| 4lbj |
| ID: | 1492603766 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 138 (134) | ||
| Sequences: | 1732 (1096.2) | ||
| Seq/Len: | 12.925 | ||
| Nf(neff/√len): | 94.7 |
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: 12.925).
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 |
| 63_T | 109_Y | 2.940 | 1.00 |
| 45_F | 99_V | 2.531 | 1.00 |
| 90_V | 97_F | 2.432 | 1.00 |
| 36_D | 46_H | 2.359 | 1.00 |
| 62_N | 72_E | 2.160 | 1.00 |
| 100_A | 105_H | 2.034 | 1.00 |
| 130_L | 133_A | 2.014 | 1.00 |
| 97_F | 119_I | 1.978 | 1.00 |
| 46_H | 50_R | 1.958 | 1.00 |
| 37_F | 90_V | 1.957 | 1.00 |
| 20_I | 37_F | 1.956 | 1.00 |
| 61_C | 107_L | 1.938 | 1.00 |
| 92_V | 111_H | 1.894 | 1.00 |
| 91_L | 100_A | 1.890 | 1.00 |
| 53_E | 74_R | 1.866 | 1.00 |
| 59_I | 106_L | 1.836 | 1.00 |
| 24_G | 86_F | 1.802 | 1.00 |
| 20_I | 135_Y | 1.757 | 1.00 |
| 30_A | 82_S | 1.742 | 1.00 |
| 19_L | 89_Q | 1.611 | 1.00 |
| 73_E | 112_R | 1.609 | 1.00 |
| 35_L | 88_I | 1.590 | 1.00 |
| 36_D | 123_G | 1.569 | 1.00 |
| 124_I | 130_L | 1.558 | 1.00 |
| 93_E | 98_K | 1.489 | 1.00 |
| 4_V | 128_I | 1.486 | 1.00 |
| 37_F | 45_F | 1.485 | 1.00 |
| 86_F | 128_I | 1.478 | 1.00 |
| 99_V | 107_L | 1.468 | 1.00 |
| 60_V | 72_E | 1.458 | 1.00 |
| 44_A | 119_I | 1.449 | 1.00 |
| 109_Y | 112_R | 1.438 | 1.00 |
| 38_Q | 123_G | 1.397 | 0.99 |
| 32_R | 52_N | 1.393 | 0.99 |
| 61_C | 73_E | 1.386 | 0.99 |
| 31_N | 52_N | 1.354 | 0.99 |
| 96_H | 108_Q | 1.335 | 0.99 |
| 14_V | 92_V | 1.325 | 0.99 |
| 47_F | 90_V | 1.298 | 0.99 |
| 65_L | 70_G | 1.292 | 0.99 |
| 34_A | 125_S | 1.288 | 0.99 |
| 49_P | 80_F | 1.247 | 0.99 |
| 31_N | 127_D | 1.233 | 0.98 |
| 10_L | 20_I | 1.217 | 0.98 |
| 34_A | 48_N | 1.206 | 0.98 |
| 5_P | 10_L | 1.160 | 0.97 |
| 50_R | 74_R | 1.155 | 0.97 |
| 102_N | 106_L | 1.148 | 0.97 |
| 28_P | 31_N | 1.137 | 0.97 |
| 61_C | 78_F | 1.135 | 0.97 |
| 80_F | 101_V | 1.118 | 0.96 |
| 93_E | 96_H | 1.086 | 0.96 |
| 14_V | 20_I | 1.085 | 0.96 |
| 19_L | 91_L | 1.075 | 0.95 |
| 15_V | 18_M | 1.072 | 0.95 |
| 29_N | 82_S | 1.065 | 0.95 |
| 92_V | 116_L | 1.063 | 0.95 |
| 39_R | 118_E | 1.059 | 0.95 |
| 50_R | 72_E | 1.057 | 0.95 |
| 62_N | 69_W | 1.057 | 0.95 |
| 36_D | 43_V | 1.045 | 0.94 |
| 30_A | 127_D | 1.044 | 0.94 |
| 46_H | 60_V | 1.041 | 0.94 |
| 81_E | 84_K | 1.040 | 0.94 |
| 60_V | 74_R | 1.032 | 0.94 |
| 23_L | 132_S | 1.029 | 0.94 |
| 105_H | 108_Q | 1.018 | 0.93 |
| 97_F | 111_H | 1.018 | 0.93 |
| 51_F | 78_F | 1.014 | 0.93 |
| 39_R | 42_D | 1.013 | 0.93 |
| 95_D | 108_Q | 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
- 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 | -0.018 | Contact Map |
| 3zsjA | 1 | 1 | 100 | -0.016 | Contact Map |
| 3vv1A | 2 | 0.9493 | 100 | -0.004 | Contact Map |
| 3vklA | 2 | 0.9783 | 100 | -0.003 | Contact Map |
| 2d6mA | 2 | 0.9783 | 100 | 0 | Contact Map |
| 3i8tA | 1 | 0.9783 | 100 | 0.001 | Contact Map |
| 3wv6A | 2 | 0 | 100 | 0.002 | Contact Map |
| 3ap9A | 1 | 0.9783 | 100 | 0.005 | Contact Map |
| 4xbqA | 2 | 0 | 100 | 0.005 | Contact Map |
| 4ym3A | 4 | 0 | 100 | 0.008 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)