| kkk |
| ID: | 1433430055 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 232 (229) | ||
| Sequences: | 6666 (4974.3) | ||
| Seq/Len: | 29.109 | ||
| Nf(neff/√len): | 328.7 |
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: 29.109).
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 |
| 51_T | 67_T | 4.199 | 1.00 |
| 53_K | 67_T | 3.926 | 1.00 |
| 93_A | 218_K | 3.675 | 1.00 |
| 163_T | 191_A | 3.655 | 1.00 |
| 10_R | 19_E | 3.272 | 1.00 |
| 90_D | 218_K | 3.099 | 1.00 |
| 22_L | 65_L | 3.017 | 1.00 |
| 44_T | 51_T | 2.851 | 1.00 |
| 21_F | 68_A | 2.816 | 1.00 |
| 10_R | 68_A | 2.658 | 1.00 |
| 173_I | 183_I | 2.630 | 1.00 |
| 69_I | 181_G | 2.508 | 1.00 |
| 13_G | 16_N | 2.385 | 1.00 |
| 100_H | 219_Y | 2.341 | 1.00 |
| 91_A | 94_V | 2.292 | 1.00 |
| 94_V | 218_K | 2.224 | 1.00 |
| 92_L | 172_L | 2.208 | 1.00 |
| 37_M | 52_I | 2.125 | 1.00 |
| 20_L | 53_K | 2.119 | 1.00 |
| 12_Y | 19_E | 2.088 | 1.00 |
| 95_F | 182_C | 2.054 | 1.00 |
| 19_E | 68_A | 2.053 | 1.00 |
| 96_L | 167_F | 1.966 | 1.00 |
| 167_F | 182_C | 1.966 | 1.00 |
| 149_E | 153_L | 1.965 | 1.00 |
| 166_D | 171_N | 1.932 | 1.00 |
| 93_A | 215_L | 1.914 | 1.00 |
| 13_G | 20_L | 1.833 | 1.00 |
| 86_E | 214_R | 1.796 | 1.00 |
| 56_I | 63_W | 1.777 | 1.00 |
| 161_V | 193_R | 1.762 | 1.00 |
| 34_T | 38_V | 1.757 | 1.00 |
| 92_L | 167_F | 1.671 | 1.00 |
| 148_K | 152_K | 1.645 | 1.00 |
| 40_L | 52_I | 1.639 | 1.00 |
| 19_E | 70_P | 1.613 | 1.00 |
| 175_D | 178_K | 1.612 | 1.00 |
| 36_E | 40_L | 1.612 | 1.00 |
| 93_A | 97_R | 1.553 | 1.00 |
| 91_A | 178_K | 1.547 | 1.00 |
| 90_D | 214_R | 1.527 | 1.00 |
| 13_G | 18_P | 1.476 | 1.00 |
| 200_L | 215_L | 1.456 | 1.00 |
| 97_R | 101_S | 1.451 | 1.00 |
| 37_M | 55_F | 1.450 | 1.00 |
| 166_D | 184_D | 1.449 | 1.00 |
| 48_P | 67_T | 1.442 | 1.00 |
| 94_V | 221_I | 1.429 | 1.00 |
| 213_K | 217_Q | 1.419 | 1.00 |
| 144_E | 148_K | 1.365 | 0.99 |
| 91_A | 95_F | 1.352 | 0.99 |
| 197_L | 215_L | 1.337 | 0.99 |
| 8_I | 21_F | 1.314 | 0.99 |
| 116_R | 119_Q | 1.306 | 0.99 |
| 41_N | 45_A | 1.300 | 0.99 |
| 163_T | 189_G | 1.299 | 0.99 |
| 214_R | 218_K | 1.294 | 0.99 |
| 140_G | 144_E | 1.288 | 0.99 |
| 73_T | 173_I | 1.288 | 0.99 |
| 99_L | 185_V | 1.277 | 0.99 |
| 217_Q | 221_I | 1.274 | 0.99 |
| 24_H | 63_W | 1.257 | 0.99 |
| 145_Q | 148_K | 1.239 | 0.98 |
| 81_Y | 84_S | 1.215 | 0.98 |
| 90_D | 94_V | 1.211 | 0.98 |
| 70_P | 175_D | 1.205 | 0.98 |
| 37_M | 41_N | 1.204 | 0.98 |
| 69_I | 180_I | 1.192 | 0.98 |
| 42_W | 46_F | 1.188 | 0.98 |
| 38_V | 41_N | 1.175 | 0.98 |
| 6_A | 186_G | 1.174 | 0.98 |
| 13_G | 17_A | 1.159 | 0.97 |
| 40_L | 185_V | 1.150 | 0.97 |
| 95_F | 98_R | 1.149 | 0.97 |
| 114_V | 118_A | 1.149 | 0.97 |
| 171_N | 184_D | 1.147 | 0.97 |
| 18_P | 67_T | 1.134 | 0.97 |
| 94_V | 97_R | 1.130 | 0.97 |
| 225_D | 228_K | 1.127 | 0.97 |
| 23_K | 36_E | 1.120 | 0.96 |
| 90_D | 217_Q | 1.115 | 0.96 |
| 20_L | 65_L | 1.106 | 0.96 |
| 34_T | 55_F | 1.101 | 0.96 |
| 104_V | 162_V | 1.091 | 0.96 |
| 91_A | 179_L | 1.087 | 0.96 |
| 214_R | 217_Q | 1.085 | 0.96 |
| 31_N | 34_T | 1.074 | 0.95 |
| 3_Q | 6_A | 1.073 | 0.95 |
| 100_H | 196_D | 1.069 | 0.95 |
| 48_P | 95_F | 1.064 | 0.95 |
| 191_A | 196_D | 1.060 | 0.95 |
| 50_P | 67_T | 1.056 | 0.95 |
| 97_R | 220_G | 1.053 | 0.95 |
| 87_N | 91_A | 1.049 | 0.94 |
| 88_I | 174_F | 1.045 | 0.94 |
| 218_K | 221_I | 1.040 | 0.94 |
| 42_W | 45_A | 1.037 | 0.94 |
| 222_D | 226_M | 1.030 | 0.94 |
| 146_V | 150_M | 1.030 | 0.94 |
| 208_S | 211_L | 1.030 | 0.94 |
| 87_N | 90_D | 1.017 | 0.93 |
| 103_P | 190_I | 1.011 | 0.93 |
| 94_V | 98_R | 1.009 | 0.93 |
| 175_D | 180_I | 1.008 | 0.93 |
| 98_R | 101_S | 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 | |
| 4gkhA | 12 | 1 | 100 | 0.193 | Contact Map |
| 4h05A | 2 | 0.9828 | 100 | 0.248 | Contact Map |
| 1nd4A | 2 | 0.9784 | 100 | 0.252 | Contact Map |
| 3tm0A | 1 | 0.9784 | 100 | 0.258 | Contact Map |
| 4dcaA | 1 | 0.9397 | 100 | 0.339 | Contact Map |
| 3dxpA | 1 | 0.931 | 100 | 0.34 | Contact Map |
| 2ppqA | 1 | 0.931 | 100 | 0.342 | Contact Map |
| 3atsA | 1 | 0.9784 | 100 | 0.348 | Contact Map |
| 3tdwA | 1 | 0.931 | 100 | 0.356 | Contact Map |
| 1nw1A | 2 | 0.9526 | 100 | 0.361 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)