.10E-30	YPL010w	8	159	PF01217	8.20E-09	0.978099	0
YDL192w	4	177	PF00025	4.30E-126	YDL137w	4	177	PF00025	2.90E-125	0.999971	1
YDL192w	4	177	PF00025	4.30E-126	YPR110c	48	330	PF01193	8.90E-20	0.727796	0
YDL236w	24	276	PF00702	6.40E-20	YNL189w	9	110	PF01749	1.10E-45	0.958621	0
YDL245c	79	484	PF07690	1.70E-24	YHR096c	93	509	PF07690	1.20E-31	0.985558	0
YDL245c	79	484	PF07690	1.70E-24	YJR160c	104	517	PF07690	0.0005	0.934402	0
YDR044w	9	327	PF01218	9.00E-161	YNL189w	9	110	PF01749	1.10E-45	0.880468	0
YDR045c	2	55	PF02150	1.20E-25	YOR116c	10	368	PF04997	6.30E-106	0.938008	0
YDR046c	94	562	PF00324	1.00E-171	YLR372w	10	321	PF01151	3.70E-232	0.94653	0
YDR099w	5	241	PF00244	2.30E-151	YBR001c	192	750	PF01204	8.20E-278	0.891849	0
YDR099w	5	241	PF00244	2.30E-151	YDR099w	5	241	PF00244	2.30E-151	1	1
YDR127w	1311	1393	PF08501	1.80E-32	YJL008c	38	549	PF00118	9.90E-164	0.979215	0
YDR127w	17	367	PF01761	1.10E-144	YOR136w	38	365	PF00180	1.70E-159	0.95761	0
YDR127w	897	1064	PF01202	1.70E-55	YPL235w	122	433	PF06068	1.90E-220	0.947078	0
YDR139c	6	74	PF00240	4.80E-25	YDR328c	4	99	PF03931	1.90E-07	0.570641	0
YDR139c	6	74	PF00240	4.80E-25	YLR306w	31	172	PF00179	6.10E-51	0.640541	0
YDR155c	3	162	PF00160	1.20E-116	YKL103c	59	501	PF02127	3.80E-263	0.744427	0
YDR155c	3	162	PF00160	1.20E-116	YNL244c	20	101	PF01253	6.80E-42	0.792188	0
YDR155c	3	162	PF00160	1.20E-116	YPL235w	122	433	PF06068	1.90E-220	0.563227	0
YDR226w	11	198	PF00406	2.10E-97	YBL036c	21	250	PF01168	3.80E-08	0.856139	0
YDR226w	11	198	PF00406	2.10E-97	YOR176w	38	357	PF00762	5.50E-174	0.93667	0
YDR226w	11	198	PF00406	2.10E-97	YPL031c	7	258	PF07714	3.50E-18	0.813632	0
YDR256c	23	410	PF00199	1.00E-277	YMR314w	29	216	PF00227	9.70E-52	0.833534	0
YDR256c	23	410	PF00199	1.00E-277	YNL189w	9	110	PF01749	1.10E-45	0.735524	0
YDR328c	4	99	PF03931	1.90E-07	YBR127c	397	500	PF00306	1.80E-24	0.911862	0
YDR328c	116	193	PF01466	1.20E-51	YEL051w	13	211	PF01813	5.90E-98	0.878649	0
YDR342c	72	488	PF07690	3.70E-29	YBL036c	21	250	PF01168	3.80E-08	0.956096	0
YDR342c	72	488	PF07690	3.70E-29	YNL323w	93	407	PF03381	1.20E-201	0.939934	0
YDR343c	72	488	PF07690	3.70E-29	YBL036c	21	250	PF01168	3.80E-08	0.956096	0
YDR343c	72	488	PF07690	3.70E-29	YGR040w	13	313	PF00069	3.30E-95	0.685304	0
YDR353w	156	249	PF00070	2.80E-29	YOL128c	41	329	PF00069	2.10E-62	0.756139	0
YDR382w	17	109	PF00428	1.30E-36	YBR006w	27	488	PF00171	2.00E-205	0.791924	0
YDR404c	1	79	PF03876	1.20E-38	YDL140c	510	669	PF04983	1.50E-69	0.971808	0
YDR404c	1	79	PF03876	1.20E-38	YGR063c	2	99	PF06093	1.60E-66	0.925248	0
YDR404c	1	79	PF03876	1.20E-38	YOR224c	7	146	PF03870	3.90E-92	0.961401	0
YDR487c	5	208	PF00926	5.80E-135	YNL189w	9	110	PF01749	1.10E-45	0.919764	0
YDR516c	243	500	PF03727	1.10E-124	YCL040w	243	500	PF03727	8.50E-148	0.999243	1
YDR529c	15	119	PF02271	1.10E-68	YBR082c	6	143	PF00179	3.90E-80	0.50018	0
YEL021w	30	251	PF00215	1.30E-89	YEL021w	30	251	PF00215	1.30E-89	1	1
YEL027w	12	77	PF00137	8.70E-21	YLR034c	31	408	PF01566	2.00E-226	0.770609	0
YEL054c	75	143	PF00298	5.60E-29	YDL081c	20	105	PF00428	6.50E-35	0.867395	0
YEL054c	75	143	PF00298	5.60E-29	YDR382w	17	109	PF00428	1.30E-36	0.850745	0
YEL054c	75	143	PF00298	5.60E-29	YOL039w	16	105	PF00428	6.80E-32	0.856575	0
YEL063c	92	557	PF00324	8.30E-189	YBL040c	1	209	PF00810	1.40E-157	0.905131	0
YEL063c	92	557	PF00324	8.30E-189	YCR034w	10	313	PF01151	7.70E-229	0.925666	0
YEL063c	92	557	PF00324	8.30E-189	YJL196c	7	309	PF01151	1.70E-227	0.914412	0
YEL063c	92	557	PF00324	8.30E-189	YLR372w	10	321	PF01151	3.70E-232	0.910386	0
YEL063c	92	557	PF00324	8.30E-189	YPL234c	96	161	PF00137	5.40E-24	0.907556	0
YEL069c	76	481	PF07690	6.20E-27	YPR110c	48	330	PF01193	8.90E-20	0.975212	0
YEL071w	243	495	PF02913	1.40E-81	YPR165w	12	185	PF00071	6.20E-87	0.633138	0
YER009w	8	121	PF02136	1.20E-46	YNL189w	9	110	PF01749	1.10E-45	0.839762	0
YER012w	1	184	PF00227	3.20E-57	YBL041w	25	226	PF00227	5.10E-40	0.982626	1
YER012w	1	184	PF00227	3.20E-57	YER094c	7	190	PF00227	5.60E-52	0.960061	1
YER012w	1	184	PF00227	3.20E-57	YJL001w	16	197	PF00227	3.70E-65	0.957508	1
YER012w	1	184	PF00227	3.20E-57	YMR314w	29	216	PF00227	9.70E-52	0.967412	1
YER020w	108	399	PF00025	0.00018	YNL037c	30	353	PF00180	7.50E-87	0.789057	0
YER057c	10	127	PF01042	6.50E-63	YNL189w	9	110	PF01749	1.10E-45	0.796174	0
YER086w	72	371	PF00291	5.90E-96	YER086w	72	371	PF00291	5.90E-96	1	1
YER086w	383	481	PF00585	3.10E-07	YER086w	383	481	PF00585	3.10E-07	1	1
YER086w	485	574	PF00585	3.40E-45	YER086w	485	574	PF00585	3.40E-45	1	1
YER126c	1	238	PF01201	6.30E-95	YPR016c	3	204	PF01912	2.40E-136	0.856728	0
YER146w	10	83	PF01423	2.20E-20	YCR024c	133	487	PF00152	4.00E-72	0.883096	0
YER146w	10	83	PF01423	2.20E-20	YDR378c	14	83	PF01423	2.20E-18	0.979358	1
YER146w	10	83	PF01423	2.20E-20	YER131w	1	113	PF01283	1.30E-82	0.634338	0
YER146w	10	83	PF01423	2.20E-20	YER146w	10	83	PF01423	2.20E-20	1	1
YER146w	10	83	PF01423	2.20E-20	YPL152w	2	305	PF03095	2.40E-193	0.751133	0
YER146w	10	83	PF01423	2.20E-20	YPR010c	652	693	PF04567	8.40E-08	0.530435	0
YER156c	11	338	PF03690	2.40E-245	YFL038c	1	169	PF00025	4.70E-06	0.515765	0
YER177w	5	241	PF00244	2.40E-151	YDR099w	5	241	PF00244	2.30E-151	0.999704	1
YER177w	5	241	PF00244	2.40E-151	YGL115w	193	318	PF00571	3.90E-21	0.69678	0
YER177w	5	241	PF00244	2.40E-151	YNL189w	9	110	PF01749	1.10E-45	0.75834	0
YFL005w	21	136	PF08477	3.00E-21	YFL038c	10	171	PF00071	4.70E-102	0.770305	0
YFL018c	28	352	PF07992	6.20E-63	YBR221c	231	355	PF02780	8.40E-56	0.807822	0
YFL045c	16	251	PF08282	0.00089	YNL189w	9	110	PF01749	1.10E-45	0.835653	0
YFR047c	26	117	PF02749	2.80E-35	YFR047c	26	117	PF02749	2.80E-35	1	0
YFR047c	119	292	PF01729	1.50E-100	YFR047c	119	292	PF01729	1.50E-100	1	1
YFR047c	26	117	PF02749	2.80E-35	YNL189w	372	412	PF00514	4.70E-13	0.855561	0
YGL040c	13	338	PF00490	3.00E-224	YGL040c	13	338	PF00490	3.00E-224	1	1
YGL040c	13	338	PF00490	3.00E-224	YNL189w	9	110	PF01749	1.10E-45	0.858525	0
YGL054c	2	125	PF03311	1.10E-77	YLR372w	10	321	PF01151	3.70E-232	0.90263	0
YGL062w	851	1059	PF02436	4.20E-133	YPR110c	48	330	PF01193	8.90E-20	0.95907	0
YGL087c	9	130	PF00179	2.10E-06	YDR092w	7	144	PF00179	1.70E-73	0.51427	1
YGL130w	28	249	PF01068	0.00054	YBR221c	39	215	PF02779	7.20E-73	0.966166	0
YGL130w	252	399	PF03919	1.70E-26	YDL140c	873	1056	PF04992	4.00E-97	0.963014	0
YGL221c	17	280	PF01784	2.30E-83	YGL221c	17	280	PF01784	2.30E-83	1	1
YGL221c	17	280	PF01784	2.30E-83	YNL189w	9	110	PF01749	1.10E-45	0.898897	0
YGL234w	345	440	PF02843	1.30E-54	YJR068w	261	350	PF08542	5.80E-27	0.917835	0
YGL234w	345	440	PF02843	1.30E-54	YOL094c	229	316	PF08542	1.90E-33	0.94671	0
YGL238w	23	96	PF03810	1.80E-22	YNL189w	372	412	PF00514	4.70E-13	0.814625	0
YGL253w	21	223	PF00349	1.10E-139	YGL253w	21	223	PF00349	1.10E-139	1	1
YGL253w	225	473	PF03727	5.10E-163	YGL253w	225	473	PF03727	5.10E-163	1	1
YGR020c	8	111	PF01990	2.70E-35	YEL051w	13	211	PF01813	5.90E-98	0.923643	0
YGR024c	1	237	PF04446	2.30E-184	YGR024c	1	237	PF04446	2.30E-184	1	0
YGR040w	13	313	PF00069	3.30E-95	YGL062w	851	1059	PF02436	4.20E-133	0.826408	0
YGR040w	13	313	PF00069	3.30E-95	YLL039c	234	302	PF00240	5.60E-38	0.778215	0
YGR040w	13	313	PF00069	3.30E-95	YML123c	81	507	PF07690	2.50E-21	0.820486	0
YGR040w	13	313	PF00069	3.30E-95	YPR010c	40	468	PF04563	2.30E-84	0.788234	0
YGR133w	21	174	PF00179	7.70E-55	YGR133w	21	174	PF00179	7.70E-55	1	1
YGR144w	39	306	PF01946	5.30E-180	YGR144w	39	306	PF01946	5.30E-180	1	0
YGR144w	67	296	PF01266	0.00021	YGR144w	67	296	PF01266	0.00021	1	1
YGR155w	14	320	PF00291	6.70E-114	YBR088c	1	125	PF00705	1.10E-78	0.919288	0
YGR155w	14	320	PF00291	6.70E-114	YGR040w	13	313	PF00069	3.30E-95	0.841094	0
YGR155w	371	507	PF00571	6.40E-20	YNL189w	9	110	PF01749	1.10E-45	0.853289	0
YHR007c	57	521	PF00067	7.10E-134	YPL274w	81	544	PF00324	2.50E-132	0.90946	0
YHR039c-a	1	106	PF03179	4.50E-55	YBR127c	397	500	PF00306	1.80E-24	0.858839	0
YHR039c-a	1	106	PF03179	4.50E-55	YGR020c	8	111	PF01990	2.70E-35	0.900294	0
YHR068w	45	377	PF01916	1.40E-230	YNL189w	9	110	PF01749	1.10E-45	0.875549	0
YHR094c	72	488	PF07690	4.20E-29	YLR372w	10	321	PF01151	3.70E-232	0.940889	0
YHR113w	25	478	PF02127	9.20E-301	YHR113w	25	478	PF02127	9.20E-301	1	0
YHR179w	16	368	PF00724	3.10E-200	YOL128c	41	329	PF00069	2.10E-62	0.710313	0
YHR183w	178	476	PF00393	2.00E-210	YKL085w	18	163	PF00056	7.70E-70	0.787604	0
YHR183w	178	476	PF00393	2.00E-210	YPR110c	48	330	PF01193	8.90E-20	0.913366	0
YHR208w	68	373	PF01063	3.10E-164	YJR148w	51	356	PF01063	2.30E-166	0.999337	1
YHR216w	35	512	PF00478	6.90E-230	YNL189w	9	110	PF01749	1.10E-45	0.866763	0
YIL021w	16	260	PF01193	1.30E-19	YBR154c	142	215	PF01191	7.60E-49	0.926415	0
YIL021w	16	260	PF01193	1.30E-19	YDR404c	1	79	PF03876	1.20E-38	0.943482	0
YIL021w	16	260	PF01193	1.30E-19	YOR224c	7	146	PF03870	3.90E-92	0.958503	1
YIL034c	1	287	PF01115	6.20E-231	YBR264c	1	167	PF00025	0.00042	0.891858	0
YIL034c	1	287	PF01115	6.20E-231	YBR291c	107	204	PF00153	3.50E-21	0.887304	0
YIL035c	40	363	PF00069	3.20E-69	YGL115w	193	318	PF00571	3.90E-21	0.844288	0
YIL035c	40	363	PF00069	3.20E-69	YIL118w	18	212	PF00071	3.70E-88	0.780596	0
YIL035c	40	363	PF00069	3.20E-69	YOR061w	50	334	PF00069	6.50E-66	0.988947	1
YIL035c	40	363	PF00069	3.20E-69	YPR016c	3	204	PF01912	2.40E-136	0.710527	0
YIL094c	25	367	PF00180	9.70E-178	YBL039c	1	280	PF06418	2.50E-194	0.800427	0
YIL118w	18	212	PF00071	3.70E-88	YEL020c	3	171	PF02776	4.00E-80	0.784339	0
YIL142w	29	519	PF00118	3.20E-166	YDL080c	15	191	PF02776	6.90E-56	0.957956	0
YIL142w	29	519	PF00118	3.20E-166	YDR212w	36	549	PF00118	8.70E-163	0.972817	1
YIL142w	29	519	PF00118	3.20E-166	YGR040w	13	313	PF00069	3.30E-95	0.864403	0
YIL145c	1	309	PF02569	1.10E-223	YLR447c	12	343	PF01992	2.50E-169	0.954206	0
YIR034c	175	323	PF01262	1.40E-20	YLR354c	25	329	PF00923	1.10E-199	0.929727	0
YJL001w	16	197	PF00227	3.70E-65	YPR054w	38	337	PF00069	1.00E-72	0.656586	0
YJL053w	5	364	PF03643	1.10E-258	YDR372c	59	340	PF05719	5.80E-206	0.910236	0
YJL060w	54	437	PF00155	3.00E-111	YBR160w	8	295	PF00069	4.30E-98	0.650912	0
YJL153c	66	515	PF07994	1.80E-199	YJL190c	5	130	PF00410	2.10E-56	0.822388	0
YJL167w	39	313	PF00348	3.50E-135	YJL167w	39	313	PF00348	3.50E-135	1	1
YJL167w	39	313	PF00348	3.50E-135	YNL244c	20	101	PF01253	6.80E-42	0.835558	0
YJL196c	7	309	PF01151	1.70E-227	YCR034w	10	313	PF01151	7.70E-229	0.957972	0
YJL196c	7	309	PF01151	1.70E-227	YLR372w	10	321	PF01151	3.70E-232	0.964207	0
YJL214w	73	490	PF07690	8.10E-24	YLR372w	10	321	PF01151	3.70E-232	0.943671	0
YJL219w	68	486	PF07690	1.70E-26	YLR447c	12	343	PF01992	2.50E-169	0.909469	0
YJR017c	64	170	PF00639	2.00E-61	YDL140c	873	1056	PF04992	4.00E-97	0.900094	0
YJR017c	64	170	PF00639	2.00E-61	YDR343c	72	488	PF07690	3.70E-29	0.906018	0
YJR017c	64	170	PF00639	2.00E-61	YIL021w	16	260	PF01193	1.30E-19	0.913003	0
YJR024c	18	235	PF00596	1.00E-71	YJR024c	18	235	PF00596	1.00E-71	1	1
YJR068w	60	243	PF00004	1.10E-08	YNL189w	9	110	PF01749	1.10E-45	0.812293	0
YJR068w	261	350	PF08542	5.80E-27	YNL290w	237	327	PF08542	4.10E-28	0.705802	1
YJR068w	60	243	PF00004	1.10E-08	YOL094c	229	316	PF08542	1.90E-33	0.865888	1
YJR103w	1	280	PF06418	5.70E-194	YJR103w	1	280	PF06418	5.70E-194	1	0
YJR103w	314	557	PF00117	2.40E-76	YJR103w	314	557	PF00117	2.40E-76	1	1
YJR121w	401	508	PF00306	2.30E-48	YBR039w	34	310	PF00231	9.50E-131	0.913245	1
YJR121w	46	113	PF02874	1.40E-27	YDR298c	32	208	PF00213	1.20E-73	0.872075	0
YJR121w	46	113	PF02874	1.40E-27	YJR121w	46	113	PF02874	1.40E-27	1	1
YJR121w	169	388	PF00006	1.10E-96	YJR121w	169	388	PF00006	1.10E-96	1	1
YJR121w	401	508	PF00306	2.30E-48	YJR121w	401	508	PF00306	2.30E-48	1	1
YJR160c	104	517	PF07690	0.0005	YLR372w	10	321	PF01151	3.70E-232	0.919537	0
YKL013c	1	169	PF05856	9.20E-112	YMR109w	759	961	PF06017	1.00E-77	0.945236	0
YKL013c	1	169	PF05856	9.20E-112	YNR035c	55	318	PF04045	2.50E-198	0.949778	0
YKL060c	16	359	PF01116	1.50E-218	YOR116c	10	368	PF04997	6.30E-106	0.813904	0
YKL067w	6	140	PF00334	4.60E-104	YKL067w	6	140	PF00334	4.60E-104	1	1
YKL080w	8	392	PF03223	3.50E-84	YEL051w	13	211	PF01813	5.90E-98	0.938925	0
YKL085w	165	331	PF02866	3.50E-83	YOL128c	41	329	PF00069	2.10E-62	0.672584	0
YKL085w	165	331	PF02866	3.50E-83	YPR110c	48	330	PF01193	8.90E-20	0.949242	0
YKL103c	59	501	PF02127	3.80E-263	YKL103c	59	501	PF02127	3.80E-263	1	0
YKL103c	59	501	PF02127	3.80E-263	YNL189w	9	110	PF01749	1.10E-45	0.916494	0
YKL106w	44	441	PF00155	1.60E-119	YLR447c	12	343	PF01992	2.50E-169	0.831604	0
YKL144c	79	211	PF08292	5.80E-89	YOR116c	855	1386	PF04998	4.80E-158	0.955007	0
YKL144c	79	211	PF08292	5.80E-89	YPR110c	48	330	PF01193	8.90E-20	0.953026	0
YKL152c	3	189	PF00300	6.30E-43	YMR109w	38	702	PF00063	1.10E-285	0.963435	0
