| wb 31-202 |
| ID: | 1444831544 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 172 (137) | ||
| Sequences: | 2074 (1616.2) | ||
| Seq/Len: | 15.139 | ||
| Nf(neff/√len): | 138.1 |
Jackhmmer Results: (2015_08)
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: 15.139).
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 |
| 139_K | 142_K | 3.659 | 1.00 |
| 135_L | 143_A | 3.247 | 1.00 |
| 125_K | 129_K | 3.246 | 1.00 |
| 37_E | 141_T | 3.080 | 1.00 |
| 44_D | 149_T | 2.932 | 1.00 |
| 30_D | 72_I | 2.923 | 1.00 |
| 71_F | 84_L | 2.589 | 1.00 |
| 85_N | 99_V | 2.372 | 1.00 |
| 31_Q | 38_R | 2.350 | 1.00 |
| 44_D | 145_T | 2.272 | 1.00 |
| 119_I | 124_F | 2.123 | 1.00 |
| 34_T | 37_E | 2.123 | 1.00 |
| 103_S | 106_D | 2.094 | 1.00 |
| 98_M | 119_I | 2.043 | 1.00 |
| 120_S | 124_F | 2.034 | 1.00 |
| 51_R | 156_Q | 2.023 | 1.00 |
| 48_L | 152_G | 2.002 | 1.00 |
| 34_T | 141_T | 1.966 | 1.00 |
| 134_L | 146_T | 1.921 | 1.00 |
| 45_L | 148_F | 1.781 | 1.00 |
| 32_Q | 104_T | 1.743 | 1.00 |
| 113_A | 117_S | 1.739 | 1.00 |
| 102_L | 144_L | 1.734 | 1.00 |
| 142_K | 146_T | 1.707 | 1.00 |
| 90_I | 99_V | 1.643 | 1.00 |
| 78_E | 110_Y | 1.593 | 1.00 |
| 119_I | 154_S | 1.555 | 1.00 |
| 134_L | 139_K | 1.522 | 1.00 |
| 123_S | 154_S | 1.521 | 1.00 |
| 98_M | 151_L | 1.518 | 1.00 |
| 69_T | 90_I | 1.488 | 1.00 |
| 81_A | 101_V | 1.473 | 1.00 |
| 100_F | 144_L | 1.458 | 1.00 |
| 25_Y | 46_L | 1.451 | 1.00 |
| 70_L | 144_L | 1.444 | 1.00 |
| 120_S | 123_S | 1.443 | 1.00 |
| 40_R | 145_T | 1.424 | 1.00 |
| 46_L | 50_Q | 1.413 | 1.00 |
| 82_H | 85_N | 1.408 | 1.00 |
| 82_H | 112_A | 1.402 | 0.99 |
| 118_P | 158_K | 1.397 | 0.99 |
| 131_Q | 150_N | 1.385 | 0.99 |
| 25_Y | 49_S | 1.375 | 0.99 |
| 111_Y | 151_L | 1.330 | 0.99 |
| 32_Q | 72_I | 1.311 | 0.99 |
| 82_H | 86_T | 1.300 | 0.99 |
| 53_S | 96_K | 1.295 | 0.99 |
| 78_E | 112_A | 1.277 | 0.99 |
| 91_D | 97_S | 1.277 | 0.99 |
| 84_L | 88_W | 1.273 | 0.99 |
| 109_L | 132_Q | 1.268 | 0.99 |
| 119_I | 151_L | 1.261 | 0.99 |
| 41_L | 141_T | 1.257 | 0.99 |
| 47_Q | 51_R | 1.251 | 0.99 |
| 134_L | 142_K | 1.239 | 0.98 |
| 81_A | 85_N | 1.189 | 0.98 |
| 109_L | 128_I | 1.168 | 0.97 |
| 33_F | 144_L | 1.165 | 0.97 |
| 134_L | 137_E | 1.161 | 0.97 |
| 24_G | 42_N | 1.155 | 0.97 |
| 131_Q | 146_T | 1.108 | 0.96 |
| 98_M | 117_S | 1.092 | 0.96 |
| 146_T | 149_T | 1.085 | 0.96 |
| 38_R | 42_N | 1.083 | 0.96 |
| 44_D | 152_G | 1.074 | 0.95 |
| 113_A | 121_I | 1.038 | 0.94 |
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 | |
| 2kw7A | 1 | 0.8547 | 99.9 | 0.411 | Contact Map |
| 4oa3A | 1 | 0.7616 | 99.9 | 0.474 | Contact Map |
| 3pvhA | 1 | 0.8314 | 99.8 | 0.492 | Contact Map |
| 2kptA | 1 | 0.8023 | 99.8 | 0.506 | Contact Map |
| 2zvfA | 8 | 0.7849 | 21.6 | 0.926 | Contact Map |
| 4tkxL | 1 | 0.8023 | 17.1 | 0.93 | Contact Map |
| 3g98A | 2 | 0.564 | 10.8 | 0.936 | Contact Map |
| 4afmA | 1 | 0.3953 | 8.7 | 0.938 | Contact Map |
| 1cvrA | 1 | 0.7907 | 8.2 | 0.939 | Contact Map |
| 2ypjA | 1 | 0.3721 | 8.1 | 0.939 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)