| T0856 |
| ID: | 1405450263 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 159 (152) | ||
| Sequences: | 3301 (2131.7) | ||
| Seq/Len: | 21.717 | ||
| Nf(neff/√len): | 172.9 |
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: 21.717).
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 |
| 40_Q | 105_T | 4.176 | 1.00 |
| 33_G | 137_Y | 2.867 | 1.00 |
| 10_C | 19_T | 2.859 | 1.00 |
| 30_A | 138_P | 2.789 | 1.00 |
| 42_K | 105_T | 2.577 | 1.00 |
| 38_C | 109_D | 2.261 | 1.00 |
| 41_W | 108_L | 2.208 | 1.00 |
| 63_P | 134_A | 2.118 | 1.00 |
| 3_D | 6_K | 2.014 | 1.00 |
| 70_R | 75_M | 1.897 | 1.00 |
| 85_L | 88_N | 1.881 | 1.00 |
| 33_G | 135_E | 1.881 | 1.00 |
| 12_V | 16_Q | 1.839 | 1.00 |
| 34_V | 39_Y | 1.760 | 1.00 |
| 40_Q | 107_V | 1.734 | 1.00 |
| 109_D | 112_A | 1.572 | 1.00 |
| 86_Y | 89_G | 1.566 | 1.00 |
| 71_T | 74_D | 1.556 | 1.00 |
| 2_F | 28_G | 1.544 | 1.00 |
| 107_V | 116_S | 1.544 | 1.00 |
| 62_W | 137_Y | 1.523 | 1.00 |
| 62_W | 135_E | 1.517 | 1.00 |
| 19_T | 28_G | 1.496 | 1.00 |
| 122_E | 125_K | 1.484 | 1.00 |
| 147_P | 150_K | 1.472 | 1.00 |
| 9_C | 21_G | 1.463 | 1.00 |
| 102_D | 120_N | 1.459 | 1.00 |
| 2_F | 7_A | 1.453 | 1.00 |
| 105_T | 118_G | 1.443 | 1.00 |
| 41_W | 106_C | 1.435 | 1.00 |
| 149_E | 153_I | 1.428 | 1.00 |
| 58_G | 69_H | 1.420 | 1.00 |
| 87_H | 90_E | 1.414 | 1.00 |
| 44_Y | 103_F | 1.356 | 0.99 |
| 123_E | 127_A | 1.339 | 0.99 |
| 72_T | 75_M | 1.330 | 0.99 |
| 37_G | 41_W | 1.326 | 0.99 |
| 60_S | 137_Y | 1.311 | 0.99 |
| 116_S | 123_E | 1.309 | 0.99 |
| 27_Y | 139_C | 1.299 | 0.99 |
| 4_P | 12_V | 1.294 | 0.99 |
| 41_W | 59_V | 1.269 | 0.99 |
| 5_E | 16_Q | 1.244 | 0.98 |
| 1_G | 24_G | 1.230 | 0.98 |
| 45_I | 55_T | 1.219 | 0.98 |
| 33_G | 138_P | 1.207 | 0.98 |
| 11_L | 22_S | 1.196 | 0.98 |
| 34_V | 108_L | 1.192 | 0.98 |
| 40_Q | 118_G | 1.189 | 0.98 |
| 60_S | 135_E | 1.178 | 0.98 |
| 59_V | 115_I | 1.159 | 0.97 |
| 64_V | 75_M | 1.156 | 0.97 |
| 42_K | 103_F | 1.153 | 0.97 |
| 132_D | 136_L | 1.145 | 0.97 |
| 60_S | 64_V | 1.142 | 0.97 |
| 15_G | 18_L | 1.139 | 0.97 |
| 151_V | 155_D | 1.124 | 0.97 |
| 124_P | 127_A | 1.121 | 0.97 |
| 110_M | 132_D | 1.116 | 0.96 |
| 61_R | 134_A | 1.110 | 0.96 |
| 106_C | 115_I | 1.110 | 0.96 |
| 149_E | 154_C | 1.081 | 0.95 |
| 30_A | 106_C | 1.070 | 0.95 |
| 149_E | 152_K | 1.062 | 0.95 |
| 147_P | 151_V | 1.044 | 0.94 |
| 113_R | 132_D | 1.042 | 0.94 |
| 107_V | 118_G | 1.034 | 0.94 |
| 48_E | 147_P | 1.034 | 0.94 |
| 43_F | 138_P | 1.032 | 0.94 |
| 16_Q | 31_S | 1.029 | 0.94 |
| 34_V | 110_M | 1.028 | 0.94 |
| 13_E | 19_T | 1.021 | 0.93 |
| 99_T | 119_K | 1.020 | 0.93 |
| 46_V | 102_D | 1.003 | 0.93 |
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 | |
| 4b8eA | 2 | 0.9245 | 100 | 0.16 | Contact Map |
| 2vokA | 2 | 0.9497 | 100 | 0.168 | Contact Map |
| 4b3nA | 2 | 0.9308 | 100 | 0.172 | Contact Map |
| 2wl1A | 1 | 0.956 | 100 | 0.174 | Contact Map |
| 4n7iA | 1 | 0.9434 | 100 | 0.18 | Contact Map |
| 2fbeA | 4 | 0.9686 | 100 | 0.181 | Contact Map |
| 3emwA | 1 | 0.9748 | 100 | 0.188 | Contact Map |
| 2afjA | 1 | 0.9811 | 100 | 0.189 | Contact Map |
| 3uv9A | 1 | 0.9245 | 100 | 0.194 | Contact Map |
| 3tojA | 2 | 0.9748 | 100 | 0.199 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)