| Subset500RandomFix |
| ID: | 1478344766 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 92 (92) | ||
| Sequences: | 500 (500) | ||
| Seq/Len: | 5.435 | ||
| Nf(neff/√len): | 52.1 |
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: 5.435).
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 |
| 39_K | 77_L | 1.766 | 1.00 |
| 13_K | 34_L | 1.543 | 0.99 |
| 8_M | 38_N | 1.479 | 0.99 |
| 5_C | 85_T | 1.479 | 0.99 |
| 29_L | 69_N | 1.457 | 0.98 |
| 2_I | 79_Y | 1.442 | 0.98 |
| 51_T | 85_T | 1.413 | 0.98 |
| 32_N | 68_G | 1.408 | 0.98 |
| 17_N | 50_I | 1.377 | 0.97 |
| 11_G | 89_P | 1.354 | 0.97 |
| 1_K | 73_I | 1.354 | 0.97 |
| 36_T | 40_Y | 1.325 | 0.97 |
| 27_C | 43_G | 1.309 | 0.96 |
| 39_K | 65_K | 1.288 | 0.96 |
| 9_K | 44_F | 1.283 | 0.96 |
| 42_P | 82_V | 1.257 | 0.95 |
| 7_Y | 10_W | 1.250 | 0.95 |
| 40_Y | 61_Q | 1.221 | 0.94 |
| 36_T | 85_T | 1.214 | 0.94 |
| 14_A | 69_N | 1.213 | 0.94 |
| 29_L | 90_Q | 1.209 | 0.94 |
| 2_I | 17_N | 1.203 | 0.93 |
| 2_I | 45_D | 1.200 | 0.93 |
| 11_G | 62_L | 1.190 | 0.93 |
| 49_D | 89_P | 1.182 | 0.93 |
| 58_T | 78_L | 1.179 | 0.92 |
| 18_T | 43_G | 1.176 | 0.92 |
| 4_V | 17_N | 1.157 | 0.91 |
| 1_K | 75_F | 1.139 | 0.91 |
| 63_S | 66_F | 1.128 | 0.90 |
| 70_V | 90_Q | 1.114 | 0.89 |
| 29_L | 59_E | 1.108 | 0.89 |
| 13_K | 65_K | 1.108 | 0.89 |
| 40_Y | 91_Q | 1.100 | 0.89 |
| 43_G | 51_T | 1.100 | 0.89 |
| 17_N | 38_N | 1.096 | 0.88 |
| 9_K | 51_T | 1.070 | 0.87 |
| 7_Y | 53_A | 1.058 | 0.86 |
| 10_W | 74_W | 1.057 | 0.86 |
| 12_D | 28_Q | 1.057 | 0.86 |
| 36_T | 55_K | 1.055 | 0.86 |
| 54_S | 90_Q | 1.053 | 0.85 |
| 40_Y | 82_V | 1.052 | 0.85 |
| 86_V | 92_L | 1.051 | 0.85 |
| 44_F | 82_V | 1.049 | 0.85 |
| 27_C | 30_F | 1.049 | 0.85 |
| 2_I | 60_A | 1.049 | 0.85 |
| 5_C | 16_I | 1.032 | 0.84 |
| 23_S | 50_I | 1.022 | 0.83 |
| 69_N | 76_D | 1.013 | 0.82 |
| 48_V | 78_L | 1.011 | 0.82 |
| 15_P | 80_D | 1.010 | 0.82 |
| 38_N | 83_Q | 1.008 | 0.82 |
| 5_C | 81_R | 1.004 | 0.82 |
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 | |
| 1qysA | 1 | 1 | 99.7 | -0.485 | Contact Map |
| 4kyzA | 4 | 1 | 99.2 | -0.33 | Contact Map |
| 2gjhA | 2 | 0.5326 | 98.1 | -0.027 | Contact Map |
| 2mblA | 1 | 1 | 97.7 | 0.08 | Contact Map |
| 2jvfA | 1 | 1 | 2.1 | 0.79 | Contact Map |
| 2wrgI | 3 | 0 | 0.3 | 0.888 | Contact Map |
| 3gf6A | 2 | 0.6848 | 0.3 | 0.889 | Contact Map |
| 1fmeA | 1 | 0.3043 | 0.3 | 0.892 | Contact Map |
| 5bq9A | 2 | 0 | 0.2 | 0.895 | Contact Map |
| 2v0xA | 2 | 0.4457 | 0.2 | 0.896 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)