YKL165c	442	874	PF04987	3.30E-227	YLR372w	10	321	PF01151	3.70E-232	0.952886	0
YKR002w	353	532	PF04926	9.20E-103	YNL189w	9	110	PF01749	1.10E-45	0.938503	0
YKR002w	353	532	PF04926	9.20E-103	YNL222w	7	206	PF04722	2.60E-164	0.955812	0
YKR014c	5	195	PF00071	2.50E-88	YNL093w	14	181	PF00071	9.60E-87	0.826077	1
YKR026c	12	294	PF01008	5.40E-118	YBL030c	22	119	PF00153	4.40E-35	0.872628	0
YKR026c	12	294	PF01008	5.40E-118	YEL051w	13	211	PF01813	5.90E-98	0.891922	0
YKR026c	12	294	PF01008	5.40E-118	YER146w	10	83	PF01423	2.20E-20	0.704063	0
YKR026c	12	294	PF01008	5.40E-118	YKR026c	12	294	PF01008	5.40E-118	1	1
YKR026c	12	294	PF01008	5.40E-118	YLR432w	35	512	PF00478	1.50E-235	0.895836	0
YKR030w	35	273	PF05216	9.60E-167	YER031c	5	174	PF00025	3.10E-05	0.804818	0
YLL001w	31	246	PF00350	1.20E-88	YLL001w	31	246	PF00350	1.20E-88	1	0
YLL001w	255	549	PF01031	7.10E-164	YLL001w	255	549	PF01031	7.10E-164	1	0
YLL001w	665	756	PF02212	1.60E-43	YLL001w	665	756	PF02212	1.60E-43	1	0
YLL061w	77	540	PF00324	8.50E-124	YLR372w	10	321	PF01151	3.70E-232	0.931111	0
YLR027c	30	405	PF00155	5.60E-99	YLR027c	30	405	PF00155	5.60E-99	1	1
YLR027c	30	405	PF00155	5.60E-99	YNL244c	20	101	PF01253	6.80E-42	0.862034	0
YLR109w	4	176	PF08534	1.10E-48	YLR109w	4	176	PF08534	1.10E-48	1	1
YLR109w	4	176	PF08534	1.10E-48	YMR022w	8	159	PF00179	7.50E-85	0.843329	0
YLR134w	387	538	PF02775	1.50E-09	YLR447c	12	343	PF01992	2.50E-169	0.956648	0
YLR134w	4	180	PF02776	1.40E-81	YNL244c	20	101	PF01253	6.80E-42	0.945861	0
YLR180w	115	237	PF02772	1.00E-94	YBL039c	314	555	PF00117	3.20E-71	0.914165	0
YLR180w	115	237	PF02772	1.00E-94	YER090w	31	174	PF04715	1.10E-43	0.93249	0
YLR209c	37	311	PF00896	1.10E-148	YNL189w	119	160	PF00514	1.20E-12	0.858639	0
YLR215c	27	330	PF07065	5.00E-174	YLR447c	12	343	PF01992	2.50E-169	0.979042	0
YLR229c	5	178	PF00071	5.90E-81	YDL135c	1	202	PF02115	7.30E-27	0.526573	1
YLR245c	8	115	PF00383	4.90E-37	YLR245c	8	115	PF00383	4.90E-37	1	1
YLR245c	8	115	PF00383	4.90E-37	YNL189w	9	110	PF01749	1.10E-45	0.838523	0
YLR264w	1	67	PF01200	3.20E-44	YLR264w	1	67	PF01200	3.20E-44	1	0
YLR270w	1	331	PF05652	1.70E-33	YLR081w	74	534	PF00083	2.90E-242	0.973452	0
YLR303w	6	436	PF01053	2.00E-250	YNL189w	9	110	PF01749	1.10E-45	0.970749	0
YLR354c	25	329	PF00923	1.10E-199	YJL068c	13	291	PF00756	1.70E-109	0.775248	0
YLR370c	1	178	PF04062	3.40E-137	YKL013c	1	169	PF05856	9.20E-112	0.948468	0
YLR370c	1	178	PF04062	3.40E-137	YNR035c	55	318	PF04045	2.50E-198	0.903244	0
YLR377c	21	347	PF00316	1.80E-218	YLR377c	21	347	PF00316	1.80E-218	1	1
YLR377c	21	347	PF00316	1.80E-218	YML121w	99	310	PF04670	8.40E-123	0.859526	0
YLR377c	21	347	PF00316	1.80E-218	YNL189w	9	110	PF01749	1.10E-45	0.832446	0
YLR378c	76	461	PF00344	1.10E-08	YLR372w	10	321	PF01151	3.70E-232	0.931047	0
YLR438c-a	6	78	PF01423	3.30E-23	YER146w	10	83	PF01423	2.20E-20	0.940084	1
YLR438c-a	6	78	PF01423	3.30E-23	YLR438c-a	6	78	PF01423	3.30E-23	1	1
YLR438c-a	6	78	PF01423	3.30E-23	YMR142c	7	173	PF01294	1.20E-120	0.819584	0
YLR438c-a	6	78	PF01423	3.30E-23	YOR096w	4	190	PF01251	2.80E-134	0.740254	0
YLR438w	29	367	PF00202	1.20E-148	YJR017c	64	170	PF00639	2.00E-61	0.886034	0
YLR438w	29	367	PF00202	1.20E-148	YNL244c	20	101	PF01253	6.80E-42	0.905105	0
YLR438w	29	367	PF00202	1.20E-148	YPR165w	12	185	PF00071	6.20E-87	0.673595	0
YLR447c	12	343	PF01992	2.50E-169	YGR020c	8	111	PF01990	2.70E-35	0.891512	0
YML042w	73	658	PF00755	5.70E-305	YML042w	73	658	PF00755	5.70E-305	1	1
YML042w	73	658	PF00755	5.70E-305	YNL189w	330	370	PF00514	2.30E-14	0.932793	0
YML056c	36	513	PF00478	2.50E-233	YBR088c	1	125	PF00705	1.10E-78	0.793389	0
YML056c	36	513	PF00478	2.50E-233	YER117w	16	137	PF00238	2.50E-53	0.747241	0
YML060w	127	292	PF00730	2.00E-22	YOL010w	183	286	PF05189	2.70E-45	0.920471	0
YML110c	116	225	PF08241	5.30E-06	YGL115w	193	318	PF00571	3.90E-21	0.962894	0
YML121w	7	129	PF01926	0.00014	YML121w	7	129	PF01926	0.00014	1	1
YML121w	99	310	PF04670	8.40E-123	YML121w	99	310	PF04670	8.40E-123	1	0
YML123c	81	507	PF07690	2.50E-21	YLR372w	10	321	PF01151	3.70E-232	0.94182	0
YML126c	217	490	PF08540	3.40E-184	YIL094c	25	367	PF00180	9.70E-178	0.787469	0
YML126c	217	490	PF08540	3.40E-184	YLR180w	115	237	PF02772	1.00E-94	0.871644	0
YMR022w	8	159	PF00179	7.50E-85	YLL039c	6	74	PF00240	5.60E-38	0.496123	0
YMR022w	8	159	PF00179	7.50E-85	YLL039c	82	150	PF00240	5.60E-38	0.496123	0
YMR105c	450	558	PF00408	4.70E-45	YJR068w	261	350	PF08542	5.80E-27	0.863716	0
YMR109w	38	702	PF00063	1.10E-285	YMR109w	38	702	PF00063	1.10E-285	1	1
YMR109w	759	961	PF06017	1.00E-77	YMR109w	759	961	PF06017	1.00E-77	1	0
YMR109w	1088	1145	PF00018	1.90E-18	YMR109w	1088	1145	PF00018	1.90E-18	1	1
YMR109w	1089	1145	PF07653	0.0006	YMR109w	1089	1145	PF07653	0.0006	1	0
YMR297w	1	108	PF05388	1.30E-67	YLR378c	76	461	PF00344	1.10E-08	0.882639	0
YNL037c	30	353	PF00180	7.50E-87	YOR136w	38	365	PF00180	1.70E-159	0.673997	1
YNL055c	2	276	PF01459	9.70E-121	YCR009c	6	232	PF03114	3.00E-80	0.942858	0
YNL055c	2	276	PF01459	9.70E-121	YNL090w	9	179	PF00071	8.20E-80	0.811261	0
YNL055c	2	276	PF01459	9.70E-121	YNL093w	3	179	PF00025	1.20E-06	0.931602	0
YNL090w	9	179	PF00071	8.20E-80	YOR089c	1	171	PF00025	7.50E-07	0.472051	0
YNL096c	4	190	PF01251	4.60E-125	YMR243c	7	378	PF01545	2.20E-69	0.881045	0
YNL135c	17	111	PF00254	2.50E-53	YDR341c	489	607	PF05746	5.90E-42	0.81679	0
YNL135c	17	111	PF00254	2.50E-53	YJR104c	1	154	PF00080	1.30E-101	0.82163	0
YNL189w	9	110	PF01749	1.10E-45	YDR353w	5	294	PF07992	2.40E-46	0.95007	0
YNL189w	9	110	PF01749	1.10E-45	YDR453c	5	182	PF00578	1.60E-101	0.77382	0
YNL189w	372	412	PF00514	4.70E-13	YGR024c	1	237	PF04446	2.30E-184	0.799248	0
YNL189w	330	370	PF00514	2.30E-14	YGR144w	39	306	PF01946	5.30E-180	0.904475	0
YNL189w	9	110	PF01749	1.10E-45	YHR112c	5	372	PF01053	6.20E-27	0.906409	0
YNL189w	9	110	PF01749	1.10E-45	YJL052w	2	150	PF00044	4.20E-97	0.812677	0
YNL189w	9	110	PF01749	1.10E-45	YJR009c	2	150	PF00044	8.20E-98	0.77617	0
YNL189w	9	110	PF01749	1.10E-45	YKL067w	6	140	PF00334	4.60E-104	0.799804	0
YNL189w	9	110	PF01749	1.10E-45	YML028w	5	182	PF00578	1.70E-113	0.769988	0
YNL189w	9	110	PF01749	1.10E-45	YPL088w	10	336	PF00248	1.20E-90	0.923047	0
YNL244c	20	101	PF01253	6.80E-42	YDL124w	10	289	PF00248	2.50E-58	0.866411	0
YNL244c	20	101	PF01253	6.80E-42	YDR353w	5	294	PF07992	2.40E-46	0.913173	0
YNL290w	48	218	PF00004	4.60E-16	YOL094c	229	316	PF08542	1.90E-33	0.718085	1
YNL323w	93	407	PF03381	1.20E-201	YDR212w	36	549	PF00118	8.70E-163	0.923391	0
YNL323w	93	407	PF03381	1.20E-201	YLR447c	12	343	PF01992	2.50E-169	0.965593	0
YNR001c	83	460	PF00285	1.60E-222	YKL085w	165	331	PF02866	3.50E-83	0.921078	0
YNR001c	83	460	PF00285	1.60E-222	YLR447c	12	343	PF01992	2.50E-169	0.902531	0
YOL058w	7	410	PF00764	2.20E-254	YBR160w	8	295	PF00069	4.30E-98	0.712523	0
YOL058w	7	410	PF00764	2.20E-254	YNL189w	9	110	PF01749	1.10E-45	0.848415	0
YOL126c	225	416	PF02866	7.10E-78	YJR068w	261	350	PF08542	5.80E-27	0.861494	0
YOL139c	4	213	PF01652	2.80E-118	YDL087c	8	261	PF03194	5.30E-137	0.979278	0
YOL139c	4	213	PF01652	2.80E-118	YGL115w	193	318	PF00571	3.90E-21	0.926015	0
YOL139c	4	213	PF01652	2.80E-118	YNL093w	3	179	PF00025	1.20E-06	0.682102	0
YOL156w	68	486	PF07690	4.30E-27	YLR372w	10	321	PF01151	3.70E-232	0.945331	0
YOR020c	10	103	PF00166	4.70E-37	YLR259c	44	550	PF00118	6.20E-174	0.835726	1
YOR020c	10	103	PF00166	4.70E-37	YNL189w	9	110	PF01749	1.10E-45	0.934904	0
YOR020c	10	103	PF00166	4.70E-37	YOR020c	10	103	PF00166	4.70E-37	1	1
YOR061w	50	334	PF00069	6.50E-66	YBR094w	1	231	PF01975	1.20E-08	0.949798	0
YOR061w	50	334	PF00069	6.50E-66	YIL118w	18	212	PF00071	3.70E-88	0.727959	0
YOR089c	1	171	PF00025	7.50E-07	YKR014c	1	193	PF00025	0.00042	0.81967	1
YOR089c	9	173	PF00071	5.60E-94	YNL093w	14	181	PF00071	9.60E-87	0.858055	1
YOR125c	135	226	PF03232	1.50E-42	YJL068c	13	291	PF00756	1.70E-109	0.954706	0
YOR136w	38	365	PF00180	1.70E-159	YNL189w	9	110	PF01749	1.10E-45	0.738094	0
YOR136w	38	365	PF00180	1.70E-159	YPR110c	48	330	PF01193	8.90E-20	0.914313	0
YOR151c	1126	1219	PF04560	5.80E-50	YBL039c	314	555	PF00117	3.20E-71	0.733248	0
YOR151c	1126	1219	PF04560	5.80E-50	YBR154c	142	215	PF01191	7.60E-49	0.763685	0
YOR151c	42	464	PF04563	6.30E-120	YDL140c	807	1398	PF04998	2.30E-170	0.814773	1
YOR151c	42	464	PF04563	6.30E-120	YDR404c	1	79	PF03876	1.20E-38	0.848309	0
YOR151c	681	745	PF04567	6.50E-26	YIL021w	49	171	PF01000	7.10E-41	0.873951	0
YOR159c	19	92	PF01423	2.30E-19	YPR182w	17	83	PF01423	2.20E-21	0.927989	1
YOR207c	555	617	PF04566	2.10E-37	YDR045c	2	55	PF02150	1.20E-25	0.858902	1
YOR207c	555	617	PF04566	2.10E-37	YKL144c	79	211	PF08292	5.80E-89	0.914178	0
YOR207c	555	617	PF04566	2.10E-37	YOR116c	370	537	PF00623	6.40E-117	0.833982	0
YOR207c	555	617	PF04566	2.10E-37	YPR110c	48	330	PF01193	8.90E-20	0.847708	0
YOR210w	1	61	PF01194	8.40E-41	YDL140c	1141	1274	PF04990	9.50E-79	0.954371	0
YOR210w	1	61	PF01194	8.40E-41	YOR151c	42	464	PF04563	6.30E-120	0.885226	1
YOR210w	1	61	PF01194	8.40E-41	YPR110c	48	330	PF01193	8.90E-20	0.878128	1
YOR224c	7	146	PF03870	3.90E-92	YDL140c	873	1056	PF04992	4.00E-97	0.975406	1
YOR224c	7	146	PF03870	3.90E-92	YKL144c	79	211	PF08292	5.80E-89	0.981323	0
YOR224c	7	146	PF03870	3.90E-92	YOR116c	855	1386	PF04998	4.80E-158	0.974056	0
YOR224c	7	146	PF03870	3.90E-92	YPR110c	48	330	PF01193	8.90E-20	0.971116	1
YOR232w	51	224	PF01025	3.20E-82	YOR232w	51	224	PF01025	3.20E-82	1	1
YPL028w	2	267	PF00108	7.20E-159	YNL244c	20	101	PF01253	6.80E-42	0.769668	0
YPL028w	2	267	PF00108	7.20E-159	YPR165w	12	185	PF00071	6.20E-87	0.492694	0
YPL031c	7	297	PF00069	9.90E-95	YFL030w	8	370	PF00266	3.00E-08	0.810633	0
YPL031c	7	297	PF00069	9.90E-95	YJR104c	1	154	PF00080	1.30E-101	0.811332	0
YPL050c	50	392	PF03452	1.10E-257	YLR447c	12	343	PF01992	2.50E-169	0.827343	0
YPL051w	3	186	PF00025	1.40E-42	YER044c	15	131	PF03694	1.00E-83	0.847211	0
YPL051w	19	188	PF00071	1.90E-06	YKR030w	35	273	PF05216	9.60E-167	0.725219	0
YPL088w	10	336	PF00248	1.20E-90	YPL088w	10	336	PF00248	1.20E-90	1	1
YPL091w	25	339	PF07992	1.80E-62	YPL091w	25	339	PF07992	1.80E-62	1	1
YPL091w	199	294	PF00070	1.10E-28	YPL091w	199	294	PF00070	1.10E-28	1	1
YPL091w	372	483	PF02852	1.30E-52	YPL091w	372	483	PF02852	1.30E-52	1	1
YPL106c	4	644	PF00012	1.50E-248	YML028w	5	182	PF00578	1.70E-113	0.882539	0
YPL111w	11	332	PF00491	3.10E-177	YKL085w	18	163	PF00056	7.70E-70	0.930723	0
YPL111w	11	332	PF00491	3.10E-177	YNL189w	9	110	PF01749	1.10E-45	0.847276	0
YPL111w	11	332	PF00491	3.10E-177	YPL111w	11	332	PF00491	3.10E-177	1	1
YPL111w	11	332	PF00491	3.10E-177	YPL160w	22	769	PF00133	7.10E-07	0.918923	0
YPL152w	2	305	PF03095	2.40E-193	YLR447c	12	343	PF01992	2.50E-169	0.955334	0
YPL160w	806	951	PF08264	8.80E-09	YNL244c	20	101	PF01253	6.80E-42	0.926062	0
YPL160w	806	951	PF08264	8.80E-09	YPR110c	48	330	PF01193	8.90E-20	0.971631	0
YPL259c	1	142	PF01217	3.10E-05	YBR221c	231	355	PF02780	8.40E-56	0.604028	0
YPL259c	1	142	PF01217	3.10E-05	YLR170c	3	146	PF01217	3.10E-96	0.81461	0
YPL259c	1	142	PF01217	3.10E-05	YOL010w	183	286	PF05189	2.70E-45	0.757546	0
YPL259c	1	142	PF01217	3.10E-05	YOR187w	263	333	PF03144	4.00E-28	0.753804	0
YPL259c	1	142	PF01217	3.10E-05	YPR016c	3	204	PF01912	2.40E-136	0.721576	0
YPR006c	46	575	PF00463	6.40E-189	YLR447c	12	343	PF01992	2.50E-169	0.93307	0
YPR010c	652	693	PF04567	8.40E-08	YBR143c	277	413	PF03465	2.50E-61	0.850019	0
YPR010c	698	1065	PF00562	1.60E-179	YKL067w	6	140	PF00334	4.60E-104	0.892338	0
YPR010c	652	693	PF04567	8.40E-08	YOR210w	1	61	PF01194	8.40E-41	0.77082	0
YPR010c	698	1065	PF00562	1.60E-179	YPR016c	3	204	PF01912	2.40E-136	0.89537	0
YPR010c	1067	1138	PF04560	1.50E-12	YPR110c	48	330	PF01193	8.90E-20	0.94912	0
YPR035w	107	356	PF00120	1.10E-90	YBR126c	16	482	PF00982	5.90E-294	0.886741	0
YPR069c	13	256	PF01564	3.40E-152	YLR146c	13	263	PF01564	6.60E-142	0.88449	1
YPR074c	356	533	PF02779	4.70E-69	YBR117c	356	533	PF02779	1.50E-70	0.998733	1
YPR082c	5	137	PF02966	1.70E-102	YFL017w-a	5	73	PF01423	2.00E-16	0.892593	0
YPR082c	5	137	PF02966	1.70E-102	YPR182w	17	83	PF01423	2.20E-21	0.537515	0
YPR110c	48	330	PF01193	8.90E-20	YDR453c	5	182	PF00578	1.60E-101	0.905926	0
YPR110c	48	330	PF01193	8.90E-20	YGL026c	9	272	PF00290	9.30E-161	0.977752	0
YPR110c	48	330	PF01193	8.90E-20	YHR112c	5	372	PF01053	6.20E-27	0.958103	0
YPR110c	83	220	PF01000	4.50E-61	YKL218c	16	306	PF00291	1.00E-95	0.980264	0
YPR110c	48	330	PF01193	8.90E-20	YLR086w	155	1406	PF02463	1.10E-140	0.957635	0
YPR110c	48	330	PF01193	8.90E-20	YOR116c	10	368	PF04997	6.30E-106	0.937882	0
YPR165w	12	185	PF00071	6.20E-87	YFR044c	98	474	PF01546	7.50E-29	0.66954	0
YPR182w	17	83	PF01423	2.20E-21	YNL189w	9	110	PF01749	1.10E-45	0.676128	0

