| 3g0m |
| ID: | 1453972252 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (137) | ||
| Sequences: | 1589 (910.2) | ||
| Seq/Len: | 11.599 | ||
| Nf(neff/√len): | 77.8 |
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: 11.599).
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 |
| 95_M | 99_D | 3.235 | 1.00 |
| 75_D | 82_K | 3.137 | 1.00 |
| 98_Q | 102_H | 3.115 | 1.00 |
| 110_E | 115_A | 2.779 | 1.00 |
| 46_N | 49_N | 2.476 | 1.00 |
| 71_E | 94_Q | 2.231 | 1.00 |
| 71_E | 93_H | 2.224 | 1.00 |
| 16_N | 90_I | 2.154 | 1.00 |
| 30_I | 87_V | 2.109 | 1.00 |
| 44_D | 73_Q | 2.082 | 1.00 |
| 96_T | 99_D | 2.025 | 1.00 |
| 50_T | 57_Q | 1.988 | 1.00 |
| 104_D | 107_P | 1.966 | 1.00 |
| 41_N | 44_D | 1.920 | 1.00 |
| 74_G | 85_M | 1.875 | 1.00 |
| 42_P | 45_R | 1.830 | 1.00 |
| 40_L | 45_R | 1.793 | 1.00 |
| 14_L | 111_K | 1.737 | 1.00 |
| 44_D | 61_V | 1.724 | 1.00 |
| 29_Y | 32_E | 1.662 | 1.00 |
| 56_S | 78_A | 1.636 | 1.00 |
| 45_R | 75_D | 1.624 | 1.00 |
| 9_D | 95_M | 1.589 | 1.00 |
| 62_M | 136_K | 1.585 | 1.00 |
| 132_A | 136_K | 1.581 | 1.00 |
| 31_I | 34_G | 1.545 | 1.00 |
| 13_L | 90_I | 1.485 | 1.00 |
| 55_Q | 121_S | 1.475 | 1.00 |
| 63_R | 73_Q | 1.431 | 1.00 |
| 101_V | 138_A | 1.403 | 0.99 |
| 92_Y | 133_I | 1.386 | 0.99 |
| 62_M | 72_L | 1.352 | 0.99 |
| 72_L | 133_I | 1.345 | 0.99 |
| 57_Q | 77_D | 1.319 | 0.99 |
| 23_W | 117_H | 1.297 | 0.99 |
| 20_C | 25_E | 1.269 | 0.99 |
| 23_W | 27_Y | 1.264 | 0.99 |
| 64_R | 97_A | 1.259 | 0.99 |
| 91_L | 103_F | 1.240 | 0.98 |
| 91_L | 108_W | 1.237 | 0.98 |
| 40_L | 44_D | 1.236 | 0.98 |
| 53_G | 76_S | 1.230 | 0.98 |
| 29_Y | 33_L | 1.217 | 0.98 |
| 131_R | 135_A | 1.208 | 0.98 |
| 72_L | 100_I | 1.187 | 0.98 |
| 47_P | 50_T | 1.167 | 0.97 |
| 60_I | 72_L | 1.165 | 0.97 |
| 44_D | 49_N | 1.151 | 0.97 |
| 18_T | 111_K | 1.142 | 0.97 |
| 47_P | 52_H | 1.124 | 0.97 |
| 41_N | 73_Q | 1.123 | 0.97 |
| 10_K | 91_L | 1.120 | 0.96 |
| 38_A | 73_Q | 1.111 | 0.96 |
| 10_K | 51_I | 1.107 | 0.96 |
| 40_L | 73_Q | 1.090 | 0.96 |
| 16_N | 29_Y | 1.082 | 0.96 |
| 80_I | 117_H | 1.074 | 0.95 |
| 40_L | 61_V | 1.054 | 0.95 |
| 81_V | 128_A | 1.030 | 0.94 |
| 25_E | 28_L | 1.025 | 0.93 |
| 135_A | 139_T | 1.024 | 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 | |
| 3g0mA | 1 | 0.9787 | 100 | 0.004 | Contact Map |
| 4lw4C | 2 | 0.9929 | 100 | 0.005 | Contact Map |
| 1wloA | 1 | 0.9362 | 100 | 0.08 | Contact Map |
| 3lvlA | 1 | 0.7872 | 57.2 | 0.913 | Contact Map |
| 2qq4A | 10 | 0.8227 | 47.6 | 0.918 | Contact Map |
| 4jjfA | 2 | 0.8014 | 47.5 | 0.918 | Contact Map |
| 4eb5C | 2 | 0.7801 | 30.3 | 0.926 | Contact Map |
| 2z7eA | 3 | 0.844 | 27 | 0.928 | Contact Map |
| 1xjsA | 1 | 0.8582 | 15.9 | 0.935 | Contact Map |
| 4k51A | 2 | 0.5106 | 12.7 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)