| 4lbj |
| ID: | 1453972463 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 138 (135) | ||
| Sequences: | 1487 (936.5) | ||
| Seq/Len: | 11.015 | ||
| Nf(neff/√len): | 80.6 |
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: 11.015).
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 |
| 45_F | 99_V | 2.900 | 1.00 |
| 63_T | 109_Y | 2.814 | 1.00 |
| 46_H | 50_R | 2.457 | 1.00 |
| 53_E | 74_R | 2.441 | 1.00 |
| 90_V | 97_F | 2.297 | 1.00 |
| 62_N | 72_E | 2.151 | 1.00 |
| 97_F | 119_I | 2.111 | 1.00 |
| 20_I | 37_F | 2.088 | 1.00 |
| 37_F | 90_V | 2.082 | 1.00 |
| 36_D | 46_H | 2.028 | 1.00 |
| 100_A | 105_H | 1.993 | 1.00 |
| 92_V | 111_H | 1.983 | 1.00 |
| 35_L | 88_I | 1.871 | 1.00 |
| 4_V | 128_I | 1.863 | 1.00 |
| 130_L | 133_A | 1.751 | 1.00 |
| 61_C | 107_L | 1.698 | 1.00 |
| 80_F | 101_V | 1.648 | 1.00 |
| 91_L | 100_A | 1.637 | 1.00 |
| 59_I | 106_L | 1.637 | 1.00 |
| 19_L | 89_Q | 1.628 | 1.00 |
| 31_N | 52_N | 1.605 | 1.00 |
| 24_G | 86_F | 1.605 | 1.00 |
| 93_E | 98_K | 1.565 | 1.00 |
| 10_L | 13_G | 1.532 | 1.00 |
| 32_R | 52_N | 1.497 | 1.00 |
| 60_V | 72_E | 1.494 | 1.00 |
| 36_D | 123_G | 1.488 | 1.00 |
| 14_V | 92_V | 1.475 | 1.00 |
| 30_A | 127_D | 1.463 | 1.00 |
| 37_F | 45_F | 1.419 | 1.00 |
| 20_I | 135_Y | 1.418 | 1.00 |
| 38_Q | 123_G | 1.390 | 0.99 |
| 47_F | 90_V | 1.390 | 0.99 |
| 124_I | 130_L | 1.366 | 0.99 |
| 31_N | 127_D | 1.356 | 0.99 |
| 34_A | 125_S | 1.345 | 0.99 |
| 39_R | 118_E | 1.324 | 0.99 |
| 62_N | 69_W | 1.322 | 0.99 |
| 96_H | 108_Q | 1.320 | 0.99 |
| 86_F | 128_I | 1.319 | 0.99 |
| 92_V | 116_L | 1.319 | 0.99 |
| 61_C | 73_E | 1.313 | 0.99 |
| 49_P | 80_F | 1.292 | 0.99 |
| 50_R | 74_R | 1.289 | 0.99 |
| 99_V | 107_L | 1.254 | 0.99 |
| 23_L | 132_S | 1.253 | 0.99 |
| 30_A | 82_S | 1.245 | 0.98 |
| 65_L | 70_G | 1.232 | 0.98 |
| 73_E | 112_R | 1.211 | 0.98 |
| 50_R | 72_E | 1.197 | 0.98 |
| 35_L | 90_V | 1.191 | 0.98 |
| 93_E | 96_H | 1.180 | 0.98 |
| 44_A | 119_I | 1.174 | 0.98 |
| 46_H | 60_V | 1.172 | 0.98 |
| 81_E | 84_K | 1.167 | 0.97 |
| 105_H | 108_Q | 1.166 | 0.97 |
| 51_F | 78_F | 1.164 | 0.97 |
| 109_Y | 112_R | 1.158 | 0.97 |
| 62_N | 70_G | 1.156 | 0.97 |
| 14_V | 119_I | 1.155 | 0.97 |
| 28_P | 31_N | 1.151 | 0.97 |
| 23_L | 85_P | 1.108 | 0.96 |
| 14_V | 37_F | 1.091 | 0.96 |
| 19_L | 91_L | 1.087 | 0.96 |
| 124_I | 128_I | 1.075 | 0.95 |
| 58_V | 74_R | 1.049 | 0.94 |
| 34_A | 48_N | 1.046 | 0.94 |
| 29_N | 82_S | 1.030 | 0.94 |
| 65_L | 113_V | 1.029 | 0.94 |
| 43_V | 46_H | 1.012 | 0.93 |
| 15_V | 18_M | 1.004 | 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 | |
| 4xbnA | 1 | 0 | 100 | -0.007 | Contact Map |
| 3zsjA | 1 | 1 | 100 | -0.006 | Contact Map |
| 3vv1A | 2 | 0.9493 | 100 | 0.003 | Contact Map |
| 3vklA | 2 | 0.971 | 100 | 0.01 | Contact Map |
| 2d6mA | 2 | 0.971 | 100 | 0.012 | Contact Map |
| 3i8tA | 1 | 0.971 | 100 | 0.015 | Contact Map |
| 4xbqA | 2 | 0 | 100 | 0.015 | Contact Map |
| 3wv6A | 2 | 0 | 100 | 0.016 | Contact Map |
| 4ym3A | 4 | 0 | 100 | 0.017 | Contact Map |
| 4gxlA | 1 | 0.9638 | 100 | 0.02 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)