We compared our prediction results with those of Chen and Liu's RDFF method³² and Riley et al.'s DPEA method.³³ The objective of this comparison is to find what percent of RCDP's predictions are confirmed by the other two methods. Chen and Liu used 9834 yeast protein interactions to infer 4366 domain–domain interactions, out of which 2475 are between Pfam-A domains while the rest involve Pfam-B domains. Riley et al.'s DPEA method is a statistical approach, which uses expectation maximization (EM) algorithm as a subroutine. They used a network of 26,032 protein–protein interactions from 69 organisms to infer a total of 3005 domain–domain interactions, out of which 1812 of them are between Pfam-A domain pairs. The comparison summary is shown in Figure 8(a), in which we refer to our method as RCDP (relative co-evolution of domain pairs). Although our analysis shows that the predictions by the RCDP method are more likely to be in iPfam than those by RDFF or DPEA methods, one needs to keep in mind that the prediction accuracies of the three methods are not directly comparable as they all use different datasets of varying sizes. However, the dataset used in our study is a subset of that used by Chen and Liu, and Riley et al. So, one would expect a good fraction of our predictions to be confirmed by the other two methods. Interestingly, only about 5% of RCDP's predictions are confirmed by both the RDFF and DPEA methods (Figure 8(b)). About 14% of RCDP's predictions are confirmed by DPEA alone, and about 23% of RCDP's predictions are confirmed by RDFF alone. Overall, 31% of RCDP's predictions are confirmed by DPEA and/or RDFF, indicating that RCDP can predict known domain–domain interactions missed by the other two. Thus, the RCDP method can be used with other methods to detect unrecognized domain–domain interactions on a genome scale with wider coverage.

