Table 2.
Comparison of IC, GGSEARCH, HMMER and SAM: Results for Homologous Proteins in Four Superfamilies1.
| Superfamily | Family TC# | Profile | Database | IC/GAP score (S.D.) | GGSEARCH (FASTA) e-value | HMMER e-value | SAM e-value | ||
|---|---|---|---|---|---|---|---|---|---|
| Protein-12 | Acc# | Protein-22 | Acc# | ||||||
| CDF Vs Orai | 2.A.4.1 | PfuCDF | AAL80682 | CelOrai | NP_497230 | 14.6 | 0.0049 | 0.09 | 0.72 |
| Orai Vs CDF | 1.A.52.1 | CelOrai | NP_497230 | PfuCDF | AAL80682 | 5.4 e-5 | 0.22 | 0.29 | |
| CDF 3-4 TMSs Vs Orai 1-2 TMSs | 2.A.4.1 | PfuCDF | AAL80682 | CelOrai | NP_497230 | 14.6 | 1.6 e-18 | 0.11 | 0.18 |
| Orai 1-2 TMSs Vs CDF 3-4 TMSs | 1.A.52.1 | CelOrai | NP_497230 | PfuCDF | AAL80682 | 4.7 e-6 | 0.11 | 0.02 | |
| DMT | 2.A.7.20 | PfCRT | Q86M68 | AthCRT | Q8RWL5 | 16 | 0 | 9.2 e-226 | 0 |
| DMT | 2.A.7.20 | AthCRT | Q8RWL5 | PfCRT | Q86M68 | 0 | 2.6 e-149 | 3.26 e-163 | |
| DMT | 2.A.7.12 | SLC35A1 | Q8BRW7 | PfCRT | Q86M68 | 9 | 6.9 e-10 | 3.2 e-6 | 8.55 e-9 |
| DMT | 2.A.7.20 | PfCRT | Q86M68 | SLC35A1 | Q8BRW7 | 3.8 e-8 | 9.5 e-6 | 2.17 e-6 | |
| BART | 2.A.87.2 (P-RFT) | YpaA | NP_390186 | Ade1 | YP_464235 | 9 | 0.0002 | 0.007 | 5.4 |
| BART | 2.A.59.1 (Acr3) | Ade1 | YP_464235 | YpaA | NP_390186 | 0.02 | 0.11 | 0.2 | |
| BART | 9.B.33 (SHK) | LytS | NP_847838 | Rba2 | NP_868846 | 8 | 0.04 | 0.08 | 0.03 |
| BART | 2.A.93 (UNK) | Rba2 | NP_868846 | LytS | NP_847838 | 0.09 | 0.007 | 0.28 | |
| BART | 9.B.34 (KPSH) | Dge1 | YP_604037 | Rba2 | NP_868846 | 9 | 0.004 | 2.2 | 0.3 |
| BART | 2.A.93 (UNK) | Rba2 | NP_868846 | Dge1 | YP_604037 | 0.024 | 0.06 | 7.2 | |
| OPT ABvsCD | 2.A.67.3 | Spr1 | YP_001477255.1 | Lsa1 | YP_394932.1 | 13 | 3.5 e-8 | 4 e-4 | 0.1 |
| OPT CDvsAB | 2.A.67.4 | Lsa1 | YP_394932.1 | Spr1 | YP_001477255.1 | 2.3 e-6 | 0.004 | 0.004 | |
| OPT AvsB | 2.A.67.4 | Ngo1 | YP_208927.1 | Sde1 | YP_526125.1 | 11 | 7.1 e-6 | 0.06 | 0.5 |
| OPT BvsA | 2.A.67.4 | Sde1 | YP_526125.1 | Ngo1 | YP_208927.1 | 5.9 e-5 | 0.2 | 0.09 | |
| OPT AvsC | 2.A.67.2 | Zma1 | NP_001104952.1 | Chy1 | YP_361078.1 | 12 | 5.9 e-5 | 0.03 | 0.002 |
| OPT CvsA | 2.A.67.4 | Chy1 | YP_361078.1 | Zma1 | NP_001104952.1 | 0.0015 | 0.03 | 0.02 | |
| OPT AvsD | 2.A.67.1 | Gze4 | XP_389463.1 | Sus1 | YP_822933.1 | 12 | 0.0008 | 0.09 | 2 |
| OPT DvsA | 2.A.67.4 | Sus1 | YP_822933.1 | Gze4 | XP_389463.1 | 0.0001 | 0.03 | 0.2 | |
| OPT BvsC | 2.A.67.1 | Sco1 | AAF26618.1 | Mtu1 | NP_216911.1 | 12 | 0.007 | 0.07 | 0.01 |
| OPT CvsB | 2.A.67.4 | Mtu1 | NP_216911.1 | Sco1 | AAF26618.1 | 0.003 | 0.08 | 0.003 | |
| OPT BvsD | 2.A.67.2 | Osa28 | CAE02279.2 | Asu1 | YP_001343430.1 | 14 | 2.2 e-8 | 0.006 | 0.02 |
| OPT DvsB | 2.A.67.4 | Asu1 | YP_001343430.1 | Osa28 | CAE02279.2 | 7 e-5 | 0.007 | 0.001 | |
| OPT CvsD | 2.A.67.4 | Pgi1 | NP_904744.1 | Ani11 | XP_658304.1 | 10 | 0.0002 | 0.2 | 2 |
| OPT DvsC | 2.A.67.2 | Ani11 | XP_658304.1 | Pgi1 | NP_904744.1 | 9.2 e-6 | 0.05 | 0.5 | |
1The comparison scores obtained with the IC and GAP programs, other than the CRAC/CDF comparisons, are published as follows: DMT superfamily: Tran & Saier, 2004; see also Jack et al., 2001; BART superfamily: Mansour et al., 2007. The HMMER and IC/GAP values for comparison of the CRAC (Orai) and CDF families, as well as the OPT family, have not been published previously.
2Top entry in each set of comparisons: Protein-2 was used as the Blast query sequence to generate the target sequences; Protein-1 was used as the query sequence to generate the HMM profile. The opposite was used for the bottom entry in each set of comparisons.