| TR |
| ID: | 1507797556 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 143 (134) | ||
| Sequences: | 2827 (2055.5) | ||
| Seq/Len: | 21.097 | ||
| Nf(neff/√len): | 177.6 |
HHblits Results: (2016_02)
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: 21.097).
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 |
| 3_D | 55_R | 3.687 | 1.00 |
| 4_V | 31_V | 2.805 | 1.00 |
| 17_A | 60_V | 2.545 | 1.00 |
| 3_D | 30_S | 2.203 | 1.00 |
| 32_F | 38_L | 2.052 | 1.00 |
| 7_S | 82_E | 1.973 | 1.00 |
| 7_S | 65_A | 1.927 | 1.00 |
| 20_L | 60_V | 1.913 | 1.00 |
| 57_F | 86_A | 1.912 | 1.00 |
| 62_S | 65_A | 1.817 | 1.00 |
| 65_A | 79_V | 1.713 | 1.00 |
| 21_K | 36_E | 1.706 | 1.00 |
| 76_K | 79_V | 1.678 | 1.00 |
| 56_N | 92_N | 1.591 | 1.00 |
| 21_K | 25_Q | 1.483 | 1.00 |
| 34_D | 38_L | 1.483 | 1.00 |
| 43_F | 119_N | 1.467 | 1.00 |
| 6_I | 60_V | 1.448 | 1.00 |
| 32_F | 50_S | 1.426 | 1.00 |
| 133_E | 137_R | 1.423 | 1.00 |
| 123_W | 131_T | 1.422 | 1.00 |
| 4_V | 58_V | 1.414 | 1.00 |
| 59_L | 65_A | 1.409 | 1.00 |
| 25_Q | 36_E | 1.393 | 0.99 |
| 97_I | 122_K | 1.381 | 0.99 |
| 56_N | 94_V | 1.347 | 0.99 |
| 38_L | 46_K | 1.332 | 0.99 |
| 63_P | 107_V | 1.316 | 0.99 |
| 9_R | 64_G | 1.280 | 0.99 |
| 135_I | 139_L | 1.280 | 0.99 |
| 48_I | 52_M | 1.275 | 0.99 |
| 133_E | 136_I | 1.270 | 0.99 |
| 18_S | 35_V | 1.261 | 0.99 |
| 128_Q | 132_I | 1.259 | 0.99 |
| 16_L | 60_V | 1.251 | 0.99 |
| 5_F | 76_K | 1.244 | 0.98 |
| 130_A | 133_E | 1.233 | 0.98 |
| 1_T | 53_G | 1.228 | 0.98 |
| 2_P | 30_S | 1.224 | 0.98 |
| 27_H | 136_I | 1.206 | 0.98 |
| 131_T | 134_K | 1.204 | 0.98 |
| 25_Q | 30_S | 1.181 | 0.98 |
| 19_L | 23_H | 1.175 | 0.98 |
| 18_S | 22_V | 1.170 | 0.97 |
| 21_K | 33_I | 1.164 | 0.97 |
| 46_K | 49_Q | 1.162 | 0.97 |
| 60_V | 98_D | 1.137 | 0.97 |
| 83_I | 112_M | 1.109 | 0.96 |
| 29_F | 140_Q | 1.102 | 0.96 |
| 57_F | 65_A | 1.100 | 0.96 |
| 33_I | 36_E | 1.094 | 0.96 |
| 32_F | 47_L | 1.093 | 0.96 |
| 63_P | 99_G | 1.091 | 0.96 |
| 133_E | 138_F | 1.088 | 0.96 |
| 4_V | 29_F | 1.084 | 0.96 |
| 32_F | 46_K | 1.081 | 0.95 |
| 81_K | 85_T | 1.080 | 0.95 |
| 8_Y | 13_G | 1.079 | 0.95 |
| 23_H | 26_L | 1.075 | 0.95 |
| 76_K | 82_E | 1.072 | 0.95 |
| 11_N | 64_G | 1.049 | 0.94 |
| 8_Y | 34_D | 1.048 | 0.94 |
| 84_V | 111_D | 1.047 | 0.94 |
| 62_S | 98_D | 1.037 | 0.94 |
| 38_L | 79_V | 1.020 | 0.93 |
| 79_V | 83_I | 1.013 | 0.93 |
| 130_A | 134_K | 1.012 | 0.93 |
| 48_I | 51_V | 1.010 | 0.93 |
| 33_I | 37_K | 1.006 | 0.93 |
| 41_G | 95_P | 1.003 | 0.93 |
| 9_R | 76_K | 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 | |
| 2js7A | 1 | 0.8951 | 99.9 | 0.216 | Contact Map |
| 4om7A | 2 | 0.9091 | 99.8 | 0.227 | Contact Map |
| 2j67A | 2 | 0.9021 | 99.8 | 0.229 | Contact Map |
| 1fyxA | 1 | 0.8881 | 99.8 | 0.239 | Contact Map |
| 4eo7A | 1 | 0.8811 | 99.8 | 0.241 | Contact Map |
| 3h16A | 4 | 0.9091 | 99.8 | 0.267 | Contact Map |
| 4lzpB | 4 | 0.8881 | 99.8 | 0.279 | Contact Map |
| 4lqcA | 2 | 0.9091 | 99.8 | 0.282 | Contact Map |
| 3ub2A | 1 | 0.7762 | 99.8 | 0.284 | Contact Map |
| 1t3gA | 2 | 0.9161 | 99.8 | 0.294 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)