| 9_1tenpdb |
| ID: | 1516869706 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 89 (89) | ||
| Sequences: | 1275 (921.7) | ||
| Seq/Len: | 14.326 | ||
| Nf(neff/√len): | 97.7 |
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: 14.326).
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 |
| 17_A | 87_F | 3.038 | 1.00 |
| 33_L | 71_L | 2.435 | 1.00 |
| 9_V | 85_E | 2.387 | 1.00 |
| 13_T | 16_T | 2.288 | 1.00 |
| 33_L | 56_Y | 2.210 | 1.00 |
| 35_Y | 58_I | 2.032 | 1.00 |
| 12_V | 87_F | 1.934 | 1.00 |
| 6_Q | 22_F | 1.895 | 1.00 |
| 73_S | 80_S | 1.874 | 1.00 |
| 61_L | 67_Y | 1.868 | 1.00 |
| 12_V | 17_A | 1.731 | 1.00 |
| 58_I | 69_V | 1.705 | 1.00 |
| 11_D | 18_L | 1.407 | 0.99 |
| 17_A | 69_V | 1.396 | 0.99 |
| 2_D | 26_A | 1.384 | 0.99 |
| 14_D | 64_D | 1.378 | 0.99 |
| 4_P | 73_S | 1.373 | 0.99 |
| 28_I | 73_S | 1.354 | 0.99 |
| 7_I | 19_I | 1.321 | 0.99 |
| 32_E | 79_S | 1.286 | 0.99 |
| 34_T | 58_I | 1.282 | 0.99 |
| 75_R | 78_M | 1.281 | 0.99 |
| 31_I | 73_S | 1.272 | 0.99 |
| 72_I | 82_P | 1.243 | 0.98 |
| 30_G | 74_R | 1.209 | 0.98 |
| 47_I | 50_T | 1.209 | 0.98 |
| 29_D | 78_M | 1.204 | 0.98 |
| 19_I | 69_V | 1.196 | 0.98 |
| 2_D | 80_S | 1.179 | 0.98 |
| 37_I | 65_T | 1.173 | 0.98 |
| 8_E | 62_K | 1.167 | 0.97 |
| 7_I | 71_L | 1.161 | 0.97 |
| 9_V | 87_F | 1.160 | 0.97 |
| 4_P | 80_S | 1.087 | 0.96 |
| 9_V | 19_I | 1.077 | 0.95 |
| 38_K | 86_T | 1.074 | 0.95 |
| 8_E | 20_T | 1.059 | 0.95 |
| 18_L | 55_Q | 1.045 | 0.94 |
| 66_E | 86_T | 1.034 | 0.94 |
| 68_E | 84_K | 1.024 | 0.93 |
| 10_K | 20_T | 1.024 | 0.93 |
| 29_D | 75_R | 1.011 | 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 | |
| 3csgA | 1 | 1 | 99.3 | 0.055 | Contact Map |
| 3qwqB | 1 | 0.9888 | 99.2 | 0.088 | Contact Map |
| 2rb8A | 1 | 1 | 99.2 | 0.091 | Contact Map |
| 4lpvA | 2 | 1 | 99.2 | 0.102 | Contact Map |
| 3teuA | 1 | 1 | 99.2 | 0.103 | Contact Map |
| 2h41A | 1 | 1 | 99.2 | 0.109 | Contact Map |
| 3b83A | 8 | 1 | 99.2 | 0.112 | Contact Map |
| 1j8kA | 1 | 1 | 99.1 | 0.115 | Contact Map |
| 2ha1A | 1 | 1 | 99.1 | 0.117 | Contact Map |
| 1qr4A | 2 | 0.9888 | 99.1 | 0.119 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)