Figure 8.

(a) An indirect comparison of RCDP's prediction results with those of RDFF³² and DPEA³³ methods. The predictions were validated against the known domain–domain interactions found in PDB crystal structures (as inferred in iPfam⁵⁰). The prediction accuracies of the three methods are not directly comparable as the results are from datasets of varying sizes. However, the dataset used to test RCDP is a subset of that used by Chen and Liu, and Riley et al. (b) Only about 5% of RCDP's predictions are confirmed by both DPEA and RDFF methods. Overall, about 31% of RCDP's predictions are confirmed by either DPEA or RDFF, with about 14% and 23% of RCDP's predictions confirmed by DPEA and RDFF, respectively. This indicates that each of these three methods can detect known domain–domain interactions missed by the other two.

Validation of predicted domain–domain interactions and estimating the true predictive power of the RCDP method

We used domain pairs found to interact in PDB⁴⁹ crystal structures, as reported in the iPfam database,⁵⁰ as our gold standard to verify the predicted domain–domain interactions. The iPfam database defines two domains from two different chains to be interacting if and only if they are close enough in at least one PDB complex to form an interaction. We consider a predicted interaction between domain P_i in protein P and domain Q_j in protein Q to be a true interaction (true positive) if and only if iPfam lists this pair of domain to be interacting based on one or more PDB crystal structure evidences.

An interacting protein pair P and Q is said to contain an iPfam domain–domain interaction xy if domain x is present in protein P and domain y is present in protein Q, or vice versa. A given protein–protein interaction may contain more than one iPfam domain–domain interaction, i.e. out of all possible domain pairs between the two interacting proteins, there may be more than one domain pair listed in iPfam.

We consider only those domain pairs found to interact in PDB crystal structures, as reported in iPfam, as true positives. Absence of a domain pair in iPfam does not necessarily mean that the two domains do not interact. Thus, it may not be fair to consider those predictions (without PDB evidence) as false positives. It could very well be that a good fraction of them could be biologically occurring domain interactions. A simple case would be a true protein–protein interaction, none of whose possible domain pairs are in iPfam. In order to estimate the true predictive power of the RCDP method, we tested it on a validation set comprising only those protein–protein interactions satisfying all of the following conditions: (i) is between proteins with at least 50% of their sequence lengths assigned with Pfam domain(s), (ii) is not between two one-domain proteins, (iii) contains a domain pair that is known to interact as per iPfam, and (iv) is between proteins having orthologs in at least a common set of ten species. The validation set contained a total of 109 protein–protein interactions (Supplementary material S6), comprising a total of 109 unique domain interactions that are in iPfam.

Supplementary material S6.

Validation set, containing 109 yeast protein interactions with SLA ≥ 50%.

