| mhc |
| ID: | 1418779608 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 181 (181) | ||
| Sequences: | 2169 (928.4) | ||
| Seq/Len: | 11.983 | ||
| Nf(neff/√len): | 69.0 |
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: 11.983).
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 |
| 144_K | 148_E | 3.122 | 1.00 |
| 3_H | 29_D | 2.504 | 1.00 |
| 36_F | 71_E | 2.363 | 1.00 |
| 77_D | 80_T | 2.319 | 1.00 |
| 63_E | 66_K | 2.119 | 1.00 |
| 24_E | 67_A | 2.070 | 1.00 |
| 7_Y | 26_G | 2.014 | 1.00 |
| 77_D | 81_L | 2.006 | 1.00 |
| 143_T | 147_W | 2.004 | 1.00 |
| 47_P | 60_W | 1.984 | 1.00 |
| 97_V | 114_Q | 1.949 | 1.00 |
| 93_H | 119_D | 1.935 | 1.00 |
| 175_G | 179_L | 1.894 | 1.00 |
| 63_E | 67_A | 1.786 | 1.00 |
| 9_V | 24_E | 1.759 | 1.00 |
| 103_V | 165_V | 1.758 | 1.00 |
| 26_G | 33_F | 1.729 | 1.00 |
| 148_E | 153_A | 1.624 | 1.00 |
| 45_Y | 67_A | 1.619 | 1.00 |
| 15_P | 18_G | 1.537 | 1.00 |
| 96_Q | 101_C | 1.494 | 1.00 |
| 76_V | 80_T | 1.491 | 1.00 |
| 126_L | 153_A | 1.483 | 1.00 |
| 12_V | 23_M | 1.464 | 1.00 |
| 34_V | 67_A | 1.457 | 1.00 |
| 157_R | 161_E | 1.441 | 1.00 |
| 110_L | 169_R | 1.406 | 0.99 |
| 34_V | 45_Y | 1.397 | 0.99 |
| 24_E | 34_V | 1.390 | 0.99 |
| 11_A | 74_F | 1.377 | 0.99 |
| 73_S | 76_V | 1.355 | 0.99 |
| 24_E | 45_Y | 1.309 | 0.99 |
| 175_G | 181_R | 1.295 | 0.99 |
| 45_Y | 63_E | 1.282 | 0.99 |
| 34_V | 59_Y | 1.279 | 0.99 |
| 61_E | 65_Q | 1.266 | 0.99 |
| 121_C | 137_D | 1.262 | 0.99 |
| 9_V | 22_Y | 1.252 | 0.99 |
| 23_M | 37_D | 1.237 | 0.98 |
| 27_Y | 30_D | 1.232 | 0.98 |
| 95_I | 116_Y | 1.226 | 0.98 |
| 41_E | 90_G | 1.218 | 0.98 |
| 138_M | 141_L | 1.209 | 0.98 |
| 93_H | 96_Q | 1.207 | 0.98 |
| 101_C | 164_C | 1.200 | 0.98 |
| 128_E | 131_K | 1.191 | 0.98 |
| 102_E | 111_R | 1.184 | 0.98 |
| 50_R | 53_E | 1.179 | 0.98 |
| 52_M | 59_Y | 1.169 | 0.97 |
| 24_E | 70_N | 1.166 | 0.97 |
| 57_P | 61_E | 1.165 | 0.97 |
| 6_R | 30_D | 1.162 | 0.97 |
| 123_Y | 140_A | 1.145 | 0.97 |
| 23_M | 58_E | 1.139 | 0.97 |
| 26_G | 34_V | 1.137 | 0.97 |
| 40_A | 43_P | 1.135 | 0.97 |
| 173_K | 180_L | 1.132 | 0.97 |
| 66_K | 70_N | 1.119 | 0.96 |
| 10_T | 14_R | 1.113 | 0.96 |
| 145_H | 148_E | 1.109 | 0.96 |
| 104_G | 121_C | 1.104 | 0.96 |
| 59_Y | 63_E | 1.102 | 0.96 |
| 9_V | 74_F | 1.102 | 0.96 |
| 97_V | 116_Y | 1.100 | 0.96 |
| 103_V | 106_D | 1.099 | 0.96 |
| 176_N | 180_L | 1.089 | 0.96 |
| 141_L | 145_H | 1.089 | 0.96 |
| 156_L | 160_L | 1.087 | 0.96 |
| 114_Q | 156_L | 1.087 | 0.96 |
| 170_R | 174_N | 1.087 | 0.96 |
| 141_L | 149_Q | 1.086 | 0.96 |
| 172_L | 176_N | 1.081 | 0.95 |
| 161_E | 177_A | 1.077 | 0.95 |
| 34_V | 63_E | 1.073 | 0.95 |
| 84_Y | 123_Y | 1.061 | 0.95 |
| 164_C | 168_L | 1.059 | 0.95 |
| 4_S | 7_Y | 1.058 | 0.95 |
| 155_R | 158_A | 1.057 | 0.95 |
| 111_R | 178_T | 1.055 | 0.95 |
| 5_L | 34_V | 1.054 | 0.95 |
| 7_Y | 34_V | 1.051 | 0.94 |
| 96_Q | 120_G | 1.045 | 0.94 |
| 124_I | 143_T | 1.045 | 0.94 |
| 133_W | 153_A | 1.042 | 0.94 |
| 24_E | 66_K | 1.039 | 0.94 |
| 116_Y | 155_R | 1.038 | 0.94 |
| 125_A | 136_A | 1.034 | 0.94 |
| 113_Y | 173_K | 1.034 | 0.94 |
| 176_N | 179_L | 1.033 | 0.94 |
| 3_H | 6_R | 1.027 | 0.94 |
| 128_E | 161_E | 1.025 | 0.93 |
| 160_L | 163_T | 1.025 | 0.93 |
| 105_S | 169_R | 1.019 | 0.93 |
| 127_N | 130_L | 1.017 | 0.93 |
| 12_V | 15_P | 1.010 | 0.93 |
| 79_R | 82_L | 1.007 | 0.93 |
| 44_R | 61_E | 1.007 | 0.93 |
| 135_A | 140_A | 1.006 | 0.93 |
| 25_V | 32_E | 1.005 | 0.93 |
| 33_F | 49_A | 1.001 | 0.92 |
| 80_T | 84_Y | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1s7qA | 1 | 1 | 100 | 0.056 | Contact Map |
| 1kcgC | 1 | 0.9282 | 100 | 0.061 | Contact Map |
| 1mhcA | 2 | 1 | 100 | 0.074 | Contact Map |
| 1k5nA | 1 | 1 | 100 | 0.074 | Contact Map |
| 4pp8C | 2 | 0.8398 | 100 | 0.08 | Contact Map |
| 3p73A | 1 | 0.9779 | 100 | 0.088 | Contact Map |
| 1zs8A | 5 | 0.9448 | 100 | 0.09 | Contact Map |
| 1a6zA | 2 | 0.9779 | 100 | 0.092 | Contact Map |
| 4g59A | 2 | 0.8895 | 100 | 0.092 | Contact Map |
| 4l4vA | 2 | 0.9724 | 100 | 0.102 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)