| test_1c2t |
| ID: | 1444257634 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 212 (197) | ||
| Sequences: | 7702 (4732.3) | ||
| Seq/Len: | 39.096 | ||
| Nf(neff/√len): | 337.2 |
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: 39.096).
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 |
| 131_E | 153_K | 3.821 | 1.00 |
| 142_E | 145_G | 3.245 | 1.00 |
| 94_P | 141_D | 2.728 | 1.00 |
| 140_T | 145_G | 2.710 | 1.00 |
| 7_I | 42_G | 2.679 | 1.00 |
| 94_P | 98_S | 2.660 | 1.00 |
| 160_D | 168_R | 2.591 | 1.00 |
| 115_Y | 127_N | 2.446 | 1.00 |
| 115_Y | 129_D | 2.443 | 1.00 |
| 152_A | 179_L | 2.338 | 1.00 |
| 2_N | 29_T | 2.310 | 1.00 |
| 2_N | 31_R | 2.279 | 1.00 |
| 114_K | 129_D | 2.277 | 1.00 |
| 160_D | 164_D | 2.273 | 1.00 |
| 135_S | 148_V | 2.206 | 1.00 |
| 4_V | 80_P | 2.115 | 1.00 |
| 18_I | 49_A | 2.112 | 1.00 |
| 138_F | 149_I | 2.087 | 1.00 |
| 15_Q | 19_D | 2.066 | 1.00 |
| 32_A | 78_Y | 2.059 | 1.00 |
| 122_R | 162_E | 2.048 | 1.00 |
| 15_Q | 45_R | 1.934 | 1.00 |
| 136_V | 180_V | 1.909 | 1.00 |
| 4_V | 32_A | 1.874 | 1.00 |
| 1_M | 185_A | 1.874 | 1.00 |
| 44_E | 47_R | 1.864 | 1.00 |
| 150_L | 176_I | 1.855 | 1.00 |
| 122_R | 126_E | 1.847 | 1.00 |
| 152_A | 175_A | 1.820 | 1.00 |
| 74_E | 77_M | 1.769 | 1.00 |
| 73_H | 77_M | 1.748 | 1.00 |
| 91_I | 143_L | 1.721 | 1.00 |
| 161_S | 164_D | 1.703 | 1.00 |
| 157_F | 168_R | 1.702 | 1.00 |
| 14_L | 33_V | 1.701 | 1.00 |
| 150_L | 180_V | 1.632 | 1.00 |
| 17_I | 181_I | 1.610 | 1.00 |
| 70_E | 73_H | 1.594 | 1.00 |
| 154_V | 172_Q | 1.594 | 1.00 |
| 138_F | 184_F | 1.574 | 1.00 |
| 43_L | 47_R | 1.568 | 1.00 |
| 45_R | 49_A | 1.561 | 1.00 |
| 152_A | 172_Q | 1.535 | 1.00 |
| 123_Q | 126_E | 1.524 | 1.00 |
| 125_L | 165_I | 1.521 | 1.00 |
| 182_S | 186_D | 1.516 | 1.00 |
| 105_L | 149_I | 1.512 | 1.00 |
| 82_V | 181_I | 1.511 | 1.00 |
| 54_H | 74_E | 1.451 | 1.00 |
| 157_F | 160_D | 1.449 | 1.00 |
| 83_V | 104_L | 1.439 | 1.00 |
| 38_A | 43_L | 1.432 | 1.00 |
| 22_K | 49_A | 1.408 | 1.00 |
| 44_E | 48_Q | 1.366 | 0.99 |
| 111_L | 133_G | 1.362 | 0.99 |
| 16_A | 178_P | 1.361 | 0.99 |
| 131_E | 155_P | 1.337 | 0.99 |
| 150_L | 183_W | 1.325 | 0.99 |
| 76_D | 99_H | 1.304 | 0.99 |
| 148_V | 151_Q | 1.294 | 0.99 |
| 52_A | 78_Y | 1.273 | 0.99 |
| 97_V | 104_L | 1.263 | 0.99 |
| 5_V | 14_L | 1.240 | 0.98 |
| 179_L | 183_W | 1.228 | 0.98 |
| 150_L | 179_L | 1.226 | 0.98 |
| 43_L | 55_T | 1.213 | 0.98 |
| 2_N | 79_A | 1.187 | 0.98 |
| 18_I | 45_R | 1.180 | 0.98 |
| 6_L | 83_V | 1.178 | 0.98 |
| 152_A | 176_I | 1.176 | 0.98 |
| 80_P | 83_V | 1.161 | 0.97 |
| 18_I | 51_I | 1.144 | 0.97 |
| 41_F | 45_R | 1.141 | 0.97 |
| 58_A | 90_R | 1.124 | 0.97 |
| 123_Q | 127_N | 1.110 | 0.96 |
| 2_N | 81_D | 1.106 | 0.96 |
| 154_V | 168_R | 1.104 | 0.96 |
| 72_I | 100_Y | 1.104 | 0.96 |
| 19_D | 49_A | 1.102 | 0.96 |
| 162_E | 166_T | 1.094 | 0.96 |
| 15_Q | 49_A | 1.092 | 0.96 |
| 38_A | 55_T | 1.088 | 0.96 |
| 16_A | 174_H | 1.077 | 0.95 |
| 41_F | 44_E | 1.066 | 0.95 |
| 15_Q | 48_Q | 1.065 | 0.95 |
| 72_I | 99_H | 1.061 | 0.95 |
| 132_H | 165_I | 1.057 | 0.95 |
| 33_V | 46_A | 1.052 | 0.95 |
| 135_S | 151_Q | 1.051 | 0.94 |
| 43_L | 53_T | 1.049 | 0.94 |
| 85_L | 139_V | 1.049 | 0.94 |
| 120_T | 123_Q | 1.048 | 0.94 |
| 52_A | 74_E | 1.034 | 0.94 |
| 28_G | 185_A | 1.029 | 0.94 |
| 3_I | 82_V | 1.029 | 0.94 |
| 172_Q | 175_A | 1.025 | 0.93 |
| 13_N | 107_I | 1.023 | 0.93 |
| 34_F | 71_L | 1.016 | 0.93 |
| 105_L | 177_Y | 1.011 | 0.93 |
| 3_I | 28_G | 1.007 | 0.93 |
| 119_H | 122_R | 1.006 | 0.93 |
| 183_W | 188_R | 1.003 | 0.93 |
| 164_D | 168_R | 1.002 | 0.92 |
| 11_G | 45_R | 1.001 | 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 | |
| 1jkxA | 4 | 0.9811 | 100 | 0.068 | Contact Map |
| 3p9xA | 2 | 0.9198 | 100 | 0.073 | Contact Map |
| 3aufA | 1 | 0.9434 | 100 | 0.074 | Contact Map |
| 3tqrA | 1 | 0.9858 | 100 | 0.075 | Contact Map |
| 3nrbA | 4 | 0.9387 | 100 | 0.083 | Contact Map |
| 3av3A | 1 | 0.8774 | 100 | 0.084 | Contact Map |
| 3w7bA | 2 | 0.9292 | 100 | 0.087 | Contact Map |
| 3o1lA | 2 | 0.9292 | 100 | 0.087 | Contact Map |
| 3louA | 4 | 0.9292 | 100 | 0.087 | Contact Map |
| 3obiA | 4 | 0.9387 | 100 | 0.088 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)