| cus-210 |
| ID: | 1419263416 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 210 (203) | ||
| Sequences: | 6533 (5445.9) | ||
| Seq/Len: | 32.182 | ||
| Nf(neff/√len): | 382.2 |
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: 32.182).
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 |
| 92_D | 96_K | 4.882 | 1.00 |
| 48_I | 149_R | 4.806 | 1.00 |
| 13_A | 207_H | 3.209 | 1.00 |
| 202_V | 206_V | 2.685 | 1.00 |
| 91_A | 97_T | 2.571 | 1.00 |
| 36_I | 184_M | 2.532 | 1.00 |
| 152_N | 168_Y | 2.530 | 1.00 |
| 89_S | 168_Y | 2.526 | 1.00 |
| 11_S | 14_T | 2.436 | 1.00 |
| 87_L | 170_A | 2.292 | 1.00 |
| 181_N | 185_N | 2.285 | 1.00 |
| 33_W | 37_H | 2.265 | 1.00 |
| 55_S | 153_L | 2.205 | 1.00 |
| 199_V | 203_L | 2.060 | 1.00 |
| 154_P | 166_T | 1.874 | 1.00 |
| 203_L | 207_H | 1.816 | 1.00 |
| 90_L | 167_L | 1.760 | 1.00 |
| 47_D | 176_H | 1.735 | 1.00 |
| 91_A | 168_Y | 1.714 | 1.00 |
| 55_S | 59_E | 1.667 | 1.00 |
| 91_A | 166_T | 1.645 | 1.00 |
| 39_V | 183_L | 1.628 | 1.00 |
| 56_A | 153_L | 1.545 | 1.00 |
| 40_K | 44_A | 1.536 | 1.00 |
| 17_T | 21_S | 1.528 | 1.00 |
| 192_S | 196_I | 1.505 | 1.00 |
| 20_I | 206_V | 1.502 | 1.00 |
| 34_I | 38_S | 1.494 | 1.00 |
| 162_K | 165_Y | 1.491 | 1.00 |
| 42_H | 46_Q | 1.481 | 1.00 |
| 39_V | 43_F | 1.460 | 1.00 |
| 10_F | 14_T | 1.448 | 1.00 |
| 150_M | 170_A | 1.437 | 1.00 |
| 58_L | 167_L | 1.432 | 1.00 |
| 43_F | 179_Y | 1.426 | 1.00 |
| 206_V | 210_H | 1.414 | 1.00 |
| 188_I | 192_S | 1.414 | 1.00 |
| 152_N | 166_T | 1.410 | 1.00 |
| 16_L | 20_I | 1.408 | 1.00 |
| 204_L | 208_K | 1.402 | 0.99 |
| 13_A | 17_T | 1.400 | 0.99 |
| 176_H | 179_Y | 1.392 | 0.99 |
| 50_D | 171_L | 1.375 | 0.99 |
| 20_I | 202_V | 1.362 | 0.99 |
| 157_P | 162_K | 1.339 | 0.99 |
| 147_N | 177_L | 1.334 | 0.99 |
| 89_S | 97_T | 1.331 | 0.99 |
| 17_T | 20_I | 1.324 | 0.99 |
| 28_F | 191_A | 1.311 | 0.99 |
| 32_A | 191_A | 1.308 | 0.99 |
| 41_V | 45_E | 1.279 | 0.99 |
| 55_S | 151_I | 1.279 | 0.99 |
| 36_I | 40_K | 1.275 | 0.99 |
| 52_K | 151_I | 1.275 | 0.99 |
| 154_P | 165_Y | 1.272 | 0.99 |
| 24_T | 198_I | 1.248 | 0.99 |
| 20_I | 35_M | 1.237 | 0.98 |
| 35_M | 187_L | 1.237 | 0.98 |
| 92_D | 95_G | 1.231 | 0.98 |
| 33_W | 36_I | 1.224 | 0.98 |
| 43_F | 47_D | 1.220 | 0.98 |
| 198_I | 202_V | 1.215 | 0.98 |
| 10_F | 18_F | 1.203 | 0.98 |
| 148_W | 170_A | 1.183 | 0.98 |
| 205_A | 209_G | 1.175 | 0.98 |
| 185_N | 189_M | 1.173 | 0.98 |
| 92_D | 98_V | 1.170 | 0.97 |
| 17_T | 206_V | 1.159 | 0.97 |
| 206_V | 209_G | 1.159 | 0.97 |
| 181_N | 184_M | 1.158 | 0.97 |
| 35_M | 183_L | 1.152 | 0.97 |
| 97_T | 100_H | 1.152 | 0.97 |
| 75_T | 78_D | 1.151 | 0.97 |
| 46_Q | 179_Y | 1.144 | 0.97 |
| 44_A | 48_I | 1.128 | 0.97 |
| 52_K | 56_A | 1.128 | 0.97 |
| 37_H | 40_K | 1.127 | 0.97 |
| 32_A | 187_L | 1.123 | 0.97 |
| 50_D | 53_E | 1.119 | 0.96 |
| 28_F | 32_A | 1.103 | 0.96 |
| 48_I | 51_L | 1.101 | 0.96 |
| 89_S | 170_A | 1.100 | 0.96 |
| 43_F | 46_Q | 1.097 | 0.96 |
| 200_F | 204_L | 1.089 | 0.96 |
| 196_I | 200_F | 1.063 | 0.95 |
| 180_I | 184_M | 1.063 | 0.95 |
| 176_H | 180_I | 1.055 | 0.95 |
| 31_F | 194_I | 1.054 | 0.95 |
| 202_V | 205_A | 1.042 | 0.94 |
| 37_H | 41_V | 1.040 | 0.94 |
| 21_S | 199_V | 1.039 | 0.94 |
| 193_V | 197_L | 1.008 | 0.93 |
| 20_I | 24_T | 1.007 | 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 | |
| 2kseA | 1 | 0.3667 | 99.4 | 0.364 | Contact Map |
| 3cwfA | 2 | 0.519 | 95.9 | 0.711 | Contact Map |
| 3e4oA | 2 | 0.7524 | 92.2 | 0.757 | Contact Map |
| 4cq4A | 4 | 0.1619 | 92.1 | 0.758 | Contact Map |
| 4onxA | 6 | 0.6 | 92 | 0.758 | Contact Map |
| 3by8A | 1 | 0.6095 | 79.3 | 0.8 | Contact Map |
| 1p0zA | 10 | 0.6048 | 70.6 | 0.814 | Contact Map |
| 4u65A | 4 | 0.6143 | 68.7 | 0.816 | Contact Map |
| 3pjvD | 2 | 0.6 | 33.9 | 0.852 | Contact Map |
| 2f95B | 1 | 0.2524 | 28.7 | 0.857 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)