| TR |
| ID: | 1507799600 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 143 (136) | ||
| Sequences: | 2556 (1826.9) | ||
| Seq/Len: | 18.794 | ||
| Nf(neff/√len): | 156.7 |
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: 18.794).
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 |
| 3_D | 55_R | 3.848 | 1.00 |
| 17_A | 60_V | 3.308 | 1.00 |
| 4_V | 31_V | 2.595 | 1.00 |
| 3_D | 30_S | 2.229 | 1.00 |
| 20_L | 60_V | 2.196 | 1.00 |
| 57_F | 86_A | 1.972 | 1.00 |
| 32_F | 38_L | 1.914 | 1.00 |
| 21_K | 36_E | 1.890 | 1.00 |
| 43_F | 119_N | 1.866 | 1.00 |
| 8_Y | 13_G | 1.850 | 1.00 |
| 7_S | 65_A | 1.792 | 1.00 |
| 42_K | 46_K | 1.778 | 1.00 |
| 63_P | 98_D | 1.707 | 1.00 |
| 25_Q | 36_E | 1.700 | 1.00 |
| 65_A | 79_V | 1.688 | 1.00 |
| 63_P | 107_V | 1.684 | 1.00 |
| 21_K | 25_Q | 1.676 | 1.00 |
| 16_L | 60_V | 1.598 | 1.00 |
| 7_S | 82_E | 1.578 | 1.00 |
| 34_D | 38_L | 1.576 | 1.00 |
| 18_S | 35_V | 1.564 | 1.00 |
| 46_K | 49_Q | 1.529 | 1.00 |
| 76_K | 79_V | 1.508 | 1.00 |
| 123_W | 131_T | 1.500 | 1.00 |
| 4_V | 58_V | 1.463 | 1.00 |
| 59_L | 65_A | 1.440 | 1.00 |
| 133_E | 137_R | 1.422 | 1.00 |
| 38_L | 50_S | 1.389 | 0.99 |
| 11_N | 64_G | 1.385 | 0.99 |
| 32_F | 50_S | 1.385 | 0.99 |
| 8_Y | 34_D | 1.379 | 0.99 |
| 135_I | 139_L | 1.361 | 0.99 |
| 62_S | 65_A | 1.311 | 0.99 |
| 110_E | 113_Q | 1.290 | 0.99 |
| 10_R | 34_D | 1.281 | 0.99 |
| 83_I | 112_M | 1.265 | 0.99 |
| 1_T | 53_G | 1.253 | 0.99 |
| 29_F | 139_L | 1.243 | 0.98 |
| 4_V | 29_F | 1.226 | 0.98 |
| 2_P | 30_S | 1.217 | 0.98 |
| 19_L | 23_H | 1.215 | 0.98 |
| 127_Y | 130_A | 1.209 | 0.98 |
| 49_Q | 53_G | 1.208 | 0.98 |
| 33_I | 37_K | 1.183 | 0.98 |
| 21_K | 33_I | 1.181 | 0.98 |
| 131_T | 134_K | 1.179 | 0.98 |
| 38_L | 46_K | 1.172 | 0.98 |
| 41_G | 95_P | 1.162 | 0.97 |
| 33_I | 36_E | 1.150 | 0.97 |
| 4_V | 56_N | 1.133 | 0.97 |
| 48_I | 52_M | 1.102 | 0.96 |
| 56_N | 92_N | 1.100 | 0.96 |
| 29_F | 140_Q | 1.092 | 0.96 |
| 13_G | 35_V | 1.092 | 0.96 |
| 38_L | 79_V | 1.083 | 0.96 |
| 32_F | 47_L | 1.082 | 0.96 |
| 84_V | 111_D | 1.068 | 0.95 |
| 38_L | 43_F | 1.064 | 0.95 |
| 137_R | 140_Q | 1.049 | 0.94 |
| 59_L | 83_I | 1.042 | 0.94 |
| 10_R | 43_F | 1.017 | 0.93 |
| 2_P | 54_A | 1.005 | 0.93 |
| 27_H | 132_I | 1.003 | 0.93 |
| 9_R | 64_G | 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 | |
| 2js7A | 1 | 0.8951 | 99.9 | 0.221 | Contact Map |
| 4eo7A | 1 | 0.8811 | 99.9 | 0.245 | Contact Map |
| 2j67A | 2 | 0.9021 | 99.8 | 0.25 | Contact Map |
| 4om7A | 2 | 0.9021 | 99.8 | 0.25 | Contact Map |
| 1fyxA | 1 | 0.8881 | 99.8 | 0.256 | Contact Map |
| 3ub2A | 1 | 0.7902 | 99.8 | 0.258 | Contact Map |
| 3h16A | 4 | 0.9091 | 99.8 | 0.268 | Contact Map |
| 4lzpB | 4 | 0.8881 | 99.8 | 0.281 | Contact Map |
| 1t3gA | 2 | 0.8811 | 99.8 | 0.287 | Contact Map |
| 4lqcA | 2 | 0.9091 | 99.8 | 0.289 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)