| HAB-17_-15 |
| ID: | 1447308256 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (56) | ||
| Sequences: | 2179 (2179) | ||
| Seq/Len: | 38.911 | ||
| Nf(neff/√len): | 291.2 |
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: 38.911).
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 |
| 18_K | 44_T | 1.581 | 1.00 |
| 10_K | 14_E | 1.500 | 1.00 |
| 24_G | 51_T | 1.421 | 1.00 |
| 17_I | 34_A | 1.403 | 0.99 |
| 8_N | 54_V | 1.386 | 0.99 |
| 4_K | 40_E | 1.351 | 0.99 |
| 11_Q | 37_K | 1.337 | 0.99 |
| 43_W | 48_E | 1.317 | 0.99 |
| 3_Y | 37_K | 1.315 | 0.99 |
| 24_G | 28_K | 1.305 | 0.99 |
| 24_G | 38_T | 1.299 | 0.99 |
| 19_E | 44_T | 1.215 | 0.98 |
| 41_G | 45_Y | 1.214 | 0.98 |
| 18_K | 22_D | 1.200 | 0.98 |
| 1_T | 42_V | 1.194 | 0.98 |
| 36_A | 54_V | 1.190 | 0.98 |
| 10_K | 48_E | 1.185 | 0.98 |
| 7_L | 48_E | 1.137 | 0.97 |
| 12_A | 43_W | 1.134 | 0.97 |
| 14_E | 26_A | 1.107 | 0.96 |
| 1_T | 10_K | 1.092 | 0.96 |
| 26_A | 50_K | 1.083 | 0.96 |
| 31_K | 52_F | 1.073 | 0.95 |
| 11_Q | 15_E | 1.068 | 0.95 |
| 27_E | 55_T | 1.057 | 0.95 |
| 11_Q | 27_E | 1.057 | 0.95 |
| 37_K | 55_T | 1.054 | 0.95 |
| 32_L | 39_V | 1.053 | 0.95 |
| 8_N | 53_T | 1.053 | 0.95 |
| 33_I | 56_E | 1.049 | 0.94 |
| 42_V | 49_I | 1.034 | 0.94 |
| 22_D | 34_A | 1.024 | 0.93 |
| 19_E | 27_E | 1.015 | 0.93 |
| 13_K | 32_L | 1.015 | 0.93 |
| 4_K | 32_L | 1.013 | 0.93 |
| 3_Y | 52_F | 1.008 | 0.93 |
| 32_L | 48_E | 1.007 | 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 | |
| 2fs1A | 1 | 1 | 68.6 | -0.036 | Contact Map |
| 2jwsA | 1 | 1 | 32.2 | 0.172 | Contact Map |
| 1gjsA | 1 | 0.9643 | 23.5 | 0.228 | Contact Map |
| 2j5yA | 2 | 0.9643 | 17.5 | 0.27 | Contact Map |
| 1pn5A | 1 | 0 | 0.5 | 0.676 | Contact Map |
| 1s2xA | 1 | 1 | 0.5 | 0.696 | Contact Map |
| 3jszA | 1 | 0.9464 | 0.4 | 0.699 | Contact Map |
| 4w20L | 1 | 0.4821 | 0.4 | 0.712 | Contact Map |
| 2khuA | 1 | 0 | 0.4 | 0.715 | Contact Map |
| 2es9A | 1 | 0.8214 | 0.4 | 0.719 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)