| d3zo7f_ |
| ID: | 1448598843 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 91 (90) | ||
| Sequences: | 364 (209.5) | ||
| Seq/Len: | 4.044 | ||
| Nf(neff/√len): | 22.1 |
HHblits Results: (2015_06)
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: 4.044).
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 |
| 39_Q | 63_E | 3.322 | 1.00 |
| 31_S | 43_L | 2.868 | 1.00 |
| 22_R | 26_S | 2.496 | 1.00 |
| 33_T | 37_Q | 2.464 | 1.00 |
| 30_R | 70_S | 2.449 | 1.00 |
| 4_L | 53_I | 2.048 | 1.00 |
| 18_R | 21_E | 1.982 | 1.00 |
| 19_E | 22_R | 1.976 | 1.00 |
| 62_D | 85_S | 1.921 | 1.00 |
| 62_D | 66_E | 1.852 | 1.00 |
| 11_L | 15_L | 1.832 | 1.00 |
| 23_L | 30_R | 1.806 | 1.00 |
| 41_R | 86_H | 1.726 | 0.99 |
| 10_N | 78_T | 1.706 | 0.99 |
| 4_L | 46_T | 1.597 | 0.99 |
| 6_R | 80_D | 1.589 | 0.99 |
| 11_L | 20_E | 1.547 | 0.98 |
| 20_E | 24_K | 1.538 | 0.98 |
| 15_L | 76_Y | 1.520 | 0.98 |
| 61_H | 83_P | 1.498 | 0.98 |
| 39_Q | 67_I | 1.449 | 0.97 |
| 59_N | 63_E | 1.359 | 0.95 |
| 63_E | 67_I | 1.355 | 0.95 |
| 39_Q | 59_N | 1.295 | 0.93 |
| 16_D | 19_E | 1.290 | 0.93 |
| 69_W | 74_F | 1.250 | 0.91 |
| 15_L | 20_E | 1.248 | 0.91 |
| 18_R | 70_S | 1.236 | 0.91 |
| 46_T | 53_I | 1.225 | 0.90 |
| 4_L | 85_S | 1.197 | 0.89 |
| 33_T | 36_E | 1.188 | 0.88 |
| 3_Y | 61_H | 1.186 | 0.88 |
| 85_S | 90_R | 1.132 | 0.85 |
| 29_A | 33_T | 1.113 | 0.84 |
| 86_H | 90_R | 1.093 | 0.82 |
| 45_R | 65_H | 1.060 | 0.79 |
| 49_K | 80_D | 1.051 | 0.78 |
| 7_M | 56_F | 1.044 | 0.78 |
| 6_R | 46_T | 1.003 | 0.74 |
| 25_A | 29_A | 1.002 | 0.74 |
| 7_M | 50_Y | 1.002 | 0.74 |
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 | |
| 1mliA | 10 | 1 | 100 | 0.152 | Contact Map |
| 3znuA | 10 | 1 | 100 | 0.196 | Contact Map |
| 1s7iA | 1 | 0.989 | 95.5 | 0.835 | Contact Map |
| 1mwqA | 2 | 0.9341 | 94 | 0.848 | Contact Map |
| 4lbhA | 1 | 0.8901 | 93.4 | 0.851 | Contact Map |
| 4oi3A | 2 | 0.8681 | 47.8 | 0.905 | Contact Map |
| 3pt1A | 1 | 0.5604 | 18.2 | 0.923 | Contact Map |
| 2gwnA | 1 | 0.8901 | 15 | 0.927 | Contact Map |
| 1q7sA | 2 | 0.956 | 15 | 0.927 | Contact Map |
| 3ziuA | 2 | 0.4176 | 11.7 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)