| d3vpxb1 |
| ID: | 1448772893 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 133 (131) | ||
| Sequences: | 2464 (819.9) | ||
| Seq/Len: | 18.809 | ||
| Nf(neff/√len): | 71.6 |
HHblits Results: (2015_06)
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: 18.809).
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 |
| 119_T | 122_D | 3.124 | 1.00 |
| 30_A | 62_A | 3.023 | 1.00 |
| 93_D | 97_R | 2.684 | 1.00 |
| 86_N | 89_T | 2.625 | 1.00 |
| 39_A | 79_G | 2.492 | 1.00 |
| 34_T | 39_A | 2.483 | 1.00 |
| 12_Y | 62_A | 2.474 | 1.00 |
| 36_L | 73_G | 2.398 | 1.00 |
| 85_G | 90_D | 2.379 | 1.00 |
| 101_R | 129_E | 2.322 | 1.00 |
| 32_H | 66_T | 1.986 | 1.00 |
| 104_E | 131_D | 1.883 | 1.00 |
| 118_T | 123_M | 1.769 | 1.00 |
| 96_F | 100_G | 1.761 | 1.00 |
| 88_K | 117_G | 1.637 | 1.00 |
| 103_I | 126_I | 1.629 | 1.00 |
| 97_R | 129_E | 1.620 | 1.00 |
| 104_E | 129_E | 1.596 | 1.00 |
| 46_W | 116_V | 1.589 | 1.00 |
| 32_H | 63_R | 1.571 | 1.00 |
| 99_F | 103_I | 1.522 | 1.00 |
| 92_N | 121_A | 1.489 | 1.00 |
| 81_T | 99_F | 1.463 | 1.00 |
| 65_M | 80_K | 1.457 | 1.00 |
| 50_S | 53_E | 1.389 | 0.99 |
| 14_Q | 109_R | 1.382 | 0.99 |
| 56_E | 59_L | 1.367 | 0.99 |
| 44_R | 65_M | 1.364 | 0.99 |
| 80_K | 113_A | 1.361 | 0.99 |
| 83_I | 99_F | 1.354 | 0.99 |
| 43_T | 126_I | 1.346 | 0.99 |
| 36_L | 70_A | 1.344 | 0.99 |
| 31_I | 39_A | 1.342 | 0.99 |
| 65_M | 68_K | 1.338 | 0.99 |
| 28_I | 84_I | 1.294 | 0.99 |
| 91_K | 94_E | 1.280 | 0.99 |
| 127_N | 131_D | 1.241 | 0.98 |
| 43_T | 112_T | 1.233 | 0.98 |
| 18_C | 102_Y | 1.199 | 0.98 |
| 98_A | 101_R | 1.199 | 0.98 |
| 30_A | 55_I | 1.187 | 0.98 |
| 68_K | 80_K | 1.165 | 0.97 |
| 26_K | 84_I | 1.165 | 0.97 |
| 44_R | 61_L | 1.147 | 0.97 |
| 6_Y | 9_H | 1.146 | 0.97 |
| 104_E | 132_Y | 1.145 | 0.97 |
| 123_M | 126_I | 1.139 | 0.97 |
| 97_R | 128_L | 1.119 | 0.96 |
| 125_L | 128_L | 1.112 | 0.96 |
| 33_D | 39_A | 1.098 | 0.96 |
| 6_Y | 10_Q | 1.085 | 0.96 |
| 92_N | 96_F | 1.068 | 0.95 |
| 45_M | 85_G | 1.062 | 0.95 |
| 18_C | 29_I | 1.051 | 0.94 |
| 40_L | 76_L | 1.051 | 0.94 |
| 102_Y | 105_G | 1.046 | 0.94 |
| 114_E | 123_M | 1.043 | 0.94 |
| 28_I | 55_I | 1.039 | 0.94 |
| 98_A | 102_Y | 1.027 | 0.94 |
| 3_I | 6_Y | 1.026 | 0.94 |
| 49_A | 53_E | 1.020 | 0.93 |
| 59_L | 62_A | 1.013 | 0.93 |
| 40_L | 69_N | 1.011 | 0.93 |
| 15_L | 55_I | 1.002 | 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 | |
| 1lehA | 2 | 1 | 100 | 0.056 | Contact Map |
| 1c1dA | 1 | 0.985 | 100 | 0.065 | Contact Map |
| 3mw9A | 6 | 0.9549 | 100 | 0.145 | Contact Map |
| 3aoeE | 4 | 0.9549 | 100 | 0.154 | Contact Map |
| 4xgiA | 6 | 0.9549 | 100 | 0.157 | Contact Map |
| 3aogA | 12 | 0.9549 | 100 | 0.161 | Contact Map |
| 2yfqA | 2 | 0.9549 | 100 | 0.161 | Contact Map |
| 3k92A | 6 | 0.9549 | 100 | 0.163 | Contact Map |
| 2tmgA | 6 | 0.9549 | 100 | 0.164 | Contact Map |
| 4fccA | 12 | 0.9549 | 100 | 0.174 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)