| T0787 GP41 |
| ID: | 1400714700 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 153 (153) | ||
| Sequences: | 1858 (61.6) | ||
| Seq/Len: | 12.144 | ||
| Nf(neff/√len): | 5.0 |
Jackhmmer Results: (2014_04_16)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 12.144).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 63_K | 66_Q | 1.945 | 1.00 |
| 74_R | 88_S | 1.706 | 1.00 |
| 94_C | 138_S | 1.548 | 1.00 |
| 75_Y | 78_D | 1.517 | 1.00 |
| 80_Q | 91_L | 1.482 | 1.00 |
| 15_A | 19_M | 1.461 | 1.00 |
| 126_N | 142_Q | 1.409 | 1.00 |
| 76_L | 98_P | 1.371 | 0.99 |
| 19_M | 26_L | 1.368 | 0.99 |
| 16_G | 19_M | 1.367 | 0.99 |
| 55_L | 60_W | 1.359 | 0.99 |
| 124_I | 140_N | 1.357 | 0.99 |
| 81_L | 102_S | 1.355 | 0.99 |
| 118_L | 138_S | 1.332 | 0.99 |
| 58_T | 121_D | 1.329 | 0.99 |
| 63_K | 135_L | 1.309 | 0.99 |
| 49_E | 90_K | 1.305 | 0.99 |
| 6_A | 13_G | 1.300 | 0.99 |
| 27_T | 33_L | 1.296 | 0.99 |
| 36_G | 40_Q | 1.292 | 0.99 |
| 39_Q | 47_A | 1.273 | 0.99 |
| 22_A | 26_L | 1.261 | 0.99 |
| 147_Q | 151_A | 1.257 | 0.99 |
| 57_L | 60_W | 1.256 | 0.99 |
| 26_L | 29_Q | 1.254 | 0.99 |
| 65_L | 68_R | 1.250 | 0.99 |
| 59_V | 62_I | 1.241 | 0.98 |
| 20_G | 26_L | 1.240 | 0.98 |
| 36_G | 41_Q | 1.239 | 0.98 |
| 11_F | 31_R | 1.232 | 0.98 |
| 72_V | 76_L | 1.222 | 0.98 |
| 40_Q | 45_L | 1.207 | 0.98 |
| 56_K | 63_K | 1.207 | 0.98 |
| 124_I | 132_Y | 1.204 | 0.98 |
| 81_L | 132_Y | 1.198 | 0.98 |
| 14_A | 18_T | 1.198 | 0.98 |
| 21_A | 26_L | 1.193 | 0.98 |
| 70_L | 151_A | 1.188 | 0.98 |
| 14_A | 22_A | 1.187 | 0.98 |
| 124_I | 138_S | 1.185 | 0.98 |
| 37_I | 41_Q | 1.180 | 0.98 |
| 10_G | 17_S | 1.174 | 0.98 |
| 43_N | 47_A | 1.170 | 0.97 |
| 53_H | 56_K | 1.164 | 0.97 |
| 139_Q | 143_E | 1.154 | 0.97 |
| 41_Q | 45_L | 1.142 | 0.97 |
| 66_Q | 135_L | 1.139 | 0.97 |
| 74_R | 94_C | 1.137 | 0.97 |
| 12_L | 15_A | 1.134 | 0.97 |
| 15_A | 18_T | 1.129 | 0.97 |
| 41_Q | 44_L | 1.127 | 0.97 |
| 29_Q | 33_L | 1.126 | 0.97 |
| 58_T | 138_S | 1.121 | 0.97 |
| 77_R | 97_V | 1.111 | 0.96 |
| 18_T | 64_Q | 1.107 | 0.96 |
| 58_T | 118_L | 1.105 | 0.96 |
| 98_P | 128_T | 1.105 | 0.96 |
| 19_M | 22_A | 1.104 | 0.96 |
| 144_K | 148_D | 1.104 | 0.96 |
| 51_Q | 131_I | 1.101 | 0.96 |
| 102_S | 109_S | 1.100 | 0.96 |
| 131_I | 134_L | 1.100 | 0.96 |
| 15_A | 26_L | 1.098 | 0.96 |
| 127_Y | 146_E | 1.087 | 0.96 |
| 36_G | 45_L | 1.078 | 0.95 |
| 88_S | 105_N | 1.076 | 0.95 |
| 63_K | 134_L | 1.073 | 0.95 |
| 23_S | 26_L | 1.069 | 0.95 |
| 13_G | 25_T | 1.066 | 0.95 |
| 89_G | 94_C | 1.062 | 0.95 |
| 134_L | 148_D | 1.061 | 0.95 |
| 70_L | 80_Q | 1.060 | 0.95 |
| 49_E | 78_D | 1.059 | 0.95 |
| 10_G | 16_G | 1.056 | 0.95 |
| 31_R | 34_L | 1.055 | 0.95 |
| 46_R | 62_I | 1.050 | 0.94 |
| 3_G | 17_S | 1.046 | 0.94 |
| 19_M | 29_Q | 1.043 | 0.94 |
| 80_Q | 121_D | 1.042 | 0.94 |
| 5_G | 18_T | 1.038 | 0.94 |
| 40_Q | 44_L | 1.031 | 0.94 |
| 42_S | 94_C | 1.030 | 0.94 |
| 37_I | 40_Q | 1.028 | 0.94 |
| 108_L | 136_E | 1.027 | 0.94 |
| 15_A | 22_A | 1.025 | 0.93 |
| 18_T | 22_A | 1.017 | 0.93 |
| 35_S | 48_P | 1.015 | 0.93 |
| 94_C | 118_L | 1.014 | 0.93 |
| 16_G | 20_G | 1.010 | 0.93 |
| 6_A | 10_G | 1.008 | 0.93 |
| 60_W | 65_L | 1.008 | 0.93 |
| 122_K | 133_G | 1.004 | 0.93 |
| 7_V | 18_T | 1.003 | 0.93 |
| 44_L | 53_H | 1.001 | 0.92 |
| 58_T | 115_M | 1.000 | 0.92 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 1qbzA | 3 | 0.7778 | 100 | 0.293 | Contact Map |
| 1envA | 1 | 0.732 | 100 | 0.465 | Contact Map |
| 3p30A | 1 | 0.5229 | 100 | 0.519 | Contact Map |
| 2cmrA | 1 | 0.5033 | 100 | 0.547 | Contact Map |
| 1jq0A | 1 | 0.4641 | 100 | 0.566 | Contact Map |
| 3k9aA | 1 | 0.4641 | 100 | 0.603 | Contact Map |
| 3o3xA | 1 | 0.5163 | 100 | 0.605 | Contact Map |
| 1df4A | 1 | 0.3725 | 100 | 0.648 | Contact Map |
| 2x7rA | 3 | 0.3333 | 99.9 | 0.723 | Contact Map |
| 3vh7A | 3 | 0.366 | 99.9 | 0.731 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)