Format: <Protein1> <Protein2> <#DomainsInProtein1> <#DomainsInProtein2>

Protein1	Protein2	#DomainsInProtein1	#DomainsInProtein2
YBL039c	YJR103w	2	2
YBL099w	YBR039w	3	1
YBL099w	YJR121w	3	3
YBR085w	YHR002w	3	3
YBR109c	YDR155c	3	1
YBR109c	YKL129c	3	3
YBR109c	YMR109w	3	4
YBR154c	YDL140c	2	7
YBR154c	YOR116c	2	5
YCL040w	YCL040w	2	2
YCR002c	YHR107c	2	2
YCR002c	YJR076c	2	2
YDL135c	YPR165w	1	2
YDL145c	YGL137w	7	5
YDL192w	YDL137w	3	3
YDL246c	YDL246c	2	2
YDR045c	YOR116c	2	5
YDR148c	YDR148c	2	2
YDR172w	YDR172w	3	3
YDR404c	YDL140c	2	7
YDR516c	YCL040w	2	2
YER017c	YMR089c	3	3
YER081w	YER081w	2	2
YER086w	YER086w	3	3
YER148w	YKL058w	2	2
YER148w	YPR086w	2	3
YER178w	YBR221c	1	2
YFL005w	YFL038c	3	3
YFL016c	YFL016c	3	3
YFR047c	YFR047c	2	2
YGL087c	YER125w	1	5
YGL238w	YLR293c	3	2
YGL238w	YNL189w	3	9
YGL253w	YGL253w	2	2
YGR144w	YGR144w	2	2
YHR074w	YHR074w	2	2
YHR107c	YHR107c	2	2
YHR111w	YHR111w	3	3
YHR169w	YJL138c	2	2
YIL021w	YOR224c	2	1
YIL074c	YER081w	2	2
YIL074c	YIL074c	2	2
YIL125w	YIL125w	2	2
YJL164c	YJL164c	2	2
YJL164c	YKL166c	2	2
YJL164c	YPL203w	2	2
YJR063w	YPR010c	2	7
YJR068w	YBR087w	2	1
YJR068w	YNL290w	2	2
YJR068w	YOL094c	2	2
YJR076c	YHR107c	2	2
YJR103w	YJR103w	2	2
YJR121w	YBR039w	3	1
YJR121w	YJR121w	3	3
YJR159w	YDL246c	2	2
YKL129c	YMR109w	3	4
YKL135c	YPL259c	1	2
YKL144c	YOR116c	2	5
YKL166c	YKL166c	2	2
YKR014c	YNL093w	3	3
YLR026c	YDR189w	2	1
YLR070c	YLR070c	2	2
YLR163c	YHR024c	2	2
YLR216c	YNR032w	2	1
YLR229c	YDL135c	2	1
YLR293c	YDR002w	2	1
YLR293c	YER009w	2	1
YLR293c	YOR185c	2	2
YML085c	YFL037w	2	2
YML121w	YML121w	2	2
YMR109w	YMR109w	4	4
YMR224c	YMR224c	2	2
YNL071w	YBR221c	3	2
YNL088w	YNL088w	3	3
YNL090w	YOR089c	2	3
YNL102w	YNL262w	2	3
YNL262w	YNL262w	3	3
YNL290w	YBR087w	2	1
YNL290w	YOL094c	2	2
YNR032w	YGR123c	1	3
YOL005c	YDL140c	1	7
YOL005c	YIL021w	1	2
YOL094c	YBR087w	2	1
YOR089c	YKR014c	3	3
YOR089c	YNL093w	3	3
YOR128c	YOR128c	3	3
YOR151c	YDL140c	7	7
YOR151c	YDR404c	7	2
YOR151c	YIL021w	7	2
YOR185c	YER009w	2	1
YOR207c	YDR045c	7	2
YOR207c	YKL144c	7	2
YOR207c	YNL113w	7	1
YOR207c	YOR116c	7	5
YOR207c	YPR110c	7	2
YOR210w	YOR151c	1	7
YOR210w	YPR110c	1	2
YOR224c	YDL140c	1	7
YOR224c	YOR116c	1	5
YOR224c	YPR110c	1	2
YPL091w	YPL091w	3	3
YPL203w	YKL166c	2	2
YPL259c	YLR170c	2	1
YPR010c	YOR210w	7	1
YPR010c	YPR110c	7	2
YPR074c	YBR117c	3	3
YPR110c	YOR116c	2	5
YPR181c	YIL109c	5	5
YPR181c	YNL049c	5	5

Ideally, a good domain–domain interaction prediction method should be able to recover all 109 unique known domain–domain interactions present in the validation set. To measure the percentage of recovery, we use the sensitivity measure, which is the ratio of the number of unique true positives to the number of unique positives (which is 109). On the validation set of 109 protein–protein interactions, RCDP predicted 109 unique domain–domain interactions, out of which 63 are in iPfam. This resulted in a sensitivity of 63/109=57.8%. This is an underestimation because there may more than one domain pair mediating a given protein–protein interaction, and since RCDP is designed to find only the pair(s) with the highest correlation, it may not be able to recover all 109 unique domain–domain interactions present in the set.

While it is important for any good method to be able to recover the 109 known domain–domain interactions from the validation set, it is equally important that every predicted domain–domain interaction is correct. To measure the accuracy of our predictions, we used the positive predictive value (PPV) defined as:

$$PPV=\frac{TP}{TP+FP}$$

where TP is the number of predicted domain pairs that are known to be true (in iPfam), and FP is the number of predicted domain pairs that are not in the iPfam. RCDP predicted a total of 147 domain–domain interactions (109 of them are unique) for the validation set, out of which 94 are in iPfam with a PPV of 63.95%. To ensure that the 63.95% prediction accuracy of RCDP is not by chance, we compared it against a random method. For this, we used the exact same random strategy used by Nye et al.³¹, which, for a given protein–protein interaction, picks a domain pair at random out of all possible domain pairs. Since there could be more than one interacting domain pair within each interacting protein pair, there is a certain probability that the domain pair picked at random is a true interaction. We performed 100,000 runs of this random method on our validation set. The p-value of obtaining a prediction accuracy of ≥63.95% by chance is 1.05×10⁻² (z-score: 2.39). The performance of RCDP versus the random method is shown in Figure 9. On average, the random method is expected to have 55.19 (±0.01)% of its predictions to be in iPfam (Figure 9). RCDP outperforms random by about 9%, which is significant, considering the fact that Nye et al. showed, on a different dataset, that the random method performs as good as three other popular methods for predicting domain–domain interactions. In particular, Nye et al. showed that one can expect their “lowest p-value” method, Deng et al.'s MLE method,³⁰ and the random method to have about 55% of their predictions to be true, and Sprinzak et al.'s association method²⁶ to have about 52% of its predictions to be true. Since the interaction dataset and domain annotations (SCOP domains) used in Nye et al.'s study are different from those used in this study, the results are not directly comparable.

Figure 9.

Domain–domain interaction predictions results for 109 yeast protein–protein interactions, each of which (i) is between proteins with at least 50% of their sequence lengths assigned with Pfam domain(s), (ii) is not an interaction between two one-domain proteins, (iii) contains a domain pair that is known to interact (as reported iPfam), and (iv) is between proteins having orthologs in at least a common set of ten species. The performance of RCDP versus a method that picks a domain pair at random among all possible domain pairs is plotted. The results are broken down according to the number of potential domain–domain contacts between an interacting protein pair. RCDP clearly outperforms random picks by about 9%, which is significant (p-value 1.05×10⁻²) considering the fact that it has been shown before (Figure 4 in Nye et al.³¹), on a different dataset, that random performs as good as three other popular methods²⁶,³⁰,³¹ for inferring domain–domain interactions.

Conclusion

Here, we performed co-evolutionary analysis of domains in interacting proteins to assess whether or not interacting domain pairs exhibit higher level of co-evolution than non-interacting domain pairs of a given protein–protein interaction. We used yeast protein–protein interactions from DNA-directed RNA polymerase complex and F1-ATPase complex among others in our investigation. Our results indicated that interacting domain pairs exhibit higher level of co-evolution than the non-interacting domain pairs. Motivated by the results, we designed a method, called RCDP, to confirm the observed trend, and to predict large-scale domain–domain (i.e. Pfam-Pfam) interactions using the yeast interactome. A total of 1222 domain–domain interactions from 1180 protein–protein interactions were predicted, out of which 109 are found in PDB (as reported in iPfam). Through comparison of our predictions with those from two other methods, we showed that the RCDP method can predict known domain–domain interactions missed by the other two methods.

The proposed RCDP method may not be suitable for predicting domain–domain interactions between homodimers (interaction between two copies of the same protein). The reason for this is that the domain pairs with the highest correlation will be inter-chain homodomains, which will have the maximum correlation score of one. Although this makes RCDP's results predictable for homodimers, in reality, it is mostly the case that homodimers are mediated by inter-chain homodomain interactions. In our set of 1180 protein–protein interactions (SLA ≥50%), we had 71 cases of a protein interacting with itself. For this set of 71 interactions, we predicted 112 domain–domain interactions, out of which 84 (75%) are found in PDB (as reported in iPfam).

Although relative co-evolution of interacting domains can be used to predict domain–domain interactions between two interacting proteins, there are some limitations that apply to any method based on co-evolution, which could cause false positives and false negatives that one should be aware of. First of all, this type of analysis assumes that interacting domains/proteins co-evolve, i.e. undergo correlated mutations, which may not be always true due to numerous other biological constraints on the interacting domains/proteins. If domain A with multiple interacting partners undergoes correlated mutations with its interacting partners, then there is a danger of it not having a high correlation with its partners due to “uncorrelated set of correlated mutations” (see Figure 4).

Predicted domain–domain interactions are only as good as the accuracy of the protein–protein interactions used. Domain–domain interactions are predicted under the premise that the given protein–protein interaction is accurate. If a protein–protein interaction is a false positive, then one should not expect the predicted domain–domain interaction to be true. Various studies^65–68 have reported that anywhere between 40–60% of the reported protein–protein interactions could be false-positives, which could potentially explain the false-positives (≈34%) in predictions by the RCDP method.

Not all interactions are mediated by pairs of globular domains. There are many that involve binding of a domain in one protein to a short region (approximately three to eight residues) in another.^69,70 Detecting these short length “linear motifs” using sequence comparison is difficult due to their tendency to reside in disordered regions in proteins, and limited conservation outside of closely related species.³⁷ Thus, there is a possibility that the set of interacting residues may not be part of the domains assigned to a protein. This could lead to incorrect prediction of domain–domain interactions in such cases. And, there may be more than one domain pair mediating a protein–protein interaction, and since RCDP is designed to find only the pair(s) with the highest correlation, it may not be able to recover all interacting domain pairs.

The orthology detection procedure used in this study may not be sufficiently rigorous for detecting orthologs. We did attempt to use a very stringent reciprocal BLAST best-hits approach. But, because of its stringent nature, and our requirement that interacting proteins have at least ten orthologs from a common set of species, we were unable to obtain a large enough dataset to make any statistical conclusion. Another issue is that of closely related paralogs. Since many genes in Eukaryotes are known to have numerous in-paralogs (due to recent duplications), it makes it difficult to establish one-toone orthology relationships. Our tests on a few cases to see the effect of including one in-paralog over another had little or no effect on the co-evolutionary analysis.

Despite these limitations, the RCDP method proves to be extremely useful for inferring domain–domain interactions. Unlike sophisticated statistical methods, which require a training set, the RCDP method can directly be used on a given protein–protein interaction to predict the domain pair that is most likely to mediate the interaction. Since RCDP, DPEA, and RDFF methods share a small fraction of their predictions, indicating that they can detect known domain–domain interactions missed by the other, together they can be used to detect unrecognized domain–domain interactions on a genome scale with wider coverage.

The RCDP method is simple and easy to implement (an implementation of the RCDP algorithm is available^†), and can be used as a tool to guide experimentalists in discovering previously unrecognized domain–domain interactions. In the future, we would like to investigate whether there is a possibility of transitivity in co-evolution. That is, if A interacts with B, and B interacts with C, will A and C exhibit a high degree of co-evolution (assuming that A and C do not interact) because of their association with a common interacting partner B? If they do, it would be interesting to know the biological reasons/constraints that require them to co-evolve.

Materials and Methods

Construction of multiple sequence alignments, phylogenetic trees, and similarity matrices

For each protein–protein interaction, multiple sequence alignments for the two proteins were constructed using MUSCLE⁷¹ by searching for their respective orthologs in 93 eukaryotic genomes ( Supplementary material S1 ). Ortho-logs were obtained by performing a stringent BLAST search.⁷² For a given query protein, the best hit in a genome with e-value <1e-5, sequence identity of at least 35% and an alignment length of at least 75% of the length of both the query and the hit sequence was considered to be an ortholog. Sequence identity and alignment length constraints were enforced to eliminate partial hits from consideration. Multiple sequence alignment for domain D in protein P is constructed by extracting those regions in P's multiple sequence alignment that corresponds to D.

Supplementary material S1.

Organisms (taxids) used for ortholog search.

7719
9606
31033
51511
180454
7460
7237
9615
10116
6238
99883
7245
7159
9544
9598
9913
13616
10141
31234
9361
9986
7091
10090
7227
9031
42254
227321
330879
273507
285217
226126
235443
226125
226127
226230
226231
226301
226302
237631
240176
237561
262981
283643
5037
294746
306902
38033
246410
246409
332952
307796
285006
294747
294750
321614
229533
242507
5141
325569
334819
334564
341663
332648
336963
344612
331117
39946
39947
5807
5823
31271
296543
44689
73239
184922
5664
5691
237895
6239
284593
284592
6035
33169
284590
284812
284591
4932
214684
3702
294381
280699
5693

In order to be able to compare the evolutionary histories of two domains, we require that both domains have orthologs in at least a common set of ten species. Multiple sequence alignments of both domains for a common set of species were constructed, followed by the construction of phylogenetic trees and similarity matrices using the algorithms provided in the ClustalW suite.⁷³

Assessment of the agreement between the evolutionary histories of two domains

The extent of agreement between the evolutionary histories of two domains is assessed by comparing their phylogenetic trees. For comparison of phylogenetic trees, we follow the standard practice of comparing the corresponding similarity matrices.^{14,16,39–44} The extent of agreement between two similarity matrices, A and B, is evaluated using Pearson's correlation coefficient, given by:

$$r_{AB}=\frac{\sum _{i=1}^{n-1}\sum _{j=i+1}^n(A_{ij}-\overline{A})(B_{ij}-\overline{B})}{\sqrt{\sum _{j=i+1}^{n-1}\sum _{j=i+1}^n{(A_{ij}-\overline{A})}^2\sum _{i=1}^{n-1}\sum _{j=i+1}^n{(B_{ij}-\overline{B})}^2}},$$

where n is the number of species (rows/columns) represented in the matrices, A_ij and B_ij are the evolutionary distances between species i and j in the tree of domains A and B, respectively, and $\overline{A}$ and $\overline{B}$ are the mean values of all A_ij and B_ij respectively. The value of r ranges from −1.0 to +1.0, with higher r indicating greater agreement between the two matrices, and thus higher level of co-evolution between the corresponding families.

Inferring domain–domain interactions

For every interacting protein pair, P and Q, all possible domain–domain interactions between them are considered. Let protein P contain domains {P₁, P₂, …, P_m} and protein Q contain domains {Q₁, Q₂, …, Q_n}. The correlation of evolutionary histories of all possible domain pairs between P and Q is computed, and the domain pair P_iQ_j with the highest level of co-evolution (whose evolutionary histories correlate the most) is inferred to be the one (or one of many domain–domain contacts) that is most likely to mediate the interaction between P and Q. In cases of more than one domain pair having the highest correlation score, all domain pairs with the highest score are inferred to be interacting. Interestingly, and more often, more than one domain pair mediate a given protein–protein interaction.

Protein–protein interaction test set

Protein–protein interaction data for Saccharomyces cere-visiae (yeast) from the DIP database⁷⁴ (February 2005 release) were used. This set contained a total of 17,471 interactions underlying 4931 yeast proteins. For domain definition, we used the Pfam database of Hidden Markov Model (HMM) profiles.⁵¹ Only Pfam-A profiles were used to assign domain definitions to the 4931 interacting proteins, using e-value cutoff of 1e-3.

