| d3qijb2 |
| ID: | 1450782389 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (106) | ||
| Sequences: | 1059 (650.1) | ||
| Seq/Len: | 9.991 | ||
| Nf(neff/√len): | 63.1 |
HHblits Results: (2015_06)
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: 9.991).
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 |
| 59_Y | 81_H | 3.727 | 1.00 |
| 49_D | 86_S | 3.050 | 1.00 |
| 23_I | 96_F | 2.344 | 1.00 |
| 40_S | 84_Y | 2.309 | 1.00 |
| 22_D | 27_R | 2.178 | 1.00 |
| 13_Y | 93_D | 2.093 | 1.00 |
| 8_E | 11_T | 2.063 | 1.00 |
| 73_L | 77_V | 1.986 | 1.00 |
| 87_M | 95_E | 1.898 | 1.00 |
| 21_Q | 25_A | 1.697 | 1.00 |
| 9_D | 12_R | 1.607 | 1.00 |
| 52_P | 55_H | 1.563 | 1.00 |
| 3_P | 6_L | 1.540 | 1.00 |
| 37_L | 41_Y | 1.525 | 1.00 |
| 103_L | 106_Y | 1.495 | 1.00 |
| 43_I | 60_V | 1.486 | 1.00 |
| 36_A | 73_L | 1.423 | 1.00 |
| 80_L | 83_S | 1.414 | 1.00 |
| 6_L | 11_T | 1.390 | 0.99 |
| 18_Q | 22_D | 1.350 | 0.99 |
| 37_L | 40_S | 1.337 | 0.99 |
| 90_A | 93_D | 1.246 | 0.98 |
| 44_Q | 49_D | 1.233 | 0.98 |
| 16_C | 93_D | 1.231 | 0.98 |
| 1_P | 5_Q | 1.228 | 0.98 |
| 16_C | 20_R | 1.218 | 0.98 |
| 19_L | 97_L | 1.218 | 0.98 |
| 99_N | 102_K | 1.213 | 0.98 |
| 13_Y | 17_L | 1.198 | 0.98 |
| 16_C | 42_T | 1.193 | 0.98 |
| 11_T | 15_L | 1.190 | 0.98 |
| 55_H | 58_D | 1.186 | 0.98 |
| 98_E | 102_K | 1.176 | 0.98 |
| 78_M | 81_H | 1.151 | 0.97 |
| 6_L | 12_R | 1.148 | 0.97 |
| 8_E | 12_R | 1.145 | 0.97 |
| 42_T | 96_F | 1.140 | 0.97 |
| 54_L | 59_Y | 1.121 | 0.97 |
| 22_D | 26_G | 1.115 | 0.96 |
| 89_P | 93_D | 1.100 | 0.96 |
| 88_T | 91_Q | 1.100 | 0.96 |
| 50_Y | 55_H | 1.099 | 0.96 |
| 34_T | 37_L | 1.094 | 0.96 |
| 97_L | 106_Y | 1.082 | 0.95 |
| 47_L | 59_Y | 1.076 | 0.95 |
| 74_E | 77_V | 1.068 | 0.95 |
| 95_E | 98_E | 1.061 | 0.95 |
| 86_S | 93_D | 1.053 | 0.95 |
| 101_K | 105_M | 1.048 | 0.94 |
| 44_Q | 48_G | 1.039 | 0.94 |
| 67_P | 71_K | 1.035 | 0.94 |
| 3_P | 101_K | 1.020 | 0.93 |
| 20_R | 46_E | 1.018 | 0.93 |
| 15_L | 20_R | 1.013 | 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 | |
| 2j0jA | 1 | 0.9906 | 99.9 | 0.108 | Contact Map |
| 3qijA | 2 | 1 | 99.9 | 0.188 | Contact Map |
| 2i1jA | 1 | 1 | 99.9 | 0.215 | Contact Map |
| 1h4rA | 2 | 1 | 99.9 | 0.216 | Contact Map |
| 4yl8A | 1 | 1 | 99.9 | 0.219 | Contact Map |
| 1mixA | 1 | 1 | 99.9 | 0.224 | Contact Map |
| 4f7gA | 1 | 0.9245 | 99.9 | 0.253 | Contact Map |
| 4hdoA | 1 | 1 | 99.9 | 0.256 | Contact Map |
| 4ekuA | 1 | 1 | 99.8 | 0.261 | Contact Map |
| 3ivfA | 1 | 0.9906 | 99.8 | 0.264 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)