| T0759 |
| ID: | 1399946362 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 109 (102) | ||
| Sequences: | 465 (312.3) | ||
| Seq/Len: | 4.559 | ||
| Nf(neff/√len): | 30.9 |
Jackhmmer Results: (2014_04_16)
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: 4.559).
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 |
| 84_T | 87_H | 2.599 | 1.00 |
| 28_H | 33_I | 2.143 | 1.00 |
| 13_V | 24_P | 1.734 | 0.99 |
| 75_E | 79_Q | 1.676 | 0.99 |
| 14_I | 32_L | 1.583 | 0.99 |
| 32_L | 81_G | 1.574 | 0.99 |
| 89_D | 92_V | 1.563 | 0.99 |
| 19_G | 68_S | 1.487 | 0.98 |
| 34_D | 37_M | 1.479 | 0.98 |
| 14_I | 41_L | 1.399 | 0.97 |
| 50_E | 55_G | 1.374 | 0.96 |
| 57_N | 65_D | 1.354 | 0.96 |
| 50_E | 56_P | 1.346 | 0.96 |
| 44_Q | 47_D | 1.327 | 0.95 |
| 23_S | 26_E | 1.317 | 0.95 |
| 92_V | 95_D | 1.294 | 0.94 |
| 33_I | 38_F | 1.286 | 0.94 |
| 98_I | 102_A | 1.282 | 0.94 |
| 104_L | 107_G | 1.272 | 0.94 |
| 92_V | 98_I | 1.265 | 0.94 |
| 27_A | 81_G | 1.264 | 0.93 |
| 77_A | 80_S | 1.242 | 0.93 |
| 50_E | 57_N | 1.235 | 0.92 |
| 22_L | 30_A | 1.233 | 0.92 |
| 34_D | 40_K | 1.216 | 0.92 |
| 85_P | 94_K | 1.207 | 0.91 |
| 34_D | 41_L | 1.206 | 0.91 |
| 19_G | 23_S | 1.200 | 0.91 |
| 60_S | 63_I | 1.196 | 0.91 |
| 77_A | 82_R | 1.180 | 0.90 |
| 70_K | 81_G | 1.178 | 0.90 |
| 21_E | 26_E | 1.164 | 0.89 |
| 15_H | 18_P | 1.148 | 0.88 |
| 14_I | 21_E | 1.144 | 0.88 |
| 50_E | 53_V | 1.111 | 0.86 |
| 6_H | 9_S | 1.075 | 0.83 |
| 99_Q | 104_L | 1.073 | 0.83 |
| 86_A | 90_R | 1.072 | 0.83 |
| 22_L | 26_E | 1.066 | 0.83 |
| 61_S | 65_D | 1.065 | 0.83 |
| 51_I | 57_N | 1.046 | 0.81 |
| 35_W | 91_Y | 1.040 | 0.80 |
| 12_V | 21_E | 1.038 | 0.80 |
| 74_I | 91_Y | 1.029 | 0.79 |
| 14_I | 20_R | 1.020 | 0.79 |
| 62_V | 69_G | 1.019 | 0.79 |
| 15_H | 20_R | 1.018 | 0.78 |
| 74_I | 78_L | 1.016 | 0.78 |
| 62_V | 71_K | 1.012 | 0.78 |
| 55_G | 58_G | 1.008 | 0.77 |
| 6_H | 106_S | 1.008 | 0.77 |
| 53_V | 60_S | 1.008 | 0.77 |
| 33_I | 36_N | 1.005 | 0.77 |
| 33_I | 40_K | 1.000 | 0.77 |
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 | |
| 1lm7A | 2 | 1 | 99.3 | 0.376 | Contact Map |
| 1lm5A | 2 | 0.8349 | 99.3 | 0.382 | Contact Map |
| 4gm2A | 7 | 0.3578 | 16.1 | 0.87 | Contact Map |
| 2j5gA | 11 | 0.844 | 15.4 | 0.87 | Contact Map |
| 3p2lA | 7 | 0.3761 | 14.5 | 0.872 | Contact Map |
| 1y7oA | 7 | 0.3761 | 14.2 | 0.873 | Contact Map |
| 3qwdA | 14 | 0.4495 | 13.5 | 0.874 | Contact Map |
| 1yg6A | 14 | 0.3761 | 12.7 | 0.876 | Contact Map |
| 3fduA | 6 | 0.8807 | 10.6 | 0.88 | Contact Map |
| 3vivA | 2 | 0.7431 | 10.2 | 0.88 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)