Only interacting proteins with at least 50% of their sequence lengths assigned onto Pfam domain(s), and interactions involving them, were considered. This reduced the number of interactions to 3266 among 1397 proteins. Because of the limitation that interacting protein pairs have orthologs in at least a common set of ten species, our final test set contained 1180 interactions, underlying 654 proteins (Supplementary material S2). We also considered a restricted set of interactions, with each interacting protein having at least 75% of its sequence length assigned onto Pfam domain(s). This restricted set contained a total of 374 interactions among 298 proteins (Supplementary material S4).

Supplementary material S2.

Test set 1, containing 1180 yeast protein interactions with SLA ≥ 50%.

Format: <Protein1> <Protein2> <#DomainsInProtein1> <#DomainsInProtein2>

Protein1	Protein2	#DomainsInProtein1	#DomainsInProtein2
YAL012w	YMR101c	1	1
YAL036c	YJL138c	2	2
YAL038w	YNL307c	2	1
YAL038w	YOR226c	2	1
YAL054c	YNL189w	1	9
YAL062w	YNL189w	2	9
YBL002w	YKR001c	1	3
YBL002w	YKR048c	1	1
YBL002w	YNL262w	1	3
YBL002w	YOL006c	1	2
YBL002w	YOR116c	1	5
YBL002w	YOR207c	1	7
YBL002w	YPR010c	1	7
YBL003c	YDL188c	1	1
YBL022c	YLR180w	5	3
YBL026w	YDR378c	1	1
YBL026w	YER146w	1	1
YBL026w	YIL048w	1	2
YBL026w	YLR264w	1	1
YBL026w	YLR275w	1	1
YBL026w	YLR438c-a	1	1
YBL026w	YNL147w	1	1
YBL026w	YNL287w	1	1
YBL026w	YPL249c-a	1	1
YBL030c	YEL020w-a	3	1
YBL030c	YGL137w	3	5
YBL039c	YJR103w	2	2
YBL040c	YGR060w	1	1
YBL040c	YOL020w	1	1
YBL078c	YOR100c	1	3
YBL091c	YNL290w	1	2
YBL099w	YBR039w	3	1
YBL099w	YDR298c	3	1
YBL099w	YJR121w	3	3
YBL099w	YPL078c	3	1
YBR009c	YBR010w	1	1
YBR009c	YDR224c	1	1
YBR009c	YDR225w	1	1
YBR009c	YKL067w	1	1
YBR009c	YLR180w	1	3
YBR009c	YLR340w	1	2
YBR009c	YPR010c	1	7
YBR009c	YPR110c	1	2
YBR010w	YDR224c	1	1
YBR010w	YDR225w	1	1
YBR010w	YPL209c	1	1
YBR011c	YGL120c	1	4
YBR011c	YHR030c	1	1
YBR011c	YMR267w	1	1
YBR018c	YER081w	2	2
YBR018c	YGL137w	2	5
YBR018c	YHR030c	2	1
YBR018c	YPR054w	2	1
YBR021w	YHR042w	1	3
YBR024w	YBR024w	1	1
YBR039w	YDL047w	1	1
YBR039w	YDL145c	1	7
YBR039w	YJR068w	1	2
YBR061c	YJL097w	1	1
YBR068c	YDR046c	1	1
YBR068c	YDR385w	1	5
YBR069c	YLR343w	1	2
YBR069c	YNL064c	1	3
YBR085w	YHR002w	3	3
YBR087w	YNL088w	1	3
YBR088c	YBR087w	2	1
YBR088c	YJR068w	2	2
YBR088c	YKL113c	2	2
YBR088c	YNL290w	2	2
YBR088c	YOL094c	2	2
YBR088c	YOR116c	2	5
YBR089c-a	YJL026w	1	1
YBR089c-a	YPL235w	1	2
YBR109c	YBR011c	3	1
YBR109c	YDR032c	3	1
YBR109c	YDR155c	3	1
YBR109c	YEL034w	3	2
YBR109c	YFR014c	3	2
YBR109c	YGR144w	3	2
YBR109c	YHR028c	3	2
YBR109c	YHR179w	3	1
YBR109c	YIL021w	3	2
YBR109c	YJR073c	3	1
YBR109c	YJR104c	3	1
YBR109c	YKL067w	3	1
YBR109c	YKL129c	3	3
YBR109c	YLL050c	3	1
YBR109c	YMR105c	3	4
YBR109c	YMR109w	3	4
YBR109c	YMR250w	3	1
YBR109c	YNL202w	3	1
YBR109c	YOL016c	3	2
YBR117c	YLR447c	3	1
YBR118w	YKL081w	3	3
YBR121c	YNL244c	2	1
YBR126c	YOR089c	1	3
YBR127c	YKL080w	3	1
YBR127c	YLR447c	3	1
YBR132c	YHR042w	1	3
YBR154c	YDL140c	2	7
YBR154c	YDR404c	2	2
YBR154c	YER125w	2	5
YBR154c	YKL144c	2	2
YBR154c	YOR116c	2	5
YBR154c	YPR110c	2	2
YBR159w	YMR279c	1	1
YBR160w	YBR038w	1	3
YBR160w	YDR097c	1	5
YBR160w	YDR212w	1	1
YBR160w	YHL035c	1	4
YBR160w	YKL129c	1	3
YBR160w	YLR086w	1	2
YBR160w	YNL102w	1	2
YBR160w	YPL209c	1	1
YBR170c	YER081w	2	2
YBR170c	YGR048w	2	1
YBR170c	YLR044c	2	3
YBR176w	YBR176w	1	1
YBR176w	YNL189w	1	9
YBR192w	YER078c	3	2
YBR205w	YFL038c	1	3
YBR218c	YPR110c	7	2
YBR221c	YER081w	2	2
YBR247c	YHR148w	1	2
YBR247c	YLR180w	1	3
YBR247c	YNL075w	1	1
YBR247c	YNL244c	1	1
YBR247c	YOL010w	1	2
YBR249c	YER081w	1	2
YBR249c	YPR110c	1	2
YBR252w	YNL189w	1	9
YBR291c	YHR096c	3	2
YBR296c	YLL028w	1	1
YBR298c	YBR159w	2	1
YBR298c	YLR372w	2	1
YBR298c	YMR279c	2	1
YCL025c	YBR159w	1	1
YCL025c	YCR034w	1	1
YCL025c	YER026c	1	1
YCL025c	YFL041w	1	3
YCL025c	YGR060w	1	1
YCL025c	YHL003c	1	2
YCL025c	YJR095w	1	3
YCL025c	YKL008c	1	2
YCL025c	YLR343w	1	2
YCL025c	YLR372w	1	1
YCL025c	YPL227c	1	1
YCL025c	YPL234c	1	2
YCL025c	YPL265w	1	1
YCL030c	YLR044c	3	3
YCL030c	YLR180w	3	3
YCL030c	YML124c	3	2
YCL040w	YCL040w	2	2
YCL040w	YNL189w	2	9
YCR002c	YFL018c	2	4
YCR002c	YHR107c	2	2
YCR002c	YJR076c	2	2
YCR002c	YLR314c	2	1
YCR005c	YCR005c	1	1
YCR005c	YKL085w	1	2
YCR009c	YGL137w	1	5
YCR010c	YEL063c	1	1
YCR012w	YGL137w	1	5
YCR028c	YLR372w	1	1
YCR034w	YBR069c	1	1
YCR034w	YGL055w	1	2
YCR034w	YHR094c	1	2
YCR034w	YJL219w	1	2
YCR034w	YLL028w	1	1
YCR034w	YLL061w	1	1
YCR034w	YMR058w	1	4
YCR034w	YOL020w	1	1
YCR034w	YOL030w	1	1
YCR034w	YPL274w	1	1
YCR034w	YPR156c	1	2
YDL004w	YBL099w	1	3
YDL004w	YJR121w	1	3
YDL047w	YJR072c	1	1
YDL047w	YNL101w	1	1
YDL055c	YNL189w	2	9
YDL064w	YDL064w	1	1
YDL081c	YPR086w	1	3
YDL100c	YDR304c	2	1
YDL100c	YHR057c	2	1
YDL100c	YJL153c	2	2
YDL100c	YNL055c	2	1
YDL100c	YOL126c	2	2
YDL108w	YDL140c	1	7
YDL108w	YOR151c	1	7
YDL126c	YBR170c	5	2
YDL126c	YDR037w	5	2
YDL126c	YGR048w	5	1
YDL126c	YGR078c	5	1
YDL126c	YLL039c	5	5
YDL134c	YDL188c	1	1
YDL134c	YIL021w	1	2
YDL134c	YPR110c	1	2
YDL135c	YPR165w	1	2
YDL137w	YPR110c	3	2
YDL140c	YER125w	7	5
YDL143w	YKR026c	1	1
YDL145c	YCR012w	7	1
YDL145c	YDR238c	7	2
YDL145c	YGL137w	7	5
YDL145c	YNL287w	7	1
YDL145c	YPL010w	7	1
YDL164c	YBR088c	3	2
YDL164c	YEL030w	3	1
YDL164c	YLR276c	3	2
YDL171c	YBL087c	5	1
YDL171c	YDL047w	5	1
YDL171c	YPR086w	5	3
YDL188c	YBL041w	1	1
YDL188c	YDR190c	1	1
YDL188c	YER012w	1	1
YDL188c	YER094c	1	1
YDL188c	YFR050c	1	1
YDL188c	YGL011c	1	1
YDL188c	YGR135w	1	1
YDL188c	YJR009c	1	2
YDL188c	YML092c	1	1
YDL188c	YMR314w	1	1
YDL188c	YOL005c	1	1
YDL188c	YOL038w	1	1
YDL188c	YOR157c	1	1
YDL188c	YPR010c	1	7
YDL188c	YPR103w	1	1
YDL192w	YDL137w	3	3
YDL192w	YNL287w	3	1
YDL192w	YPR110c	3	2
YDL192w	YPR176c	3	5
YDL219w	YDL047w	1	1
YDL229w	YNL064c	1	3
YDL236w	YNL189w	1	9
YDL245c	YHR096c	2	2
YDL245c	YJR160c	2	2
YDL246c	YDL246c	2	2
YDR012w	YER081w	1	2
YDR021w	YJR007w	2	2
YDR023w	YBL036c	2	1
YDR032c	YCR004c	1	1
YDR032c	YDR032c	1	1
YDR044w	YNL189w	1	9
YDR045c	YOR116c	2	5
YDR046c	YBR159w	1	1
YDR046c	YGR060w	1	1
YDR046c	YLR372w	1	1
YDR062w	YDR502c	1	3
YDR062w	YIL094c	1	1
YDR062w	YJR077c	1	3
YDR062w	YLR180w	1	3
YDR075w	YDR212w	1	1
YDR091c	YPR041w	4	2
YDR097c	YKR001c	5	3
YDR097c	YPL235w	5	2
YDR099w	YBR001c	1	2
YDR099w	YDR062w	1	1
YDR099w	YDR099w	1	1
YDR099w	YGR123c	1	3
YDR127w	YJL008c	6	1
YDR127w	YOR136w	6	1
YDR127w	YPL235w	6	2
YDR129c	YDR353w	4	2
YDR139c	YDR328c	1	2
YDR139c	YLR306w	1	1
YDR148c	YDR148c	2	2
YDR148c	YDR510w	2	1
YDR148c	YFL018c	2	4
YDR148c	YLR180w	2	3
YDR148c	YNL189w	2	9
YDR155c	YBR009c	1	1
YDR155c	YDR510w	1	1
YDR155c	YER081w	1	2
YDR155c	YGL194c	1	1
YDR155c	YKL103c	1	1
YDR155c	YNL244c	1	1
YDR155c	YPL235w	1	2
YDR172w	YBR143c	3	3
YDR172w	YDR172w	3	3
YDR188w	YDL047w	1	1
YDR188w	YGL137w	1	5
YDR190c	YPL235w	1	2
YDR212w	YJL164c	1	2
YDR224c	YGL058w	1	1
YDR224c	YKL103c	1	1
YDR224c	YPR041w	1	2
YDR225w	YDR224c	1	1
YDR225w	YGR103w	1	2
YDR225w	YHL001w	1	2
YDR225w	YKR048c	1	1
YDR225w	YOR116c	1	5
YDR225w	YOR207c	1	7
YDR226w	YBL036c	2	1
YDR226w	YDR177w	2	1
YDR226w	YOR176w	2	1
YDR226w	YPL031c	2	2
YDR238c	YGL137w	2	5
YDR256c	YMR314w	1	1
YDR256c	YNL189w	1	9
YDR280w	YNL189w	2	9
YDR297w	YBR159w	1	1
YDR297w	YLL028w	1	1
YDR297w	YLR372w	1	1
YDR328c	YBR127c	2	3
YDR328c	YEL051w	2	1
YDR342c	YBL036c	2	1
YDR342c	YLR340w	2	2
YDR342c	YNL323w	2	1
YDR343c	YBL036c	2	1
YDR343c	YER081w	2	2
YDR343c	YER125w	2	5
YDR343c	YGR040w	2	1
YDR353w	YOL128c	2	1
YDR378c	YLR275w	1	1
YDR378c	YNL147w	1	1
YDR382w	YBR006w	1	1
YDR385w	YDR328c	5	2
YDR404c	YDL140c	2	7
YDR404c	YGR063c	2	1
YDR404c	YOR224c	2	1
YDR430c	YBR221c	3	2
YDR430c	YER178w	3	1
YDR430c	YFL018c	3	4
YDR430c	YNL071w	3	3
YDR487c	YNL189w	1	9
YDR497c	YLL028w	2	1
YDR508c	YBR159w	1	1
YDR508c	YMR279c	1	1
YDR510w	YDL064w	1	1
YDR510w	YDR510w	1	1
YDR510w	YNL088w	1	3
YDR510w	YNL189w	1	9
YDR516c	YCL040w	2	2
YDR529c	YBR082c	1	1
YEL011w	YPR086w	2	3
YEL021w	YEL021w	1	1
YEL027w	YBR298c	2	2
YEL027w	YLL028w	2	1
YEL027w	YLR034c	2	1
YEL034w	YLR340w	2	2
YEL046c	YEL046c	1	1
YEL046c	YNL189w	1	9
YEL054c	YDL081c	2	1
YEL054c	YDR382w	2	1
YEL054c	YOL039w	2	1
YEL063c	YBL040c	1	1
YEL063c	YBR159w	1	1
YEL063c	YCR034w	1	1
YEL063c	YFL041w	1	3
YEL063c	YJL196c	1	1
YEL063c	YLR343w	1	2
YEL063c	YLR372w	1	1
YEL063c	YOR161c	1	1
YEL063c	YPL234c	1	2
YEL069c	YPR110c	2	2
YEL071w	YPR165w	2	2
YER009w	YNL189w	1	9
YER012w	YBL041w	1	1
YER012w	YER094c	1	1
YER012w	YFR050c	1	1
YER012w	YGL011c	1	1
YER012w	YGR135w	1	1
YER012w	YJL001w	1	1
YER012w	YML092c	1	1
YER012w	YMR314w	1	1
YER012w	YOL038w	1	1
YER012w	YPR103w	1	1
YER017c	YBR247c	3	1
YER017c	YFL018c	3	4
YER017c	YMR089c	3	3
YER020w	YGL245w	2	2
YER020w	YNL037c	2	1
YER020w	YPL036w	2	3
YER025w	YBL026w	2	1
YER025w	YER146w	2	1
YER025w	YJR007w	2	2
YER025w	YKR026c	2	1
YER025w	YPR110c	2	2
YER026c	YDR297w	1	1
YER026c	YGR060w	1	1
YER026c	YMR058w	1	4
YER036c	YNL142w	2	1
YER043c	YKL161c	2	1
YER057c	YNL189w	1	9
YER073w	YPR086w	1	3
YER081w	YBR143c	2	3
YER081w	YCR072c	2	8
YER081w	YDL168w	2	2
YER081w	YDR105c	2	1
YER081w	YER078c	2	2
YER081w	YER081w	2	2
YER081w	YFL037w	2	2
YER081w	YGR020c	2	1
YER081w	YPL234c	2	2
YER081w	YPR016c	2	1
YER086w	YER086w	3	3
YER086w	YKL081w	3	3
YER094c	YGL011c	1	1
YER126c	YCR072c	1	8
YER126c	YKR081c	1	1
YER126c	YPR016c	1	1
YER133w	YGR103w	1	2
YER133w	YJR007w	1	2
YER133w	YKL085w	1	2
YER133w	YKR002w	1	3
YER133w	YLR134w	1	3
YER146w	YCR024c	1	2
YER146w	YDR378c	1	1
YER146w	YER131w	1	1
YER146w	YER146w	1	1
YER146w	YIL048w	1	2
YER146w	YLR058c	1	1
YER146w	YLR275w	1	1
YER146w	YNL147w	1	1
YER146w	YPL090c	1	1
YER146w	YPL152w	1	1
YER146w	YPR010c	1	7
YER148w	YKL058w	2	2
YER148w	YKR001c	2	3
YER148w	YPR086w	2	3
YER156c	YFL038c	1	3
YER170w	YKL002w	2	1
YER177w	YDR062w	1	1
YER177w	YDR099w	1	1
YER177w	YGL115w	1	2
YER177w	YNL189w	1	9
YER178w	YBR221c	1	2
YER178w	YGL137w	1	5
YFL005w	YFL038c	3	3
YFL016c	YFL016c	3	3
YFL016c	YJR045c	3	1
YFL017c	YBL072c	1	1
YFL017c	YNL189w	1	9
YFL017c	YOL059w	1	2
YFL018c	YBR221c	4	2
YFL022c	YKR026c	1	1
YFL028c	YFL028c	1	1
YFL041w	YLL028w	3	1
YFL041w	YML123c	3	2
YFL041w	YPR156c	3	2
YFL045c	YLR343w	2	2
YFL045c	YNL189w	2	9
YFL059w	YFL059w	1	1
YFL059w	YNL189w	1	9
YFL060c	YFL059w	2	1
YFL060c	YMR096w	2	1
YFR009w	YLR058c	2	1
YFR047c	YFR047c	2	2
YFR047c	YNL189w	2	9
YFR050c	YGL011c	1	1
YFR050c	YML092c	1	1
YFR053c	YER081w	2	2
YGL006w	YDR339c	4	1
YGL008c	YHR030c	3	1
YGL019w	YBR009c	1	1
YGL019w	YGL019w	1	1
YGL019w	YGL115w	1	2
YGL019w	YIL118w	1	2
YGL019w	YNL088w	1	3
YGL019w	YOR039w	1	1
YGL040c	YGL040c	1	1
YGL040c	YNL189w	1	9
YGL054c	YLR372w	1	1
YGL055w	YBR159w	2	1
YGL062w	YPR110c	9	2
YGL087c	YDR092w	1	1
YGL087c	YER125w	1	5
YGL120c	YPR182w	4	1
YGL130w	YBR221c	3	2
YGL130w	YDL140c	3	7
YGL130w	YGL120c	3	4
YGL135w	YER081w	1	2
YGL137w	YBR187w	5	2
YGL137w	YDR212w	5	1
YGL137w	YKL081w	5	3
YGL137w	YKL166c	5	2
YGL156w	YPR110c	2	2
YGL206c	YBR169c	7	1
YGL206c	YIL094c	7	1
YGL206c	YKR026c	7	1
YGL206c	YPL106c	7	1
YGL221c	YGL221c	1	1
YGL221c	YNL189w	1	9
YGL234w	YBL026w	5	1
YGL234w	YJR068w	5	2
YGL234w	YKL166c	5	2
YGL234w	YOL094c	5	2
YGL238w	YLR293c	3	2
YGL238w	YNL189w	3	9
YGL253w	YGL253w	2	2
YGR020c	YEL051w	1	1
YGR024c	YGR024c	1	1
YGR040w	YBL022c	1	5
YGR040w	YDR190c	1	1
YGR040w	YGL008c	1	3
YGR040w	YGL062w	1	9
YGR040w	YGL245w	1	2
YGR040w	YJR072c	1	1
YGR040w	YKR048c	1	1
YGR040w	YLL039c	1	5
YGR040w	YML123c	1	2
YGR040w	YOL033w	1	1
YGR040w	YPR010c	1	7
YGR048w	YHR039c-a	1	1
YGR060w	YBR159w	1	1
YGR060w	YDR343c	1	2
YGR060w	YGL001c	1	4
YGR060w	YKL008c	1	2
YGR060w	YLL028w	1	1
YGR060w	YLR343w	1	2
YGR060w	YLR372w	1	1
YGR060w	YPR028w	1	1
YGR078c	YLR200w	1	1
YGR078c	YLR212c	1	2
YGR087c	YHR030c	3	1
YGR088w	YNL189w	1	9
YGR103w	YFR031c-a	2	2
YGR103w	YHR066w	2	1
YGR103w	YKR081c	2	1
YGR103w	YNL189w	2	9
YGR103w	YPR016c	2	1
YGR103w	YPR041w	2	2
YGR133w	YGR133w	1	1
YGR135w	YGL011c	1	1
YGR135w	YNL244c	1	1
YGR144w	YGR144w	2	2
YGR155w	YBR088c	2	2
YGR155w	YGR040w	2	1
YGR155w	YJR045c	2	1
YGR155w	YNL189w	2	9
YHR005c-a	YBL030c	1	3
YHR005c-a	YEL020w-a	1	1
YHR007c	YPL274w	1	1
YHR008c	YBR061c	2	1
YHR018c	YGL137w	1	5
YHR018c	YNL189w	1	9
YHR018c	YNL244c	1	1
YHR019c	YNL244c	2	1
YHR030c	YJL138c	1	2
YHR030c	YLR262c	1	3
YHR030c	YPR054w	1	1
YHR039c-a	YBR127c	1	3
YHR039c-a	YGR020c	1	1
YHR042w	YAL067c	3	1
YHR068w	YNL189w	1	9
YHR074w	YHR074w	2	2
YHR075c	YDL134c	1	1
YHR075c	YDL188c	1	1
YHR088w	YPR016c	1	1
YHR094c	YLR372w	2	1
YHR096c	YDL047w	2	1
YHR096c	YDL095w	2	2
YHR107c	YER091c	2	2
YHR107c	YFL045c	2	2
YHR107c	YGL062w	2	9
YHR107c	YGL245w	2	2
YHR107c	YHR107c	2	2
YHR107c	YKL056c	2	1
YHR107c	YLR314c	2	1
YHR107c	YML056c	2	2
YHR111w	YHR111w	3	3
YHR113w	YHR113w	1	1
YHR169w	YDR238c	2	2
YHR169w	YHR179w	2	1
YHR169w	YIL125w	2	2
YHR169w	YJL026w	2	1
YHR169w	YJL138c	2	2
