| 1RA9 |
| ID: | 1429470643 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 71 (67) | ||
| Sequences: | 3563 (1873.8) | ||
| Seq/Len: | 53.179 | ||
| Nf(neff/√len): | 228.9 |
HHblits Results: (2013_03)
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: 53.179).
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 |
| 32_V | 67_V | 3.479 | 1.00 |
| 56_E | 65_A | 3.329 | 1.00 |
| 54_S | 66_N | 2.599 | 1.00 |
| 64_A | 67_V | 2.498 | 1.00 |
| 24_V | 50_K | 2.260 | 1.00 |
| 6_T | 52_T | 2.064 | 1.00 |
| 23_P | 26_G | 1.974 | 1.00 |
| 23_P | 53_F | 1.949 | 1.00 |
| 23_P | 27_S | 1.860 | 1.00 |
| 8_L | 50_K | 1.838 | 1.00 |
| 10_K | 29_D | 1.829 | 1.00 |
| 6_T | 50_K | 1.804 | 1.00 |
| 57_S | 62_P | 1.582 | 1.00 |
| 36_A | 65_A | 1.564 | 1.00 |
| 49_Q | 70_T | 1.534 | 1.00 |
| 34_F | 43_R | 1.497 | 1.00 |
| 14_A | 46_F | 1.458 | 1.00 |
| 5_M | 23_P | 1.453 | 1.00 |
| 32_V | 45_L | 1.434 | 1.00 |
| 52_T | 69_I | 1.375 | 0.99 |
| 6_T | 24_V | 1.342 | 0.99 |
| 34_F | 37_I | 1.337 | 0.99 |
| 58_G | 63_A | 1.329 | 0.99 |
| 9_V | 51_V | 1.254 | 0.99 |
| 38_Q | 66_N | 1.235 | 0.98 |
| 21_I | 51_V | 1.201 | 0.98 |
| 7_G | 21_I | 1.180 | 0.98 |
| 58_G | 61_G | 1.174 | 0.98 |
| 8_L | 22_S | 1.145 | 0.97 |
| 12_F | 34_F | 1.123 | 0.97 |
| 30_V | 55_V | 1.101 | 0.96 |
| 37_I | 45_L | 1.086 | 0.96 |
| 10_K | 22_S | 1.083 | 0.96 |
| 20_F | 31_F | 1.077 | 0.95 |
| 9_V | 12_F | 1.029 | 0.94 |
| 37_I | 43_R | 1.026 | 0.94 |
| 14_A | 42_F | 1.017 | 0.93 |
| 46_F | 49_Q | 1.004 | 0.93 |
| 5_M | 25_D | 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 | |
| 3i2zB | 2 | 0.9859 | 99.8 | 0.051 | Contact Map |
| 2lssA | 1 | 0.9859 | 99.8 | 0.061 | Contact Map |
| 3camA | 2 | 0.9437 | 99.8 | 0.072 | Contact Map |
| 1h95A | 1 | 1 | 99.8 | 0.072 | Contact Map |
| 3uljA | 2 | 1 | 99.8 | 0.092 | Contact Map |
| 1c9oA | 2 | 0.9296 | 99.8 | 0.096 | Contact Map |
| 2k5nA | 1 | 0.9296 | 99.8 | 0.097 | Contact Map |
| 2lxjA | 1 | 0.9296 | 99.8 | 0.103 | Contact Map |
| 3ts2A | 2 | 1 | 99.8 | 0.115 | Contact Map |
| 1g6pA | 1 | 0.9296 | 99.8 | 0.115 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)