| 1r69 |
| ID: | 1485574679 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 69 (65) | ||
| Sequences: | 33279 (25837.9) | ||
| Seq/Len: | 511.985 | ||
| Nf(neff/√len): | 3204.8 |
Jackhmmer Results: (2016_04)
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: 511.985).
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 |
| 10_R | 35_E | 3.457 | 1.00 |
| 23_K | 51_A | 2.431 | 1.00 |
| 18_A | 28_Q | 2.425 | 1.00 |
| 33_Q | 38_K | 2.155 | 1.00 |
| 9_K | 13_L | 1.992 | 1.00 |
| 9_K | 12_Q | 1.937 | 1.00 |
| 30_S | 34_L | 1.806 | 1.00 |
| 15_L | 51_A | 1.621 | 1.00 |
| 20_L | 31_I | 1.587 | 1.00 |
| 18_A | 22_Q | 1.581 | 1.00 |
| 32_E | 36_N | 1.538 | 1.00 |
| 8_S | 12_Q | 1.479 | 1.00 |
| 34_L | 44_F | 1.479 | 1.00 |
| 5_R | 58_W | 1.478 | 1.00 |
| 19_E | 23_K | 1.476 | 1.00 |
| 44_F | 47_E | 1.466 | 1.00 |
| 33_Q | 39_T | 1.419 | 1.00 |
| 28_Q | 32_E | 1.405 | 0.99 |
| 5_R | 8_S | 1.389 | 0.99 |
| 13_L | 53_G | 1.306 | 0.99 |
| 24_V | 51_A | 1.279 | 0.99 |
| 9_K | 52_L | 1.269 | 0.99 |
| 9_K | 54_V | 1.245 | 0.98 |
| 55_S | 58_W | 1.239 | 0.98 |
| 7_K | 11_I | 1.231 | 0.98 |
| 3_S | 37_G | 1.211 | 0.98 |
| 45_L | 56_V | 1.195 | 0.98 |
| 40_K | 43_R | 1.171 | 0.98 |
| 29_Q | 32_E | 1.152 | 0.97 |
| 49_A | 56_V | 1.148 | 0.97 |
| 16_N | 19_E | 1.115 | 0.96 |
| 15_L | 23_K | 1.109 | 0.96 |
| 20_L | 52_L | 1.100 | 0.96 |
| 54_V | 58_W | 1.097 | 0.96 |
| 17_Q | 32_E | 1.090 | 0.96 |
| 15_L | 19_E | 1.070 | 0.95 |
| 34_L | 41_R | 1.062 | 0.95 |
| 19_E | 22_Q | 1.052 | 0.95 |
| 56_V | 60_L | 1.037 | 0.94 |
| 26_T | 44_F | 1.034 | 0.94 |
| 30_S | 33_Q | 1.024 | 0.93 |
| 46_P | 50_S | 1.012 | 0.93 |
| 50_S | 62_G | 1.004 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1r69A | 1 | 0.913 | 99.4 | 0.205 | Contact Map |
| 4ndwA | 2 | 1 | 99.4 | 0.227 | Contact Map |
| 3u3wA | 2 | 0.9855 | 99.4 | 0.227 | Contact Map |
| 1y9qA | 1 | 1 | 99.4 | 0.23 | Contact Map |
| 4yarA | 1 | 1 | 99.4 | 0.234 | Contact Map |
| 3r1fA | 18 | 1 | 99.3 | 0.24 | Contact Map |
| 3mlfA | 5 | 1 | 99.3 | 0.242 | Contact Map |
| 2kpjA | 1 | 1 | 99.3 | 0.248 | Contact Map |
| 4mctA | 2 | 1 | 99.3 | 0.249 | Contact Map |
| 3op9A | 1 | 0.971 | 99.3 | 0.25 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)