YHR169w	YMR105c	2	4
YHR174w	YIL091c	2	1
YHR179w	YHR030c	1	1
YHR179w	YOL128c	1	1
YHR183w	YHR030c	2	1
YHR183w	YKL085w	2	2
YHR183w	YPR110c	2	2
YHR193c	YHR030c	2	1
YHR208w	YJR148w	1	1
YHR216w	YNL189w	2	9
YIL021w	YBR154c	2	2
YIL021w	YDR404c	2	2
YIL021w	YER125w	2	5
YIL021w	YOR224c	2	1
YIL033c	YER133w	3	1
YIL033c	YIL035c	3	1
YIL033c	YJL164c	3	2
YIL033c	YJR017c	3	2
YIL033c	YKL166c	3	2
YIL033c	YMR022w	3	1
YIL033c	YNL093w	3	3
YIL033c	YNL189w	3	9
YIL033c	YPL203w	3	2
YIL033c	YPR086w	3	3
YIL034c	YBR264c	1	3
YIL034c	YBR291c	1	3
YIL034c	YCL035c	1	1
YIL035c	YBL002w	1	1
YIL035c	YBR009c	1	1
YIL035c	YBR010w	1	1
YIL035c	YDR225w	1	1
YIL035c	YGL019w	1	1
YIL035c	YGL115w	1	2
YIL035c	YGR103w	1	2
YIL035c	YHL035c	1	4
YIL035c	YIL118w	1	2
YIL035c	YJL087c	1	2
YIL035c	YLR197w	1	3
YIL035c	YML069w	1	2
YIL035c	YNL262w	1	3
YIL035c	YNL330c	1	1
YIL035c	YOR039w	1	1
YIL035c	YOR061w	1	1
YIL035c	YPR016c	1	1
YIL074c	YER081w	2	2
YIL074c	YIL074c	2	2
YIL094c	YBL039c	1	2
YIL094c	YHR030c	1	1
YIL094c	YKR048c	1	1
YIL109c	YLR026c	5	2
YIL118w	YEL020c	2	3
YIL125w	YDR148c	2	2
YIL125w	YFL018c	2	4
YIL125w	YIL125w	2	2
YIL142w	YDL047w	1	1
YIL142w	YDL080c	1	3
YIL142w	YDR075w	1	1
YIL142w	YDR212w	1	1
YIL142w	YGL137w	1	5
YIL142w	YGR040w	1	1
YIL145c	YLR447c	1	1
YIR034c	YLR354c	2	1
YJL001w	YGL011c	1	1
YJL001w	YOR157c	1	1
YJL001w	YPR054w	1	1
YJL014w	YDR075w	1	1
YJL026w	YDL047w	1	1
YJL026w	YGL137w	1	5
YJL026w	YJL026w	1	1
YJL026w	YPR054w	1	1
YJL034w	YJL034w	1	1
YJL034w	YMR214w	1	3
YJL034w	YMR297w	1	2
YJL053w	YDR372c	1	1
YJL060w	YBR160w	1	1
YJL060w	YLR314c	1	1
YJL087c	YLR447c	2	1
YJL138c	YBL039c	2	2
YJL138c	YBR126c	2	1
YJL153c	YJL190c	2	1
YJL164c	YJL164c	2	2
YJL164c	YKL166c	2	2
YJL164c	YNL093w	2	3
YJL164c	YPL203w	2	2
YJL167w	YJL167w	1	1
YJL167w	YNL244c	1	1
YJL196c	YBR159w	1	1
YJL196c	YCR034w	1	1
YJL196c	YDR297w	1	1
YJL196c	YIL048w	1	2
YJL196c	YLR372w	1	1
YJL196c	YMR058w	1	4
YJL196c	YNL101w	1	1
YJL214w	YBR159w	2	1
YJL214w	YLR372w	2	1
YJL219w	YBR159w	2	1
YJL219w	YLR447c	2	1
YJR007w	YCR053w	2	1
YJR007w	YJL138c	2	2
YJR017c	YDL140c	2	7
YJR017c	YDR343c	2	2
YJR017c	YIL021w	2	2
YJR017c	YPR086w	2	3
YJR024c	YJR024c	1	1
YJR045c	YJL143w	1	1
YJR045c	YJR045c	1	1
YJR063w	YBR154c	2	2
YJR063w	YDR196c	2	1
YJR063w	YOR224c	2	1
YJR063w	YPR010c	2	7
YJR063w	YPR110c	2	2
YJR068w	YBR087w	2	1
YJR068w	YEL013w	2	8
YJR068w	YNL189w	2	9
YJR068w	YNL290w	2	2
YJR068w	YOL094c	2	2
YJR072c	YLR243w	1	1
YJR076c	YDL064w	2	1
YJR076c	YHR107c	2	2
YJR076c	YLR314c	2	1
YJR076c	YNL088w	2	3
YJR077c	YBR069c	3	1
YJR103w	YJR103w	2	2
YJR105w	YDL047w	1	1
YJR109c	YBL039c	5	2
YJR109c	YHR169w	5	2
YJR109c	YJR068w	5	2
YJR121w	YBR039w	3	1
YJR121w	YDR298c	3	1
YJR121w	YJR121w	3	3
YJR121w	YPL078c	3	1
YJR159w	YDL246c	2	2
YJR159w	YLR447c	2	1
YJR159w	YNL189w	2	9
YJR160c	YLR372w	2	1
YKL002w	YER031c	1	3
YKL002w	YER044c	1	1
YKL002w	YGR020c	1	1
YKL008c	YBR159w	2	1
YKL008c	YHL003c	2	2
YKL008c	YLR372w	2	1
YKL013c	YKL129c	1	3
YKL013c	YMR109w	1	4
YKL013c	YNR035c	1	1
YKL029c	YDL047w	2	1
YKL029c	YGL137w	2	5
YKL029c	YLR447c	2	1
YKL029c	YPR054w	2	1
YKL060c	YOR116c	1	5
YKL067w	YKL067w	1	1
YKL078w	YGL137w	4	5
YKL080w	YEL051w	1	1
YKL081w	YBR025c	3	2
YKL081w	YGL245w	3	2
YKL085w	YDR129c	2	4
YKL085w	YOL128c	2	1
YKL085w	YPR110c	2	2
YKL103c	YKL103c	1	1
YKL103c	YNL189w	1	9
YKL104c	YBL087c	3	1
YKL104c	YDR062w	3	1
YKL104c	YGR040w	3	1
YKL104c	YKL081w	3	3
YKL104c	YKL161c	3	1
YKL104c	YLR058c	3	1
YKL104c	YPR110c	3	2
YKL106w	YLR447c	1	1
YKL113c	YLR447c	2	1
YKL129c	YMR109w	3	4
YKL135c	YGL206c	1	7
YKL135c	YHR068w	1	1
YKL135c	YLR170c	1	1
YKL135c	YNL189w	1	9
YKL135c	YPL259c	1	2
YKL135c	YPR010c	1	7
YKL144c	YOR116c	2	5
YKL144c	YPR110c	2	2
YKL152c	YDL090c	1	5
YKL152c	YKL129c	1	3
YKL152c	YMR109w	1	4
YKL165c	YLR372w	2	1
YKL165c	YPR028w	2	1
YKL166c	YKL166c	2	2
YKL166c	YML001w	2	3
YKL166c	YNL093w	2	3
YKL180w	YGR118w	1	1
YKR002w	YGR048w	3	1
YKR002w	YNL189w	3	9
YKR002w	YNL222w	3	1
YKR014c	YNL093w	3	3
YKR026c	YBL030c	1	3
YKR026c	YEL051w	1	1
YKR026c	YER146w	1	1
YKR026c	YHL032c	1	2
YKR026c	YJR007w	1	2
YKR026c	YJR072c	1	1
YKR026c	YKR026c	1	1
YKR026c	YLR289w	1	5
YKR026c	YLR432w	1	2
YKR026c	YMR145c	1	2
YKR026c	YMR267w	1	1
YKR030w	YER031c	1	3
YKR039w	YBR159w	1	1
YKR048c	YDR002w	1	1
YKR048c	YJR045c	1	1
YKR048c	YMR139w	1	2
YKR081c	YPR016c	1	1
YLL001w	YLL001w	3	3
YLL028w	YBR159w	1	1
YLL057c	YLL057c	1	1
YLL061w	YBR159w	1	1
YLL061w	YLR372w	1	1
YLR005w	YLR005w	2	2
YLR026c	YDR189w	2	1
YLR026c	YNL049c	2	5
YLR027c	YLR027c	1	1
YLR027c	YLR314c	1	1
YLR027c	YNL244c	1	1
YLR038c	YML125c	1	2
YLR044c	YBR069c	3	1
YLR056w	YBR159w	1	1
YLR056w	YIL074c	1	2
YLR056w	YLL028w	1	1
YLR058c	YNL189w	1	9
YLR070c	YLR070c	2	2
YLR109w	YLR109w	1	1
YLR109w	YLR340w	1	2
YLR109w	YMR022w	1	1
YLR134w	YLR447c	3	1
YLR134w	YNL244c	3	1
YLR153c	YNL244c	1	1
YLR153c	YPR165w	1	2
YLR163c	YHR024c	2	2
YLR163c	YLR086w	2	2
YLR172c	YOR159c	1	1
YLR175w	YBR247c	3	1
YLR175w	YDL208w	3	1
YLR175w	YHR072w-a	3	1
YLR175w	YLR134w	3	3
YLR175w	YLR197w	3	3
YLR175w	YMR205c	3	2
YLR175w	YNL189w	3	9
YLR175w	YNL307c	3	1
YLR180w	YBL039c	3	2
YLR180w	YER090w	3	2
YLR186w	YBR247c	1	1
YLR186w	YHR179w	1	1
YLR197w	YNL088w	3	3
YLR209c	YNL189w	1	9
YLR212c	YLR200w	2	1
YLR215c	YER025w	1	2
YLR215c	YLR447c	1	1
YLR216c	YDR353w	2	2
YLR216c	YGL137w	2	5
YLR216c	YHR030c	2	1
YLR216c	YHR039c-a	2	1
YLR216c	YHR074w	2	2
YLR216c	YIR037w	2	1
YLR216c	YJR017c	2	2
YLR216c	YKL166c	2	2
YLR216c	YNL330c	2	1
YLR216c	YNR032w	2	1
YLR229c	YDL135c	2	1
YLR245c	YLR245c	1	1
YLR245c	YNL189w	1	9
YLR264w	YLR264w	1	1
YLR270w	YLR081w	1	2
YLR275w	YFL017w-a	1	1
YLR275w	YOR159c	1	1
YLR275w	YPR182w	1	1
YLR276c	YKR081c	2	1
YLR293c	YDR002w	2	1
YLR293c	YER009w	2	1
YLR293c	YNL189w	2	9
YLR293c	YOR185c	2	2
YLR300w	YOL126c	1	2
YLR303w	YNL189w	3	9
YLR304c	YGR040w	2	1
YLR304c	YLR262c	2	3
YLR304c	YOL006c	2	2
YLR304c	YOL094c	2	2
YLR314c	YCR053w	1	1
YLR314c	YDR158w	1	2
YLR340w	YDL081c	2	1
YLR340w	YDR382w	2	1
YLR340w	YPR016c	2	1
YLR354c	YJL068c	1	1
YLR355c	YHR030c	2	1
YLR370c	YKL013c	1	1
YLR370c	YNR035c	1	1
YLR372w	YBR069c	1	1
YLR372w	YLL028w	1	1
YLR372w	YLR241w	1	1
YLR372w	YNL101w	1	1
YLR372w	YPR156c	1	2
YLR377c	YLR377c	1	1
YLR377c	YML121w	1	2
YLR377c	YNL189w	1	9
YLR378c	YBR159w	1	1
YLR378c	YDR086c	1	1
YLR378c	YLR372w	1	1
YLR438c-a	YER146w	1	1
YLR438c-a	YLR438c-a	1	1
YLR438c-a	YMR142c	1	1
YLR438c-a	YNL147w	1	1
YLR438c-a	YOR096w	1	1
YLR438w	YHR169w	1	2
YLR438w	YJR017c	1	2
YLR438w	YLR186w	1	1
YLR438w	YNL244c	1	1
YLR438w	YPR165w	1	2
YLR447c	YBR028c	1	3
YLR447c	YGR020c	1	1
YLR447c	YIR035c	1	1
YML008c	YPR113w	4	1
YML022w	YDR441c	1	1
YML022w	YLR447c	1	1
YML042w	YML042w	1	1
YML042w	YNL189w	1	9
YML056c	YBR088c	2	2
YML056c	YER117w	2	1
YML060w	YOL010w	2	2
YML085c	YFL037w	2	2
YML092c	YER094c	1	1
YML092c	YGL011c	1	1
YML092c	YGR135w	1	1
YML092c	YOR157c	1	1
YML094w	YGR078c	1	1
YML094w	YLR200w	1	1
YML094w	YLR212c	1	2
YML110c	YGL115w	3	2
YML121w	YML121w	2	2
YML123c	YBR159w	2	1
YML123c	YDL198c	2	2
YML123c	YER125w	2	5
YML123c	YLR372w	2	1
YML126c	YDL188c	2	1
YML126c	YIL094c	2	1
YML126c	YLR180w	2	3
YMR022w	YLL039c	1	5
YMR058w	YBR159w	4	1
YMR058w	YGL084c	4	1
YMR058w	YKL008c	4	2
YMR058w	YLR372w	4	1
YMR058w	YOR161c	4	1
YMR058w	YPL234c	4	2
YMR058w	YPL274w	4	1
YMR095c	YFL059w	2	1
YMR095c	YMR096w	2	1
YMR095c	YNL333w	2	1
YMR096w	YFL059w	1	1
YMR096w	YNL333w	1	1
YMR105c	YJR068w	4	2
YMR109w	YMR109w	4	4
YMR116c	YGL120c	5	4
YMR116c	YLR197w	5	3
YMR116c	YOR116c	5	5
YMR116c	YPL106c	5	1
YMR145c	YDL047w	2	1
YMR205c	YDL047w	2	1
YMR205c	YER148w	2	2
YMR205c	YJL138c	2	2
YMR224c	YMR224c	2	2
YMR246w	YDL047w	1	1
YMR246w	YDR129c	1	4
YMR246w	YNL088w	1	3
YMR246w	YOL126c	1	2
YMR296c	YDR062w	1	1
YMR297w	YLR378c	2	1
YMR300c	YAL012w	2	1
YMR303c	YLR216c	2	2
YMR303c	YLR229c	2	2
YMR303c	YOL094c	2	2
YMR303c	YPR110c	2	2
YMR314w	YDL084w	1	2
YMR314w	YGL011c	1	1
YMR314w	YML092c	1	1
YNL007c	YHR030c	2	1
YNL037c	YGL137w	1	5
YNL037c	YHR030c	1	1
YNL037c	YOR136w	1	1
YNL055c	YCR009c	1	1
YNL055c	YNL090w	1	2
YNL055c	YNL093w	1	3
YNL071w	YBR221c	3	2
YNL088w	YBR025c	3	2
YNL088w	YNL088w	3	3
YNL090w	YOR089c	2	3
YNL096c	YMR243c	1	1
YNL096c	YPR086w	1	3
YNL102w	YIR008c	2	1
YNL102w	YNL262w	2	3
YNL135c	YDR037w	1	2
YNL135c	YDR129c	1	4
YNL135c	YDR341c	1	3
YNL135c	YIL078w	1	4
YNL135c	YJR104c	1	1
YNL135c	YLR005w	1	2
YNL135c	YMR205c	1	2
YNL147w	YLR275w	1	1
YNL153c	YGR078c	1	1
YNL153c	YLR212c	1	2
YNL169c	YLR447c	1	1
YNL189w	YDL246c	9	2
YNL189w	YDR353w	9	2
YNL189w	YDR453c	9	2
YNL189w	YGR024c	9	1
YNL189w	YGR144w	9	2
YNL189w	YHR112c	9	1
YNL189w	YJL052w	9	2
YNL189w	YJR009c	9	2
YNL189w	YKL067w	9	1
YNL189w	YML028w	9	2
YNL189w	YMR226c	9	1
YNL189w	YPL088w	9	1
YNL220w	YEL046c	1	1
YNL244c	YCR053w	1	1
YNL244c	YDL124w	1	1
YNL244c	YDR353w	1	2
YNL244c	YPR041w	1	2
YNL262w	YIR008c	3	1
YNL262w	YKL045w	3	1
YNL262w	YNL262w	3	3
YNL287w	YGL137w	1	5
YNL290w	YBR087w	2	1
YNL290w	YLR058c	2	1
YNL290w	YMR226c	2	1
YNL290w	YOL094c	2	2
YNL323w	YDR212w	1	1
YNL323w	YLR447c	1	1
YNL330c	YKR001c	1	3
YNL330c	YOL006c	1	2
YNL333w	YFL059w	1	1
YNL333w	YNL189w	1	9
YNL333w	YNL333w	1	1
YNR001c	YKL085w	1	2
YNR001c	YLR447c	1	1
YNR032w	YBR187w	1	2
YNR032w	YGR123c	1	3
YNR035c	YBR109c	1	3
YNR053c	YER126c	2	1
YNR053c	YPR016c	2	1
YNR070w	YBR159w	5	1
YOL005c	YDL140c	1	7
YOL005c	YDR404c	1	2
YOL005c	YIL021w	1	2
YOL012c	YKR048c	1	1
YOL038w	YGL011c	1	1
YOL038w	YML092c	1	1
YOL058w	YBR160w	1	1
YOL058w	YNL189w	1	9
YOL062c	YFL045c	1	2
YOL062c	YJR058c	1	1
YOL077c	YKR081c	1	1
YOL086c	YGL009c	2	2
YOL086c	YML085c	2	2
YOL090w	YBR025c	5	2
YOL090w	YJL138c	5	2
YOL094c	YBR087w	2	1
YOL094c	YGL245w	2	2
YOL126c	YJR068w	2	2
YOL139c	YDL087c	1	1
YOL139c	YER165w	1	5
YOL139c	YGL115w	1	2
YOL139c	YJL138c	1	2
YOL139c	YJR007w	1	2
YOL139c	YMR246w	1	1
YOL139c	YNL093w	1	3
YOL139c	YNL147w	1	1
YOL139c	YNL262w	1	3
YOL156w	YBR159w	2	1
YOL156w	YLR372w	2	1
YOR020c	YLR259c	1	1
YOR020c	YML092c	1	1
YOR020c	YNL189w	1	9
YOR020c	YOR020c	1	1
YOR039w	YGR103w	1	2
YOR039w	YNL330c	1	1
YOR039w	YOR039w	1	1
YOR039w	YPL235w	1	2
YOR061w	YBR094w	1	2
YOR061w	YGL019w	1	1
YOR061w	YGR103w	1	2
YOR061w	YIL118w	1	2
YOR061w	YNL088w	1	3
YOR061w	YOR039w	1	1
YOR074c	YPR086w	1	3
YOR089c	YKR014c	3	3
YOR089c	YNL093w	3	3
YOR125c	YJL068c	2	1
YOR128c	YBR021w	3	1
YOR128c	YCR012w	3	1
YOR128c	YKR026c	3	1
YOR128c	YMR323w	3	2
YOR128c	YOR128c	3	3
YOR128c	YPR054w	3	1
YOR128c	YPR088c	3	3
YOR136w	YBL022c	1	5
YOR136w	YNL189w	1	9
YOR136w	YPR110c	1	2
YOR150w	YDR172w	1	3
YOR150w	YER081w	1	2
YOR151c	YBL039c	7	2
YOR151c	YBR154c	7	2
YOR151c	YDL140c	7	7
YOR151c	YDR404c	7	2
YOR151c	YIL021w	7	2
YOR157c	YER094c	1	1
YOR159c	YPR182w	1	1
YOR176w	YDL134c	1	1
YOR176w	YGR123c	1	3
YOR185c	YER009w	2	1
YOR185c	YOL128c	2	1
YOR190w	YLR447c	1	1
YOR202w	YOR202w	1	1
YOR202w	YPR016c	1	1
YOR207c	YDR045c	7	2
YOR207c	YKL144c	7	2
YOR207c	YNL113w	7	1
YOR207c	YOR116c	7	5
YOR207c	YPR110c	7	2
YOR210w	YDL140c	1	7
YOR210w	YOR151c	1	7
YOR210w	YPR110c	1	2
YOR224c	YDL140c	1	7
YOR224c	YKL144c	1	2
YOR224c	YOR116c	1	5
YOR224c	YPR110c	1	2
YOR232w	YJR045c	1	1
YOR232w	YOR232w	1	1
YPL002c	YPR086w	1	3
YPL010w	YGL137w	1	5
YPL028w	YNL244c	2	1
YPL028w	YPR165w	2	2
YPL031c	YDL246c	2	2
YPL031c	YFL030w	2	1
YPL031c	YJR104c	2	1
YPL031c	YJR159w	2	2
YPL046c	YPL046c	1	1
YPL048w	YBR118w	3	3
YPL050c	YLR447c	1	1
YPL051w	YER044c	3	1
YPL051w	YKR030w	3	1
YPL051w	YPR086w	3	3
YPL088w	YPL088w	1	1
YPL091w	YPL091w	3	3
YPL106c	YML028w	1	2
YPL111w	YBR011c	1	1
YPL111w	YEL034w	1	2
YPL111w	YKL085w	1	2
YPL111w	YKL104c	1	3
YPL111w	YNL189w	1	9
YPL111w	YPL111w	1	1
YPL111w	YPL160w	1	2
YPL135w	YCL017c	1	3
YPL152w	YLR447c	1	1
YPL160w	YNL244c	2	1
YPL160w	YPR110c	2	2
YPL189w	YBR159w	1	1
YPL203w	YKL166c	2	2
YPL211w	YKR081c	1	1
YPL227c	YEL063c	1	1
YPL227c	YGR060w	1	1
YPL227c	YJL026w	1	1
YPL227c	YJL196c	1	1
YPL227c	YPL274w	1	1
YPL234c	YLL028w	2	1
YPL259c	YBR221c	2	2
YPL259c	YER165w	2	5
YPL259c	YLR170c	2	1
YPL259c	YOL010w	2	2
YPL259c	YOL077c	2	1
YPL259c	YOR187w	2	4
YPL259c	YPR016c	2	1
YPL262w	YPR165w	1	2
YPL274w	YBR159w	1	1
YPR006c	YLR447c	1	1
YPR010c	YBR143c	7	3
YPR010c	YKL067w	7	1
YPR010c	YOR210w	7	1
YPR010c	YPR016c	7	1
YPR010c	YPR110c	7	2
YPR035w	YBR126c	2	1
YPR069c	YLR146c	1	1
YPR074c	YBR117c	3	3
YPR082c	YFL017w-a	1	1
YPR082c	YNL147w	1	1
YPR082c	YPR182w	1	1
YPR086w	YDL086w	3	1
YPR086w	YFL038c	3	3
YPR086w	YKL058w	3	2
YPR086w	YPR041w	3	2
YPR086w	YPR066w	3	2
YPR103w	YER094c	1	1
YPR103w	YFR050c	1	1
YPR103w	YGL011c	1	1
YPR103w	YJL001w	1	1
YPR103w	YNL244c	1	1
YPR110c	YDR453c	2	2
YPR110c	YGL026c	2	2
YPR110c	YGL137w	2	5
YPR110c	YGL245w	2	2
YPR110c	YHR112c	2	1
YPR110c	YKL218c	2	1
YPR110c	YLR086w	2	2
YPR110c	YOR116c	2	5
YPR145w	YHR113w	2	1
YPR156c	YBR159w	2	1
YPR165w	YFR044c	2	2
YPR181c	YIL109c	5	5
YPR181c	YLR026c	5	2
YPR181c	YNL049c	5	5
YPR182w	YNL189w	1	9

