| 1BHTA |
| ID: | 1411599872 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (166) | ||
| Sequences: | 543 (353.7) | ||
| Seq/Len: | 3.271 | ||
| Nf(neff/√len): | 27.5 |
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: 3.271).
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 |
| 111_S | 165_E | 3.322 | 1.00 |
| 68_N | 71_S | 2.868 | 1.00 |
| 50_C | 62_C | 2.501 | 1.00 |
| 116_Q | 123_P | 2.480 | 1.00 |
| 116_Q | 124_H | 1.965 | 1.00 |
| 123_P | 126_H | 1.929 | 1.00 |
| 116_Q | 157_T | 1.912 | 1.00 |
| 138_L | 147_R | 1.798 | 0.99 |
| 123_P | 163_R | 1.709 | 0.99 |
| 105_T | 142_Y | 1.544 | 0.97 |
| 123_P | 157_T | 1.518 | 0.97 |
| 94_C | 102_Y | 1.479 | 0.96 |
| 94_C | 118_W | 1.453 | 0.95 |
| 116_Q | 126_H | 1.444 | 0.95 |
| 83_D | 87_N | 1.421 | 0.95 |
| 116_Q | 163_R | 1.420 | 0.95 |
| 126_H | 163_R | 1.409 | 0.94 |
| 14_T | 18_K | 1.377 | 0.93 |
| 45_G | 48_F | 1.376 | 0.93 |
| 102_Y | 118_W | 1.365 | 0.93 |
| 157_T | 163_R | 1.344 | 0.92 |
| 11_S | 14_T | 1.334 | 0.92 |
| 121_M | 126_H | 1.332 | 0.92 |
| 113_I | 159_N | 1.330 | 0.92 |
| 62_C | 66_P | 1.329 | 0.92 |
| 159_N | 162_V | 1.324 | 0.91 |
| 61_Q | 64_W | 1.321 | 0.91 |
| 109_T | 157_T | 1.320 | 0.91 |
| 134_R | 157_T | 1.298 | 0.90 |
| 104_G | 115_C | 1.289 | 0.90 |
| 81_E | 86_E | 1.267 | 0.89 |
| 27_T | 30_V | 1.262 | 0.89 |
| 49_T | 52_A | 1.262 | 0.89 |
| 108_I | 112_G | 1.257 | 0.88 |
| 102_Y | 115_C | 1.244 | 0.88 |
| 15_T | 18_K | 1.240 | 0.87 |
| 14_T | 19_I | 1.235 | 0.87 |
| 124_H | 163_R | 1.234 | 0.87 |
| 48_F | 53_F | 1.228 | 0.87 |
| 157_T | 160_P | 1.214 | 0.86 |
| 51_K | 54_V | 1.206 | 0.85 |
| 18_K | 23_L | 1.206 | 0.85 |
| 124_H | 157_T | 1.204 | 0.85 |
| 121_M | 163_R | 1.191 | 0.84 |
| 62_C | 65_F | 1.187 | 0.84 |
| 135_G | 147_R | 1.183 | 0.84 |
| 50_C | 53_F | 1.177 | 0.83 |
| 45_G | 49_T | 1.167 | 0.83 |
| 15_T | 20_D | 1.166 | 0.83 |
| 130_P | 133_Y | 1.165 | 0.83 |
| 10_K | 15_T | 1.161 | 0.82 |
| 36_C | 153_P | 1.153 | 0.82 |
| 77_E | 86_E | 1.137 | 0.80 |
| 12_A | 15_T | 1.136 | 0.80 |
| 17_I | 20_D | 1.131 | 0.80 |
| 115_C | 118_W | 1.123 | 0.79 |
| 99_G | 118_W | 1.112 | 0.78 |
| 107_S | 141_N | 1.107 | 0.78 |
| 13_K | 20_D | 1.104 | 0.78 |
| 18_K | 21_P | 1.103 | 0.78 |
| 103_K | 138_L | 1.099 | 0.77 |
| 28_K | 31_N | 1.096 | 0.77 |
| 104_G | 118_W | 1.088 | 0.76 |
| 77_E | 83_D | 1.087 | 0.76 |
| 16_L | 19_I | 1.084 | 0.76 |
| 83_D | 86_E | 1.080 | 0.76 |
| 72_S | 82_F | 1.078 | 0.75 |
| 10_K | 17_I | 1.060 | 0.74 |
| 94_C | 115_C | 1.059 | 0.73 |
| 159_N | 163_R | 1.056 | 0.73 |
| 12_A | 18_K | 1.051 | 0.73 |
| 123_P | 160_P | 1.045 | 0.72 |
| 12_A | 17_I | 1.045 | 0.72 |
| 113_I | 165_E | 1.044 | 0.72 |
| 11_S | 15_T | 1.037 | 0.71 |
| 13_K | 16_L | 1.037 | 0.71 |
| 15_T | 19_I | 1.028 | 0.70 |
| 11_S | 18_K | 1.028 | 0.70 |
| 45_G | 53_F | 1.027 | 0.70 |
| 138_L | 156_F | 1.024 | 0.70 |
| 94_C | 104_G | 1.018 | 0.69 |
| 17_I | 22_A | 1.017 | 0.69 |
| 122_I | 174_E | 1.016 | 0.69 |
| 19_I | 22_A | 1.013 | 0.69 |
| 107_S | 128_F | 1.008 | 0.68 |
| 103_K | 137_D | 1.000 | 0.67 |
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 | |
| 2qj2A | 2 | 0.9943 | 100 | 0.166 | Contact Map |
| 3sp8A | 2 | 1 | 100 | 0.174 | Contact Map |
| 4durA | 2 | 0.9375 | 100 | 0.212 | Contact Map |
| 3nxpA | 1 | 0.4773 | 100 | 0.367 | Contact Map |
| 1i71A | 1 | 0.4716 | 100 | 0.376 | Contact Map |
| 3e6pL | 1 | 0.4773 | 100 | 0.381 | Contact Map |
| 4bvwA | 2 | 0.4489 | 100 | 0.382 | Contact Map |
| 1jfnA | 1 | 0.6023 | 100 | 0.385 | Contact Map |
| 3k65A | 1 | 0.4545 | 100 | 0.39 | Contact Map |
| 5hpgA | 2 | 0.4716 | 100 | 0.395 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)