| gpJ2 |
| ID: | 1479767266 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (104) | ||
| Sequences: | 155 (130.2) | ||
| Seq/Len: | 1.490 | ||
| Nf(neff/√len): | 12.8 |
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: 1.490).
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 |
| 8_N | 15_C | 3.319 | 1.00 |
| 8_N | 17_I | 2.689 | 1.00 |
| 11_I | 15_C | 2.361 | 1.00 |
| 10_T | 15_C | 2.294 | 0.99 |
| 9_V | 15_C | 2.274 | 0.99 |
| 8_N | 11_I | 2.149 | 0.99 |
| 10_T | 17_I | 2.057 | 0.98 |
| 11_I | 17_I | 1.963 | 0.98 |
| 6_L | 15_C | 1.928 | 0.97 |
| 55_D | 59_F | 1.893 | 0.97 |
| 17_I | 21_L | 1.887 | 0.97 |
| 2_N | 5_T | 1.844 | 0.96 |
| 9_V | 14_N | 1.756 | 0.95 |
| 9_V | 17_I | 1.752 | 0.95 |
| 20_K | 25_Q | 1.700 | 0.93 |
| 6_L | 17_I | 1.643 | 0.92 |
| 2_N | 7_N | 1.631 | 0.91 |
| 6_L | 10_T | 1.625 | 0.91 |
| 6_L | 13_E | 1.471 | 0.85 |
| 8_N | 13_E | 1.456 | 0.84 |
| 12_N | 18_K | 1.423 | 0.82 |
| 6_L | 11_I | 1.396 | 0.80 |
| 26_I | 30_I | 1.375 | 0.79 |
| 53_I | 61_R | 1.352 | 0.77 |
| 7_N | 11_I | 1.346 | 0.77 |
| 16_Q | 22_S | 1.345 | 0.76 |
| 22_S | 26_I | 1.336 | 0.76 |
| 65_I | 68_V | 1.327 | 0.75 |
| 101_E | 104_X | 1.317 | 0.74 |
| 13_E | 17_I | 1.275 | 0.71 |
| 9_V | 13_E | 1.221 | 0.66 |
| 7_N | 12_N | 1.189 | 0.63 |
| 55_D | 61_R | 1.186 | 0.63 |
| 4_G | 7_N | 1.174 | 0.62 |
| 2_N | 49_I | 1.139 | 0.58 |
| 23_A | 26_I | 1.133 | 0.58 |
| 7_N | 15_C | 1.110 | 0.55 |
| 48_T | 63_V | 1.108 | 0.55 |
| 12_N | 15_C | 1.106 | 0.55 |
| 32_K | 61_R | 1.099 | 0.54 |
| 50_T | 67_P | 1.098 | 0.54 |
| 10_T | 13_E | 1.057 | 0.50 |
| 39_P | 93_L | 1.041 | 0.48 |
| 18_K | 24_N | 1.038 | 0.48 |
| 20_K | 26_I | 1.031 | 0.47 |
| 8_N | 12_N | 1.008 | 0.45 |
| 53_I | 59_F | 1.008 | 0.45 |
| 95_V | 99_G | 1.008 | 0.45 |
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 | |
| 3rwxA | 1 | 0.4057 | 1.8 | 0.93 | Contact Map |
| 2h0eA | 2 | 0.7075 | 1.5 | 0.933 | Contact Map |
| 4x5pA | 1 | 0 | 1.3 | 0.935 | Contact Map |
| 3fcgA | 2 | 0.3208 | 1.3 | 0.935 | Contact Map |
| 3zm8A | 1 | 0.7736 | 1.2 | 0.937 | Contact Map |
| 1hr0W | 1 | 0.4623 | 1.1 | 0.938 | Contact Map |
| 4qs4A | 1 | 0 | 1.1 | 0.939 | Contact Map |
| 2ra9A | 1 | 0.1698 | 1 | 0.939 | Contact Map |
| 3wnoA | 2 | 0.8113 | 1 | 0.939 | Contact Map |
| 3i4oA | 2 | 0.4717 | 1 | 0.94 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)