Supplementary material S4.

Test set 2, containing 374 yeast protein interactions with SLA ≥ 75%.

Format: <Protein1> <Protein2> <#DomainsInProtein1> <#DomainsInProtein2>

Protein1	Protein2	#DomainsInProtein1	#DomainsInProtein2
YAL038w	YNL307c	2	1
YAL038w	YOR226c	2	1
YAL062w	YNL189w	2	9
YBL039c	YJR103w	2	2
YBL040c	YOL020w	1	1
YBL078c	YOR100c	1	3
YBR018c	YPR054w	2	1
YBR039w	YDL145c	1	7
YBR039w	YJR068w	1	2
YBR068c	YDR046c	1	1
YBR085w	YHR002w	3	3
YBR088c	YJR068w	2	2
YBR088c	YNL290w	2	2
YBR088c	YOL094c	2	2
YBR088c	YOR116c	2	5
YBR117c	YLR447c	3	1
YBR126c	YOR089c	1	3
YBR127c	YKL080w	3	1
YBR127c	YLR447c	3	1
YBR154c	YDL140c	2	7
YBR154c	YDR404c	2	2
YBR154c	YKL144c	2	2
YBR154c	YOR116c	2	5
YBR154c	YPR110c	2	2
YBR160w	YDR212w	1	1
YBR160w	YLR086w	1	2
YBR170c	YLR044c	2	3
YBR176w	YBR176w	1	1
YBR176w	YNL189w	1	9
YBR205w	YFL038c	1	3
YBR218c	YPR110c	7	2
YBR249c	YPR110c	1	2
YBR252w	YNL189w	1	9
YBR291c	YHR096c	3	2
YCL040w	YCL040w	2	2
YCL040w	YNL189w	2	9
YCR002c	YFL018c	2	4
YCR005c	YCR005c	1	1
YCR005c	YKL085w	1	2
YCR034w	YHR094c	1	2
YCR034w	YJL219w	1	2
YCR034w	YLL061w	1	1
YCR034w	YOL020w	1	1
YCR034w	YPL274w	1	1
YDL064w	YDL064w	1	1
YDL100c	YHR057c	2	1
YDL100c	YJL153c	2	2
YDL100c	YNL055c	2	1
YDL100c	YOL126c	2	2
YDL108w	YDL140c	1	7
YDL108w	YOR151c	1	7
YDL135c	YPR165w	1	2
YDL137w	YPR110c	3	2
YDL143w	YKR026c	1	1
YDL145c	YCR012w	7	1
YDL145c	YDR238c	7	2
YDL145c	YPL010w	7	1
YDL192w	YDL137w	3	3
YDL192w	YPR110c	3	2
YDL236w	YNL189w	1	9
YDL245c	YHR096c	2	2
YDL245c	YJR160c	2	2
YDR044w	YNL189w	1	9
YDR045c	YOR116c	2	5
YDR046c	YLR372w	1	1
YDR099w	YBR001c	1	2
YDR099w	YDR099w	1	1
YDR127w	YJL008c	6	1
YDR127w	YOR136w	6	1
YDR127w	YPL235w	6	2
YDR139c	YDR328c	1	2
YDR139c	YLR306w	1	1
YDR155c	YKL103c	1	1
YDR155c	YNL244c	1	1
YDR155c	YPL235w	1	2
YDR226w	YBL036c	2	1
YDR226w	YOR176w	2	1
YDR226w	YPL031c	2	2
YDR256c	YMR314w	1	1
YDR256c	YNL189w	1	9
YDR328c	YBR127c	2	3
YDR328c	YEL051w	2	1
YDR342c	YBL036c	2	1
YDR342c	YNL323w	2	1
YDR343c	YBL036c	2	1
YDR343c	YGR040w	2	1
YDR353w	YOL128c	2	1
YDR382w	YBR006w	1	1
YDR404c	YDL140c	2	7
YDR404c	YGR063c	2	1
YDR404c	YOR224c	2	1
YDR487c	YNL189w	1	9
YDR516c	YCL040w	2	2
YDR529c	YBR082c	1	1
YEL021w	YEL021w	1	1
YEL027w	YLR034c	2	1
YEL054c	YDL081c	2	1
YEL054c	YDR382w	2	1
YEL054c	YOL039w	2	1
YEL063c	YBL040c	1	1
YEL063c	YCR034w	1	1
YEL063c	YJL196c	1	1
YEL063c	YLR372w	1	1
YEL063c	YPL234c	1	2
YEL069c	YPR110c	2	2
YEL071w	YPR165w	2	2
YER009w	YNL189w	1	9
YER012w	YBL041w	1	1
YER012w	YER094c	1	1
YER012w	YJL001w	1	1
YER012w	YMR314w	1	1
YER020w	YNL037c	2	1
YER057c	YNL189w	1	9
YER086w	YER086w	3	3
YER126c	YPR016c	1	1
YER146w	YCR024c	1	2
YER146w	YDR378c	1	1
YER146w	YER131w	1	1
YER146w	YER146w	1	1
YER146w	YPL152w	1	1
YER146w	YPR010c	1	7
YER156c	YFL038c	1	3
YER177w	YDR099w	1	1
YER177w	YGL115w	1	2
YER177w	YNL189w	1	9
YFL005w	YFL038c	3	3
YFL018c	YBR221c	4	2
YFL045c	YNL189w	2	9
YFR047c	YFR047c	2	2
YFR047c	YNL189w	2	9
YGL040c	YGL040c	1	1
YGL040c	YNL189w	1	9
YGL054c	YLR372w	1	1
YGL062w	YPR110c	9	2
YGL087c	YDR092w	1	1
YGL130w	YBR221c	3	2
YGL130w	YDL140c	3	7
YGL221c	YGL221c	1	1
YGL221c	YNL189w	1	9
YGL234w	YJR068w	5	2
YGL234w	YOL094c	5	2
YGL238w	YNL189w	3	9
YGL253w	YGL253w	2	2
YGR020c	YEL051w	1	1
YGR024c	YGR024c	1	1
YGR040w	YGL062w	1	9
YGR040w	YLL039c	1	5
YGR040w	YML123c	1	2
YGR040w	YPR010c	1	7
YGR133w	YGR133w	1	1
YGR144w	YGR144w	2	2
YGR155w	YBR088c	2	2
YGR155w	YGR040w	2	1
YGR155w	YNL189w	2	9
YHR007c	YPL274w	1	1
YHR039c-a	YBR127c	1	3
YHR039c-a	YGR020c	1	1
YHR068w	YNL189w	1	9
YHR094c	YLR372w	2	1
YHR113w	YHR113w	1	1
YHR179w	YOL128c	1	1
YHR183w	YKL085w	2	2
YHR183w	YPR110c	2	2
YHR208w	YJR148w	1	1
YHR216w	YNL189w	2	9
YIL021w	YBR154c	2	2
YIL021w	YDR404c	2	2
YIL021w	YOR224c	2	1
YIL034c	YBR264c	1	3
YIL034c	YBR291c	1	3
YIL035c	YGL115w	1	2
YIL035c	YIL118w	1	2
YIL035c	YOR061w	1	1
YIL035c	YPR016c	1	1
YIL094c	YBL039c	1	2
YIL118w	YEL020c	2	3
YIL142w	YDL080c	1	3
YIL142w	YDR212w	1	1
YIL142w	YGR040w	1	1
YIL145c	YLR447c	1	1
YIR034c	YLR354c	2	1
YJL001w	YPR054w	1	1
YJL053w	YDR372c	1	1
YJL060w	YBR160w	1	1
YJL153c	YJL190c	2	1
YJL167w	YJL167w	1	1
YJL167w	YNL244c	1	1
YJL196c	YCR034w	1	1
YJL196c	YLR372w	1	1
YJL214w	YLR372w	2	1
YJL219w	YLR447c	2	1
YJR017c	YDL140c	2	7
YJR017c	YDR343c	2	2
YJR017c	YIL021w	2	2
YJR024c	YJR024c	1	1
YJR068w	YNL189w	2	9
YJR068w	YNL290w	2	2
YJR068w	YOL094c	2	2
YJR103w	YJR103w	2	2
YJR121w	YBR039w	3	1
YJR121w	YDR298c	3	1
YJR121w	YJR121w	3	3
YJR160c	YLR372w	2	1
YKL013c	YMR109w	1	4
YKL013c	YNR035c	1	1
YKL060c	YOR116c	1	5
YKL067w	YKL067w	1	1
YKL080w	YEL051w	1	1
YKL085w	YOL128c	2	1
YKL085w	YPR110c	2	2
YKL103c	YKL103c	1	1
YKL103c	YNL189w	1	9
YKL106w	YLR447c	1	1
YKL144c	YOR116c	2	5
YKL144c	YPR110c	2	2
YKL152c	YMR109w	1	4
YKL165c	YLR372w	2	1
YKR002w	YNL189w	3	9
YKR002w	YNL222w	3	1
YKR014c	YNL093w	3	3
YKR026c	YBL030c	1	3
YKR026c	YEL051w	1	1
YKR026c	YER146w	1	1
YKR026c	YKR026c	1	1
YKR026c	YLR432w	1	2
YKR030w	YER031c	1	3
YLL001w	YLL001w	3	3
YLL061w	YLR372w	1	1
YLR027c	YLR027c	1	1
YLR027c	YNL244c	1	1
YLR109w	YLR109w	1	1
YLR109w	YMR022w	1	1
YLR134w	YLR447c	3	1
YLR134w	YNL244c	3	1
YLR180w	YBL039c	3	2
YLR180w	YER090w	3	2
YLR209c	YNL189w	1	9
YLR215c	YLR447c	1	1
YLR229c	YDL135c	2	1
YLR245c	YLR245c	1	1
YLR245c	YNL189w	1	9
YLR264w	YLR264w	1	1
YLR270w	YLR081w	1	2
YLR303w	YNL189w	3	9
YLR354c	YJL068c	1	1
YLR370c	YKL013c	1	1
YLR370c	YNR035c	1	1
YLR377c	YLR377c	1	1
YLR377c	YML121w	1	2
YLR377c	YNL189w	1	9
YLR378c	YLR372w	1	1
YLR438c-a	YER146w	1	1
YLR438c-a	YLR438c-a	1	1
YLR438c-a	YMR142c	1	1
YLR438c-a	YOR096w	1	1
YLR438w	YJR017c	1	2
YLR438w	YNL244c	1	1
YLR438w	YPR165w	1	2
YLR447c	YGR020c	1	1
YML042w	YML042w	1	1
YML042w	YNL189w	1	9
YML056c	YBR088c	2	2
YML056c	YER117w	2	1
YML060w	YOL010w	2	2
YML110c	YGL115w	3	2
YML121w	YML121w	2	2
YML123c	YLR372w	2	1
YML126c	YIL094c	2	1
YML126c	YLR180w	2	3
YMR022w	YLL039c	1	5
YMR105c	YJR068w	4	2
YMR109w	YMR109w	4	4
YMR297w	YLR378c	2	1
YNL037c	YOR136w	1	1
YNL055c	YCR009c	1	1
YNL055c	YNL090w	1	2
YNL055c	YNL093w	1	3
YNL090w	YOR089c	2	3
YNL096c	YMR243c	1	1
YNL135c	YDR341c	1	3
YNL135c	YJR104c	1	1
YNL189w	YDR353w	9	2
YNL189w	YDR453c	9	2
YNL189w	YGR024c	9	1
YNL189w	YGR144w	9	2
YNL189w	YHR112c	9	1
YNL189w	YJL052w	9	2
YNL189w	YJR009c	9	2
YNL189w	YKL067w	9	1
YNL189w	YML028w	9	2
YNL189w	YPL088w	9	1
YNL244c	YDL124w	1	1
YNL244c	YDR353w	1	2
YNL290w	YOL094c	2	2
YNL323w	YDR212w	1	1
YNL323w	YLR447c	1	1
YNR001c	YKL085w	1	2
YNR001c	YLR447c	1	1
YOL058w	YBR160w	1	1
YOL058w	YNL189w	1	9
YOL126c	YJR068w	2	2
YOL139c	YDL087c	1	1
YOL139c	YGL115w	1	2
YOL139c	YNL093w	1	3
YOL156w	YLR372w	2	1
YOR020c	YLR259c	1	1
YOR020c	YNL189w	1	9
YOR020c	YOR020c	1	1
YOR061w	YBR094w	1	2
YOR061w	YIL118w	1	2
YOR089c	YKR014c	3	3
YOR089c	YNL093w	3	3
YOR125c	YJL068c	2	1
YOR136w	YNL189w	1	9
YOR136w	YPR110c	1	2
YOR151c	YBL039c	7	2
YOR151c	YBR154c	7	2
YOR151c	YDL140c	7	7
YOR151c	YDR404c	7	2
YOR151c	YIL021w	7	2
YOR159c	YPR182w	1	1
YOR207c	YDR045c	7	2
YOR207c	YKL144c	7	2
YOR207c	YOR116c	7	5
YOR207c	YPR110c	7	2
YOR210w	YDL140c	1	7
YOR210w	YOR151c	1	7
YOR210w	YPR110c	1	2
YOR224c	YDL140c	1	7
YOR224c	YKL144c	1	2
YOR224c	YOR116c	1	5
YOR224c	YPR110c	1	2
YOR232w	YOR232w	1	1
YPL028w	YNL244c	2	1
YPL028w	YPR165w	2	2
YPL031c	YFL030w	2	1
YPL031c	YJR104c	2	1
YPL050c	YLR447c	1	1
YPL051w	YER044c	3	1
YPL051w	YKR030w	3	1
YPL088w	YPL088w	1	1
YPL091w	YPL091w	3	3
YPL106c	YML028w	1	2
YPL111w	YKL085w	1	2
YPL111w	YNL189w	1	9
YPL111w	YPL111w	1	1
YPL111w	YPL160w	1	2
YPL152w	YLR447c	1	1
YPL160w	YNL244c	2	1
YPL160w	YPR110c	2	2
YPL259c	YBR221c	2	2
YPL259c	YLR170c	2	1
YPL259c	YOL010w	2	2
YPL259c	YOR187w	2	4
YPL259c	YPR016c	2	1
YPR006c	YLR447c	1	1
YPR010c	YBR143c	7	3
YPR010c	YKL067w	7	1
YPR010c	YOR210w	7	1
YPR010c	YPR016c	7	1
YPR010c	YPR110c	7	2
YPR035w	YBR126c	2	1
YPR069c	YLR146c	1	1
YPR074c	YBR117c	3	3
YPR082c	YFL017w-a	1	1
YPR082c	YPR182w	1	1
YPR110c	YDR453c	2	2
YPR110c	YGL026c	2	2
YPR110c	YHR112c	2	1
YPR110c	YKL218c	2	1
YPR110c	YLR086w	2	2
YPR110c	YOR116c	2	5
YPR165w	YFR044c	2	2
YPR182w	YNL189w	1	9

Supplementary information

Supplementary data associated with this article, and an implementation of the RCDP algorithm is available at URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/RCDP/. The supplementary data comprises: S1, organisms used in ortholog search; S2, test set 1, containing 1180 yeast protein interactions with SLA ≥50%; S3, RCDP prediction results for the test set 1, containing 1222 domain–domain interactions; S4; test set 2, containing 374 yeast protein interactions with SLA ≥75%; S5, RCDP prediction results for the test set 2, containing 394 domain–domain interactions; S6, validation set, containing 109 yeast protein interactions with SLA ≥50%.