| HsaB160- |
| ID: | 1474642660 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 104 (98) | ||
| Sequences: | 5548 (4091.7) | ||
| Seq/Len: | 56.612 | ||
| Nf(neff/√len): | 413.3 |
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: 56.612).
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 |
| 43_D | 49_L | 2.960 | 1.00 |
| 56_S | 63_D | 2.819 | 1.00 |
| 39_R | 90_E | 2.404 | 1.00 |
| 39_R | 52_T | 2.321 | 1.00 |
| 43_D | 47_H | 2.246 | 1.00 |
| 41_T | 50_A | 2.228 | 1.00 |
| 65_E | 68_A | 2.203 | 1.00 |
| 35_V | 96_D | 2.189 | 1.00 |
| 51_V | 67_Q | 2.150 | 1.00 |
| 39_R | 54_V | 2.093 | 1.00 |
| 33_Q | 99_L | 2.058 | 1.00 |
| 32_R | 59_L | 2.055 | 1.00 |
| 43_D | 88_T | 2.013 | 1.00 |
| 37_Q | 55_S | 1.997 | 1.00 |
| 41_T | 90_E | 1.875 | 1.00 |
| 67_Q | 71_K | 1.833 | 1.00 |
| 32_R | 61_S | 1.803 | 1.00 |
| 39_R | 92_T | 1.783 | 1.00 |
| 27_A | 61_S | 1.767 | 1.00 |
| 51_V | 71_K | 1.753 | 1.00 |
| 57_A | 62_L | 1.702 | 1.00 |
| 35_V | 94_P | 1.603 | 1.00 |
| 26_D | 30_L | 1.538 | 1.00 |
| 58_G | 63_D | 1.520 | 1.00 |
| 37_Q | 94_P | 1.501 | 1.00 |
| 57_A | 63_D | 1.490 | 1.00 |
| 41_T | 88_T | 1.451 | 1.00 |
| 48_V | 51_V | 1.434 | 1.00 |
| 44_R | 88_T | 1.389 | 0.99 |
| 27_A | 32_R | 1.339 | 0.99 |
| 26_D | 61_S | 1.333 | 0.99 |
| 16_R | 72_R | 1.323 | 0.99 |
| 38_V | 70_V | 1.309 | 0.99 |
| 25_K | 29_R | 1.305 | 0.99 |
| 21_K | 69_L | 1.304 | 0.99 |
| 36_G | 53_L | 1.284 | 0.99 |
| 18_N | 21_K | 1.255 | 0.99 |
| 66_I | 97_F | 1.238 | 0.98 |
| 54_V | 92_T | 1.225 | 0.98 |
| 14_S | 18_N | 1.211 | 0.98 |
| 76_L | 79_P | 1.198 | 0.98 |
| 37_Q | 92_T | 1.156 | 0.97 |
| 49_L | 88_T | 1.154 | 0.97 |
| 51_V | 70_V | 1.134 | 0.97 |
| 23_Y | 97_F | 1.121 | 0.97 |
| 38_V | 66_I | 1.121 | 0.97 |
| 91_L | 94_P | 1.101 | 0.96 |
| 25_K | 28_L | 1.090 | 0.96 |
| 40_F | 70_V | 1.074 | 0.95 |
| 65_E | 69_L | 1.058 | 0.95 |
| 58_G | 61_S | 1.051 | 0.94 |
| 12_R | 15_G | 1.030 | 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
- 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 | |
| 2m2kA | 1 | 0.9904 | 99.7 | 0.136 | Contact Map |
| 2k9kA | 1 | 0.9423 | 99.4 | 0.252 | Contact Map |
| 1lr0A | 1 | 0.9615 | 99.4 | 0.272 | Contact Map |
| 2grxC | 2 | 0.75 | 99.3 | 0.302 | Contact Map |
| 1u07A | 2 | 0.8365 | 99.2 | 0.349 | Contact Map |
| 4g7xB | 1 | 0.875 | 99 | 0.385 | Contact Map |
| 1tolA | 1 | 0.875 | 99 | 0.393 | Contact Map |
| 3f42A | 2 | 0.8654 | 9.4 | 0.871 | Contact Map |
| 1lshA | 1 | 0.9904 | 8.5 | 0.873 | Contact Map |
| 2idlA | 2 | 0.6154 | 8 | 0.875 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)