Appendix 1—table 5. BPPS-SIPRIS analyses using MAPGAPS (MG) versus Jackhmmer (JH) generated MSAs as input.
| Protein | MSA* | SIPRIS† | BPPS-SIPRIS† | SIPRIS | Tree | Optimal BPPS pattern ∩ SIPRIS cluster# | ||
|---|---|---|---|---|---|---|---|---|
| Mode | Dist. | Init. | Term. | p-value | level‡ | |||
| Gna1 | JH | p=BDF | 21 | 69 | 87 | 1.2 × 10−5 | 1 | F93,I94,D105,K136,H95,Y68,Y135,T44,R102,E104, E90,C141,K92,L40,L43,V88,V134,Y36,L27,F58,V89 |
| MG | p=BDF | 22 | 57 | 71 | 8.5 × 10−7 | 1 | F93,I94,D105,K136,H95,Y68,Y135,T44,R102,E104, E90,C141,K92,M61,L40,L43,V134,F54,Y36,F58, G98,V89 |
|
| JH | S | 14 | 21 | 135 | 2.1 × 10−5 | 1 | E90,K92,R102,V89,V88,G101,Y135,I94,V134,K136, F93,E104,Y68,H95 |
|
| MG | S | 14 | 21 | 107 | 2.5 × 10−4 | 1 | E90,K92,R102,V89,G101,Y135,I94,V134,K136,F93, G98,E104,Y68,H95 |
|
| APE1 | JH | H | 15 | 38 | 219 | 5.0 × 10−5 | 0 | V206,L167,Q95,S66,G209,W67,P311,H309,D283, S307,N68,D210,E96,N212,R185 |
| MG | H | 16 | 33 | 218 | 4.2 × 10−7 | 0 | V206,L167,F165,Q95,S66,G209,V69,W67,H309, D283,T265,S307,N68,D210,E96,N212 |
|
| JH | H | 25 | 158 | 99 | 8.8 × 10−6 | 1 | Y128,E154,R156,Y171,P173,W188,D70,W267,N277, E236,C310,G71,R237,D219,R254,R281,V213,A214, L62,G279,K98,V131,A175,L72,R181 |
|
| MG | H | 25 | 137 | 214 | 1.7 × 10−6 | 1 | Y128,G155,E154,D152,R156,Y171,P173,R185,D70, W267,N277,W188,E236,C310,Y269,R237,D219, R254,V213,A214,Y264,G279,K98,A175,G145 |
|
| Rho1 | JH | B | 20 | 63 | 110 | 3.5 × 10−4 | 1 | S106,D28,W114,Y81,E117,Y89,A76,Q78,L84,E79, K22,W73,F176,F99,F107,V101,E163,Y161,G149, C153 |
| MG | B | 20 | 53 | 100 | 8.3 × 10−5 | 1 | S106,D28,W114,Y81,Y89,A76,Q78,L84,E79,K22, W73,F99,F107,V101,V144,R137,E163,Y161,G149, C153 |
|
| JH | C | 24 | 82 | 91 | 2.4 × 10−6 | 1 | L84,Y81,Q78,A76,E117,W114,Y89,D28,V24,E79, W73,K22,F99,F107,Y161,C153,G149,S106,V101, E163,G131,F176,F40,F57 |
|
| MG | C | 22 | 55 | 98 | 7.8 × 10−7 | 1 | L84,Y81,Q78,A76,T52,W114,Y89,D28,E79,W73,K22, F99,F107,Y161,C153,G149,V144,S106,V101,E163, G131,R137 |
|
| eIF4AIII | JH | p=J | 8 | 18 | 212 | 2.7 × 10−4 | 1 | G165,R116,D169,R166,G143,T115,G196,P164 |
| MG | p=J | 11 | 18 | 128 | 6.4 × 10-6 | 1 | G165,F197,R116,Q200,D169,R166,G143,T115, G142,G196,P164 |
|
*Input MSA: Jackhmmer, JH; MAPGAPS, MG.
†Explained in the footnotes to Table 1.
‡Codes designate BPPS category: 0, superfamily; 1, family.
§Pattern residue discrepancies between the Jackhmmer and MAPGAPS runs are shown in bold.