| T0787 GP41 |
| ID: | 1400696314 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 153 (153) | ||
| Sequences: | 1959 (72.7) | ||
| Seq/Len: | 12.804 | ||
| Nf(neff/√len): | 5.9 |
HHblits Results: (2013_03)
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: 12.804).
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 | 1.851 | 1.00 |
| 74_R | 88_S | 1.709 | 1.00 |
| 16_G | 19_M | 1.706 | 1.00 |
| 75_Y | 78_D | 1.650 | 1.00 |
| 59_V | 62_I | 1.569 | 1.00 |
| 15_A | 19_M | 1.479 | 1.00 |
| 57_L | 65_L | 1.417 | 1.00 |
| 55_L | 60_W | 1.415 | 1.00 |
| 55_L | 65_L | 1.372 | 0.99 |
| 80_Q | 91_L | 1.314 | 0.99 |
| 72_V | 76_L | 1.296 | 0.99 |
| 126_N | 142_Q | 1.294 | 0.99 |
| 2_V | 5_G | 1.281 | 0.99 |
| 42_S | 94_C | 1.278 | 0.99 |
| 57_L | 60_W | 1.271 | 0.99 |
| 147_Q | 151_A | 1.265 | 0.99 |
| 51_Q | 131_I | 1.264 | 0.99 |
| 26_L | 29_Q | 1.251 | 0.99 |
| 60_W | 65_L | 1.250 | 0.99 |
| 94_C | 138_S | 1.244 | 0.98 |
| 30_A | 35_S | 1.241 | 0.98 |
| 145_N | 149_L | 1.228 | 0.98 |
| 89_G | 94_C | 1.226 | 0.98 |
| 11_F | 31_R | 1.219 | 0.98 |
| 20_G | 26_L | 1.218 | 0.98 |
| 56_K | 63_K | 1.209 | 0.98 |
| 65_L | 68_R | 1.205 | 0.98 |
| 94_C | 135_L | 1.201 | 0.98 |
| 53_H | 56_K | 1.196 | 0.98 |
| 122_K | 129_Q | 1.196 | 0.98 |
| 81_L | 132_Y | 1.193 | 0.98 |
| 19_M | 26_L | 1.185 | 0.98 |
| 27_T | 33_L | 1.182 | 0.98 |
| 149_L | 152_L | 1.180 | 0.98 |
| 1_A | 5_G | 1.177 | 0.98 |
| 124_I | 138_S | 1.161 | 0.97 |
| 117_W | 120_W | 1.160 | 0.97 |
| 134_L | 148_D | 1.155 | 0.97 |
| 1_A | 6_A | 1.151 | 0.97 |
| 143_E | 152_L | 1.150 | 0.97 |
| 16_G | 26_L | 1.147 | 0.97 |
| 15_A | 26_L | 1.147 | 0.97 |
| 70_L | 80_Q | 1.146 | 0.97 |
| 124_I | 140_N | 1.144 | 0.97 |
| 57_L | 68_R | 1.135 | 0.97 |
| 55_L | 68_R | 1.130 | 0.97 |
| 127_Y | 146_E | 1.129 | 0.97 |
| 89_G | 104_S | 1.128 | 0.97 |
| 118_L | 138_S | 1.124 | 0.97 |
| 23_S | 26_L | 1.124 | 0.97 |
| 124_I | 132_Y | 1.123 | 0.97 |
| 31_R | 34_L | 1.120 | 0.96 |
| 88_S | 104_S | 1.118 | 0.96 |
| 31_R | 35_S | 1.118 | 0.96 |
| 19_M | 29_Q | 1.114 | 0.96 |
| 60_W | 68_R | 1.112 | 0.96 |
| 63_K | 135_L | 1.106 | 0.96 |
| 104_S | 123_E | 1.106 | 0.96 |
| 29_Q | 33_L | 1.105 | 0.96 |
| 12_L | 15_A | 1.103 | 0.96 |
| 36_G | 39_Q | 1.103 | 0.96 |
| 150_L | 153_D | 1.102 | 0.96 |
| 3_G | 7_V | 1.101 | 0.96 |
| 67_A | 71_A | 1.100 | 0.96 |
| 66_Q | 135_L | 1.100 | 0.96 |
| 144_K | 148_D | 1.093 | 0.96 |
| 76_L | 98_P | 1.089 | 0.96 |
| 100_N | 103_W | 1.069 | 0.95 |
| 23_S | 30_A | 1.062 | 0.95 |
| 132_Y | 153_D | 1.053 | 0.95 |
| 45_L | 68_R | 1.047 | 0.94 |
| 88_S | 94_C | 1.044 | 0.94 |
| 47_A | 50_A | 1.039 | 0.94 |
| 58_T | 138_S | 1.034 | 0.94 |
| 106_R | 123_E | 1.031 | 0.94 |
| 80_Q | 121_D | 1.030 | 0.94 |
| 145_N | 152_L | 1.027 | 0.94 |
| 37_I | 40_Q | 1.025 | 0.93 |
| 70_L | 151_A | 1.019 | 0.93 |
| 73_E | 79_Q | 1.017 | 0.93 |
| 48_P | 70_L | 1.013 | 0.93 |
| 58_T | 121_D | 1.010 | 0.93 |
| 37_I | 41_Q | 1.010 | 0.93 |
| 16_G | 29_Q | 1.008 | 0.93 |
| 94_C | 104_S | 1.003 | 0.93 |
| 63_K | 78_D | 1.002 | 0.92 |
| 96_N | 128_T | 1.001 | 0.92 |
| 38_V | 41_Q | 1.001 | 0.92 |
| 91_L | 150_L | 1.001 | 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 | 0.267 | Contact Map |
| 1envA | 1 | 0.732 | 100 | 0.449 | Contact Map |
| 3p30A | 1 | 0.5229 | 100 | 0.506 | Contact Map |
| 2cmrA | 1 | 0.5033 | 100 | 0.536 | Contact Map |
| 1jq0A | 1 | 0.4641 | 100 | 0.554 | Contact Map |
| 3o3xA | 1 | 0.5163 | 100 | 0.593 | Contact Map |
| 3k9aA | 1 | 0.4641 | 100 | 0.596 | Contact Map |
| 1df4A | 1 | 0.3725 | 100 | 0.64 | Contact Map |
| 2x7rA | 3 | 0.3333 | 99.9 | 0.705 | Contact Map |
| 3vh7A | 3 | 0.366 | 99.9 | 0.716 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)