| fastRelax_offset_4 |
| ID: | 1507196381 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 614 (288.4) | ||
| Seq/Len: | 7.057 | ||
| Nf(neff/√len): | 30.9 |
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: 7.057).
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 |
| 16_G | 19_A | 2.007 | 1.00 |
| 36_D | 41_R | 1.864 | 1.00 |
| 1_D | 86_I | 1.856 | 1.00 |
| 65_I | 69_N | 1.594 | 1.00 |
| 29_F | 76_S | 1.536 | 0.99 |
| 16_G | 27_A | 1.531 | 0.99 |
| 14_I | 17_A | 1.479 | 0.99 |
| 51_R | 86_I | 1.458 | 0.99 |
| 38_N | 82_V | 1.446 | 0.99 |
| 32_L | 38_N | 1.377 | 0.99 |
| 4_R | 44_V | 1.366 | 0.98 |
| 75_R | 79_A | 1.360 | 0.98 |
| 77_L | 82_V | 1.300 | 0.98 |
| 3_S | 62_L | 1.294 | 0.98 |
| 53_L | 70_A | 1.282 | 0.97 |
| 22_L | 69_N | 1.279 | 0.97 |
| 2_D | 17_A | 1.241 | 0.97 |
| 8_T | 12_I | 1.232 | 0.97 |
| 71_V | 81_F | 1.228 | 0.96 |
| 44_V | 50_I | 1.220 | 0.96 |
| 20_R | 24_E | 1.199 | 0.96 |
| 55_V | 86_I | 1.174 | 0.95 |
| 53_L | 66_H | 1.172 | 0.95 |
| 18_A | 80_L | 1.172 | 0.95 |
| 8_T | 37_L | 1.167 | 0.95 |
| 29_F | 80_L | 1.165 | 0.95 |
| 47_D | 51_R | 1.156 | 0.95 |
| 16_G | 20_R | 1.124 | 0.93 |
| 25_L | 80_L | 1.123 | 0.93 |
| 28_A | 56_P | 1.107 | 0.93 |
| 19_A | 73_T | 1.107 | 0.93 |
| 7_I | 28_A | 1.083 | 0.92 |
| 24_E | 65_I | 1.080 | 0.92 |
| 66_H | 72_L | 1.080 | 0.92 |
| 52_M | 68_S | 1.079 | 0.91 |
| 44_V | 55_V | 1.070 | 0.91 |
| 20_R | 47_D | 1.066 | 0.91 |
| 8_T | 28_A | 1.062 | 0.91 |
| 76_S | 84_Y | 1.050 | 0.90 |
| 4_R | 14_I | 1.048 | 0.90 |
| 48_G | 52_M | 1.040 | 0.89 |
| 21_L | 56_P | 1.029 | 0.89 |
| 37_L | 70_A | 1.029 | 0.89 |
| 27_A | 44_V | 1.025 | 0.88 |
| 15_N | 64_V | 1.024 | 0.88 |
| 18_A | 86_I | 1.018 | 0.88 |
| 11_P | 47_D | 1.012 | 0.88 |
| 57_R | 84_Y | 1.011 | 0.88 |
| 6_L | 34_L | 1.007 | 0.87 |
| 7_I | 33_I | 1.002 | 0.87 |
| 23_A | 61_F | 1.000 | 0.87 |
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 | |
| 1kklH | 3 | 1 | 97.2 | 0.777 | Contact Map |
| 1ka5A | 1 | 1 | 97.2 | 0.778 | Contact Map |
| 1pchA | 1 | 0.9885 | 97.2 | 0.778 | Contact Map |
| 1ptfA | 1 | 1 | 97 | 0.784 | Contact Map |
| 3ccdA | 2 | 0.977 | 97 | 0.785 | Contact Map |
| 1sphA | 2 | 0.9885 | 96.9 | 0.786 | Contact Map |
| 1y51A | 3 | 0.9885 | 96.9 | 0.786 | Contact Map |
| 3ihsA | 2 | 0.931 | 96.8 | 0.79 | Contact Map |
| 3le1A | 2 | 0.9885 | 96.3 | 0.8 | Contact Map |
| 3nasA | 2 | 0.6667 | 5.8 | 0.931 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)