| ga-1tf0 |
| ID: | 1429128284 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 53 (43) | ||
| Sequences: | 455 (386) | ||
| Seq/Len: | 10.581 | ||
| Nf(neff/√len): | 58.9 |
Jackhmmer Results: (2015_01_07)
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: 10.581).
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 |
| 15_I | 33_N | 2.809 | 1.00 |
| 18_L | 32_I | 2.585 | 1.00 |
| 6_L | 38_V | 2.313 | 1.00 |
| 19_K | 29_F | 2.282 | 1.00 |
| 28_Y | 31_A | 1.780 | 1.00 |
| 37_T | 40_E | 1.775 | 1.00 |
| 8_K | 12_E | 1.632 | 1.00 |
| 38_V | 42_N | 1.603 | 1.00 |
| 6_L | 9_N | 1.586 | 1.00 |
| 10_A | 38_V | 1.526 | 1.00 |
| 14_A | 32_I | 1.408 | 1.00 |
| 16_A | 20_K | 1.408 | 1.00 |
| 9_N | 13_D | 1.336 | 0.99 |
| 41_V | 44_L | 1.213 | 0.98 |
| 36_K | 43_A | 1.130 | 0.97 |
| 30_N | 34_K | 1.122 | 0.97 |
| 26_D | 30_N | 1.114 | 0.96 |
| 40_E | 44_L | 1.104 | 0.96 |
| 17_E | 20_K | 1.103 | 0.96 |
| 27_F | 31_A | 1.060 | 0.95 |
| 7_L | 47_E | 1.051 | 0.94 |
| 28_Y | 44_L | 1.041 | 0.94 |
| 27_F | 30_N | 1.014 | 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 | |
| 2j5yA | 2 | 1 | 98.7 | 0.237 | Contact Map |
| 2fs1A | 1 | 0.9811 | 98.5 | 0.276 | Contact Map |
| 1gjsA | 1 | 0.9811 | 97.9 | 0.387 | Contact Map |
| 2jwsA | 1 | 0.9811 | 95.9 | 0.543 | Contact Map |
| 2dgjA | 2 | 0.9811 | 93.8 | 0.593 | Contact Map |
| 4kjmA | 2 | 0.9434 | 90.4 | 0.633 | Contact Map |
| 3bzcA | 1 | 1 | 22.9 | 0.785 | Contact Map |
| 4efaG | 1 | 0.9811 | 8.5 | 0.822 | Contact Map |
| 4p72C | 2 | 0 | 7 | 0.83 | Contact Map |
| 3psiA | 1 | 0.8679 | 6.7 | 0.83 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)