| 1r69 |
| ID: | 1485911418 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 63 (62) | ||
| Sequences: | 46684 (33493.3) | ||
| Seq/Len: | 752.968 | ||
| Nf(neff/√len): | 4253.7 |
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: 752.968).
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 | 3.879 | 1.00 |
| 23_K | 51_A | 2.574 | 1.00 |
| 18_A | 28_Q | 2.193 | 1.00 |
| 9_K | 12_Q | 2.114 | 1.00 |
| 30_S | 34_L | 1.919 | 1.00 |
| 28_Q | 32_E | 1.819 | 1.00 |
| 9_K | 13_L | 1.787 | 1.00 |
| 33_Q | 38_K | 1.673 | 1.00 |
| 19_E | 23_K | 1.640 | 1.00 |
| 18_A | 22_Q | 1.471 | 1.00 |
| 15_L | 51_A | 1.470 | 1.00 |
| 8_S | 12_Q | 1.463 | 1.00 |
| 32_E | 36_N | 1.392 | 0.99 |
| 17_Q | 32_E | 1.391 | 0.99 |
| 29_Q | 32_E | 1.378 | 0.99 |
| 34_L | 44_F | 1.372 | 0.99 |
| 15_L | 19_E | 1.361 | 0.99 |
| 44_F | 47_E | 1.347 | 0.99 |
| 15_L | 23_K | 1.337 | 0.99 |
| 24_V | 51_A | 1.328 | 0.99 |
| 5_R | 8_S | 1.319 | 0.99 |
| 20_L | 31_I | 1.276 | 0.99 |
| 16_N | 19_E | 1.262 | 0.99 |
| 26_T | 44_F | 1.253 | 0.99 |
| 33_Q | 39_T | 1.201 | 0.98 |
| 5_R | 58_W | 1.192 | 0.98 |
| 20_L | 52_L | 1.146 | 0.97 |
| 29_Q | 33_Q | 1.131 | 0.97 |
| 7_K | 35_E | 1.084 | 0.96 |
| 5_R | 9_K | 1.063 | 0.95 |
| 30_S | 33_Q | 1.050 | 0.94 |
| 42_P | 60_L | 1.048 | 0.94 |
| 26_T | 30_S | 1.034 | 0.94 |
| 9_K | 54_V | 1.031 | 0.94 |
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 | |
| 1y9qA | 1 | 1 | 98.4 | -0.105 | Contact Map |
| 4pu7B | 2 | 0.9365 | 98.4 | -0.095 | Contact Map |
| 4ndwA | 2 | 1 | 98.4 | -0.095 | Contact Map |
| 2bnmA | 2 | 1 | 98.4 | -0.09 | Contact Map |
| 4o8bA | 1 | 1 | 98.4 | -0.085 | Contact Map |
| 1r69A | 1 | 1 | 98.3 | -0.079 | Contact Map |
| 3ivpA | 4 | 1 | 98.3 | -0.079 | Contact Map |
| 2p5tA | 4 | 0.0159 | 98.3 | -0.076 | Contact Map |
| 4yarA | 1 | 1 | 98.3 | -0.075 | Contact Map |
| 3r1fA | 18 | 1 | 98.3 | -0.075 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)