| test2 |
| ID: | 1463991644 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 61 (59) | ||
| Sequences: | 2216 (1591.9) | ||
| Seq/Len: | 37.559 | ||
| Nf(neff/√len): | 207.2 |
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: 37.559).
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 |
| 14_K | 18_E | 4.583 | 1.00 |
| 19_L | 23_T | 2.767 | 1.00 |
| 56_V | 59_E | 2.325 | 1.00 |
| 5_T | 12_K | 1.972 | 1.00 |
| 12_K | 34_G | 1.683 | 1.00 |
| 15_L | 25_V | 1.624 | 1.00 |
| 13_P | 17_K | 1.612 | 1.00 |
| 9_E | 13_P | 1.479 | 1.00 |
| 1_M | 25_V | 1.466 | 1.00 |
| 3_L | 28_H | 1.401 | 0.99 |
| 1_M | 8_N | 1.372 | 0.99 |
| 12_K | 16_E | 1.308 | 0.99 |
| 42_K | 51_T | 1.277 | 0.99 |
| 13_P | 21_P | 1.266 | 0.99 |
| 28_H | 50_H | 1.261 | 0.99 |
| 34_G | 37_P | 1.242 | 0.98 |
| 5_T | 29_E | 1.190 | 0.98 |
| 30_F | 46_G | 1.178 | 0.98 |
| 17_K | 20_K | 1.169 | 0.97 |
| 8_N | 55_Y | 1.123 | 0.97 |
| 1_M | 27_S | 1.118 | 0.96 |
| 45_D | 50_H | 1.113 | 0.96 |
| 17_K | 58_G | 1.107 | 0.96 |
| 19_L | 25_V | 1.083 | 0.96 |
| 36_N | 39_E | 1.072 | 0.95 |
| 13_P | 37_P | 1.038 | 0.94 |
| 47_N | 50_H | 1.029 | 0.94 |
| 4_L | 30_F | 1.027 | 0.94 |
| 4_L | 7_V | 1.019 | 0.93 |
| 38_K | 56_V | 1.018 | 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
- 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 | |
| 5bxyA | 2 | 0 | 80.2 | 0.505 | Contact Map |
| 4rv9A | 1 | 0.9508 | 79.4 | 0.509 | Contact Map |
| 4e2xA | 1 | 0.9508 | 76.4 | 0.522 | Contact Map |
| 2pxxA | 1 | 1 | 67.2 | 0.553 | Contact Map |
| 3tmaA | 1 | 0.9508 | 59.7 | 0.574 | Contact Map |
| 2qe6A | 2 | 1 | 58.5 | 0.577 | Contact Map |
| 2kw5A | 1 | 0.9016 | 58.3 | 0.577 | Contact Map |
| 3dliA | 3 | 0.9344 | 53.8 | 0.589 | Contact Map |
| 1ws6A | 1 | 0.8689 | 51.7 | 0.594 | Contact Map |
| 1l3iA | 6 | 0.9672 | 50.8 | 0.596 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)