| C2B |
| ID: | 1491865206 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 149 (134) | ||
| Sequences: | 5934 (3526.8) | ||
| Seq/Len: | 44.284 | ||
| Nf(neff/√len): | 304.7 |
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: 44.284).
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 |
| 15_V | 41_T | 3.620 | 1.00 |
| 42_R | 53_E | 3.496 | 1.00 |
| 17_E | 127_K | 3.162 | 1.00 |
| 9_F | 132_V | 2.718 | 1.00 |
| 70_P | 91_R | 2.467 | 1.00 |
| 90_F | 110_L | 2.453 | 1.00 |
| 17_E | 109_W | 2.435 | 1.00 |
| 79_R | 85_A | 2.391 | 1.00 |
| 18_G | 51_F | 2.342 | 1.00 |
| 29_V | 84_D | 2.298 | 1.00 |
| 17_E | 50_L | 2.288 | 1.00 |
| 19_R | 125_Y | 2.105 | 1.00 |
| 12_R | 56_F | 2.056 | 1.00 |
| 109_W | 127_K | 1.994 | 1.00 |
| 15_V | 30_V | 1.970 | 1.00 |
| 30_V | 73_I | 1.969 | 1.00 |
| 14_Q | 129_S | 1.967 | 1.00 |
| 76_V | 86_L | 1.949 | 1.00 |
| 26_I | 87_L | 1.943 | 1.00 |
| 72_F | 89_E | 1.927 | 1.00 |
| 26_I | 47_N | 1.921 | 1.00 |
| 75_V | 112_L | 1.892 | 1.00 |
| 19_R | 109_W | 1.794 | 1.00 |
| 14_Q | 54_T | 1.754 | 1.00 |
| 39_K | 55_L | 1.728 | 1.00 |
| 43_I | 78_S | 1.597 | 1.00 |
| 28_P | 77_D | 1.594 | 1.00 |
| 111_L | 125_Y | 1.580 | 1.00 |
| 23_G | 26_I | 1.564 | 1.00 |
| 32_V | 55_L | 1.553 | 1.00 |
| 72_F | 91_R | 1.526 | 1.00 |
| 109_W | 125_Y | 1.517 | 1.00 |
| 107_R | 127_K | 1.506 | 1.00 |
| 70_P | 93_D | 1.460 | 1.00 |
| 27_K | 79_R | 1.460 | 1.00 |
| 16_I | 129_S | 1.452 | 1.00 |
| 23_G | 47_N | 1.445 | 1.00 |
| 18_G | 21_L | 1.422 | 1.00 |
| 14_Q | 52_N | 1.416 | 1.00 |
| 12_R | 54_T | 1.354 | 0.99 |
| 110_L | 128_T | 1.339 | 0.99 |
| 33_T | 74_T | 1.321 | 0.99 |
| 73_I | 128_T | 1.317 | 0.99 |
| 21_L | 28_P | 1.299 | 0.99 |
| 12_R | 131_C | 1.278 | 0.99 |
| 30_V | 51_F | 1.244 | 0.98 |
| 20_Q | 48_S | 1.223 | 0.98 |
| 16_I | 52_N | 1.213 | 0.98 |
| 78_S | 84_D | 1.202 | 0.98 |
| 10_Q | 58_N | 1.202 | 0.98 |
| 12_R | 133_L | 1.194 | 0.98 |
| 30_V | 75_V | 1.183 | 0.98 |
| 13_V | 130_L | 1.177 | 0.98 |
| 86_L | 89_E | 1.125 | 0.97 |
| 68_D | 95_G | 1.116 | 0.96 |
| 11_I | 130_L | 1.114 | 0.96 |
| 31_K | 74_T | 1.112 | 0.96 |
| 13_V | 32_V | 1.088 | 0.96 |
| 15_V | 32_V | 1.084 | 0.96 |
| 46_G | 49_P | 1.063 | 0.95 |
| 88_G | 112_L | 1.046 | 0.94 |
| 33_T | 72_F | 1.044 | 0.94 |
| 32_V | 73_I | 1.034 | 0.94 |
| 45_K | 78_S | 1.005 | 0.93 |
| 79_R | 82_R | 1.003 | 0.93 |
| 74_T | 86_L | 1.000 | 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 | |
| 3l9bA | 1 | 0.8322 | 99.8 | 0.255 | Contact Map |
| 2fk9A | 1 | 0.7785 | 99.7 | 0.315 | Contact Map |
| 2dmhA | 1 | 0.906 | 99.7 | 0.315 | Contact Map |
| 2r83A | 2 | 0.9664 | 99.7 | 0.315 | Contact Map |
| 4npjA | 2 | 0.906 | 99.7 | 0.321 | Contact Map |
| 3m7fB | 1 | 0.7987 | 99.7 | 0.323 | Contact Map |
| 4iqhA | 3 | 0.8255 | 99.7 | 0.326 | Contact Map |
| 3b7yA | 2 | 0.8591 | 99.7 | 0.326 | Contact Map |
| 1wfjA | 1 | 0.8658 | 99.7 | 0.327 | Contact Map |
| 4v29A | 2 | 0.8523 | 99.7 | 0.328 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)