| nef |
| ID: | 1508990912 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 206 (206) | ||
| Sequences: | 2435 (126.6) | ||
| Seq/Len: | 11.820 | ||
| Nf(neff/√len): | 8.8 |
HHblits Results: (2016_02)
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: 11.820).
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 |
| 89_H | 191_F | 3.508 | 1.00 |
| 144_K | 186_D | 3.305 | 1.00 |
| 157_N | 169_S | 2.937 | 1.00 |
| 85_V | 89_H | 2.842 | 1.00 |
| 101_I | 182_E | 2.492 | 1.00 |
| 33_V | 43_I | 2.373 | 1.00 |
| 188_R | 191_F | 2.313 | 1.00 |
| 89_H | 188_R | 2.225 | 1.00 |
| 155_E | 158_K | 2.075 | 1.00 |
| 85_V | 191_F | 2.050 | 1.00 |
| 89_H | 104_Q | 1.943 | 1.00 |
| 48_T | 56_A | 1.882 | 1.00 |
| 99_G | 105_R | 1.874 | 1.00 |
| 35_R | 38_E | 1.844 | 1.00 |
| 83_A | 120_Y | 1.786 | 1.00 |
| 82_K | 93_E | 1.785 | 1.00 |
| 77_R | 86_D | 1.730 | 1.00 |
| 148_V | 182_E | 1.715 | 1.00 |
| 81_Y | 133_V | 1.703 | 1.00 |
| 90_F | 93_E | 1.696 | 1.00 |
| 104_Q | 108_D | 1.679 | 1.00 |
| 163_S | 169_S | 1.660 | 1.00 |
| 89_H | 192_H | 1.617 | 1.00 |
| 188_R | 192_H | 1.608 | 1.00 |
| 82_K | 90_F | 1.601 | 1.00 |
| 19_R | 22_R | 1.592 | 1.00 |
| 135_Y | 138_T | 1.584 | 1.00 |
| 25_P | 35_R | 1.561 | 1.00 |
| 31_G | 36_D | 1.512 | 1.00 |
| 11_I | 14_P | 1.503 | 1.00 |
| 82_K | 94_K | 1.484 | 1.00 |
| 148_V | 163_S | 1.470 | 1.00 |
| 194_V | 198_L | 1.458 | 1.00 |
| 1_M | 6_S | 1.451 | 1.00 |
| 81_Y | 85_V | 1.451 | 1.00 |
| 48_T | 52_N | 1.417 | 1.00 |
| 78_P | 91_L | 1.414 | 1.00 |
| 85_V | 192_H | 1.390 | 0.99 |
| 70_V | 73_Q | 1.370 | 0.99 |
| 48_T | 116_H | 1.362 | 0.99 |
| 104_Q | 174_D | 1.333 | 0.99 |
| 2_G | 6_S | 1.317 | 0.99 |
| 79_M | 86_D | 1.308 | 0.99 |
| 82_K | 92_K | 1.305 | 0.99 |
| 152_K | 182_E | 1.295 | 0.99 |
| 114_I | 120_Y | 1.290 | 0.99 |
| 102_H | 135_Y | 1.287 | 0.99 |
| 35_R | 152_K | 1.269 | 0.99 |
| 98_E | 143_Y | 1.251 | 0.99 |
| 192_H | 197_E | 1.250 | 0.99 |
| 16_V | 20_M | 1.241 | 0.98 |
| 12_G | 17_R | 1.239 | 0.98 |
| 108_D | 174_D | 1.237 | 0.98 |
| 36_D | 47_N | 1.234 | 0.98 |
| 102_H | 163_S | 1.232 | 0.98 |
| 152_K | 192_H | 1.217 | 0.98 |
| 87_L | 91_L | 1.182 | 0.98 |
| 169_S | 194_V | 1.164 | 0.97 |
| 196_R | 202_Y | 1.162 | 0.97 |
| 174_D | 177_E | 1.162 | 0.97 |
| 32_A | 47_N | 1.162 | 0.97 |
| 79_M | 140_G | 1.162 | 0.97 |
| 54_A | 60_A | 1.161 | 0.97 |
| 85_V | 149_E | 1.146 | 0.97 |
| 161_N | 168_V | 1.145 | 0.97 |
| 59_E | 77_R | 1.128 | 0.97 |
| 44_T | 48_T | 1.127 | 0.97 |
| 153_V | 162_T | 1.125 | 0.97 |
| 112_L | 121_F | 1.108 | 0.96 |
| 187_S | 191_F | 1.108 | 0.96 |
| 20_M | 152_K | 1.091 | 0.96 |
| 24_E | 35_R | 1.083 | 0.96 |
| 102_H | 186_D | 1.075 | 0.95 |
| 88_S | 91_L | 1.071 | 0.95 |
| 191_F | 194_V | 1.067 | 0.95 |
| 1_M | 7_K | 1.065 | 0.95 |
| 79_M | 111_D | 1.061 | 0.95 |
| 154_E | 162_T | 1.056 | 0.95 |
| 148_V | 184_R | 1.054 | 0.95 |
| 41_G | 59_E | 1.053 | 0.95 |
| 195_A | 200_P | 1.046 | 0.94 |
| 112_L | 115_Y | 1.037 | 0.94 |
| 40_H | 46_S | 1.035 | 0.94 |
| 71_T | 116_H | 1.033 | 0.94 |
| 101_I | 133_V | 1.028 | 0.94 |
| 101_I | 184_R | 1.028 | 0.94 |
| 120_Y | 178_R | 1.024 | 0.93 |
| 89_H | 151_D | 1.018 | 0.93 |
| 87_L | 196_R | 1.016 | 0.93 |
| 157_N | 168_V | 1.013 | 0.93 |
| 170_L | 173_M | 1.013 | 0.93 |
| 13_W | 16_V | 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 | |
| 4en2B | 2 | 0.7573 | 100 | 0.023 | Contact Map |
| 3reaA | 2 | 0.6408 | 100 | 0.16 | Contact Map |
| 4u5wA | 2 | 0.5777 | 100 | 0.238 | Contact Map |
| 3ik5A | 2 | 0.5825 | 100 | 0.26 | Contact Map |
| 1vx7g | 1 | 0.1214 | 15.9 | 0.976 | Contact Map |
| 3j61n | 1 | 0.1214 | 13.5 | 0.977 | Contact Map |
| 4ujra | 1 | 0.1214 | 13.4 | 0.977 | Contact Map |
| 4w20n | 1 | 0.1117 | 13 | 0.977 | Contact Map |
| 3j39n | 1 | 0.1214 | 12.7 | 0.977 | Contact Map |
| 3j21h | 1 | 0.1165 | 12.1 | 0.977 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)