| 1tk7 |
| ID: | 1496033946 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 88 (83) | ||
| Sequences: | 1468 (940) | ||
| Seq/Len: | 17.687 | ||
| Nf(neff/√len): | 103.2 |
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: 17.687).
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 |
| 13_L | 16_G | 2.509 | 1.00 |
| 21_I | 27_V | 2.176 | 1.00 |
| 57_L | 60_G | 2.046 | 1.00 |
| 65_Y | 71_R | 1.868 | 1.00 |
| 31_N | 38_Q | 1.797 | 1.00 |
| 18_E | 32_H | 1.761 | 1.00 |
| 62_E | 76_H | 1.760 | 1.00 |
| 75_D | 78_T | 1.760 | 1.00 |
| 60_G | 77_N | 1.669 | 1.00 |
| 19_K | 27_V | 1.655 | 1.00 |
| 20_K | 30_V | 1.587 | 1.00 |
| 63_I | 71_R | 1.544 | 1.00 |
| 31_N | 34_N | 1.477 | 1.00 |
| 64_R | 70_E | 1.471 | 1.00 |
| 64_R | 74_V | 1.468 | 1.00 |
| 8_D | 11_G | 1.322 | 0.99 |
| 66_T | 70_E | 1.293 | 0.99 |
| 66_T | 72_F | 1.285 | 0.99 |
| 22_Q | 66_T | 1.282 | 0.99 |
| 76_H | 81_T | 1.270 | 0.99 |
| 73_F | 85_D | 1.263 | 0.99 |
| 6_H | 9_A | 1.259 | 0.99 |
| 63_I | 73_F | 1.248 | 0.99 |
| 22_Q | 26_R | 1.244 | 0.98 |
| 32_H | 36_T | 1.241 | 0.98 |
| 26_R | 70_E | 1.233 | 0.98 |
| 65_Y | 69_G | 1.232 | 0.98 |
| 17_W | 29_F | 1.214 | 0.98 |
| 30_V | 37_T | 1.196 | 0.98 |
| 20_K | 64_R | 1.188 | 0.98 |
| 29_F | 41_D | 1.107 | 0.96 |
| 26_R | 35_R | 1.102 | 0.96 |
| 24_D | 40_E | 1.091 | 0.96 |
| 32_H | 37_T | 1.074 | 0.95 |
| 28_Y | 39_W | 1.073 | 0.95 |
| 14_P | 17_W | 1.069 | 0.95 |
| 31_N | 36_T | 1.066 | 0.95 |
| 46_G | 49_V | 1.046 | 0.94 |
| 37_T | 42_P | 1.036 | 0.94 |
| 81_T | 86_P | 1.020 | 0.93 |
| 72_F | 83_F | 1.012 | 0.93 |
| 20_K | 36_T | 1.004 | 0.93 |
| 28_Y | 63_I | 1.002 | 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 | |
| 1tk7A | 1 | 1 | 99.8 | 0.114 | Contact Map |
| 2kxqA | 1 | 0.9659 | 99.8 | 0.177 | Contact Map |
| 4rohA | 1 | 0.7955 | 99.8 | 0.183 | Contact Map |
| 2l5fA | 1 | 0.9545 | 99.7 | 0.211 | Contact Map |
| 2jxwA | 1 | 0.8523 | 99.7 | 0.252 | Contact Map |
| 1o6wA | 1 | 0.8182 | 99.6 | 0.277 | Contact Map |
| 3l4hA | 1 | 0.8068 | 99.3 | 0.412 | Contact Map |
| 2dwvA | 2 | 0.5114 | 98.9 | 0.502 | Contact Map |
| 1eg3A | 1 | 0.4773 | 98.8 | 0.511 | Contact Map |
| 2ysdA | 1 | 0.625 | 98.7 | 0.526 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)