| msa |
| ID: | 1485848694 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (100) | ||
| Sequences: | 9716 (6268.3) | ||
| Seq/Len: | 97.160 | ||
| Nf(neff/√len): | 626.8 |
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: 97.160).
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 |
| 44_V | 85_A | 2.539 | 1.00 |
| 17_T | 59_Q | 2.401 | 1.00 |
| 11_V | 46_N | 2.339 | 1.00 |
| 12_F | 71_Y | 2.213 | 1.00 |
| 10_C | 23_I | 2.179 | 1.00 |
| 63_L | 67_Y | 2.140 | 1.00 |
| 16_N | 19_S | 2.058 | 1.00 |
| 61_Q | 65_R | 2.017 | 1.00 |
| 27_R | 31_K | 2.017 | 1.00 |
| 48_C | 80_Q | 2.004 | 1.00 |
| 57_S | 61_Q | 1.942 | 1.00 |
| 7_G | 89_L | 1.937 | 1.00 |
| 60_A | 64_A | 1.893 | 1.00 |
| 7_G | 93_I | 1.878 | 1.00 |
| 8_F | 30_I | 1.812 | 1.00 |
| 14_I | 48_C | 1.806 | 1.00 |
| 72_I | 88_T | 1.719 | 1.00 |
| 31_K | 41_M | 1.708 | 1.00 |
| 14_I | 45_G | 1.652 | 1.00 |
| 17_T | 21_E | 1.646 | 1.00 |
| 70_P | 88_T | 1.591 | 1.00 |
| 24_H | 66_S | 1.571 | 1.00 |
| 62_D | 66_S | 1.568 | 1.00 |
| 46_N | 76_A | 1.556 | 1.00 |
| 60_A | 71_Y | 1.498 | 1.00 |
| 24_H | 63_L | 1.483 | 1.00 |
| 56_E | 59_Q | 1.467 | 1.00 |
| 2_M | 29_Q | 1.445 | 1.00 |
| 88_T | 92_E | 1.430 | 1.00 |
| 23_I | 43_L | 1.346 | 0.99 |
| 92_E | 95_Q | 1.325 | 0.99 |
| 12_F | 60_A | 1.320 | 0.99 |
| 42_V | 72_I | 1.295 | 0.99 |
| 81_G | 84_D | 1.272 | 0.99 |
| 27_R | 67_Y | 1.240 | 0.98 |
| 88_T | 91_R | 1.231 | 0.98 |
| 74_T | 85_A | 1.200 | 0.98 |
| 22_D | 26_Y | 1.186 | 0.98 |
| 70_P | 92_E | 1.180 | 0.98 |
| 43_L | 69_I | 1.168 | 0.97 |
| 42_V | 85_A | 1.156 | 0.97 |
| 27_R | 41_M | 1.113 | 0.96 |
| 18_K | 21_E | 1.113 | 0.96 |
| 57_S | 73_E | 1.106 | 0.96 |
| 20_F | 63_L | 1.104 | 0.96 |
| 44_V | 74_T | 1.087 | 0.96 |
| 12_F | 45_G | 1.075 | 0.95 |
| 5_G | 8_F | 1.074 | 0.95 |
| 44_V | 72_I | 1.070 | 0.95 |
| 83_E | 87_Y | 1.060 | 0.95 |
| 75_S | 81_G | 1.049 | 0.94 |
| 40_P | 96_H | 1.036 | 0.94 |
| 13_A | 16_N | 1.032 | 0.94 |
| 23_I | 63_L | 1.022 | 0.93 |
| 20_F | 55_V | 1.013 | 0.93 |
| 22_D | 25_Q | 1.005 | 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 | |
| 2g3yA | 1 | 0.8235 | 99.7 | 0.343 | Contact Map |
| 4dsuA | 1 | 0.9244 | 99.7 | 0.348 | Contact Map |
| 2gf0A | 4 | 0.8487 | 99.7 | 0.35 | Contact Map |
| 2iwrA | 1 | 0.8403 | 99.7 | 0.365 | Contact Map |
| 2cjwA | 1 | 0.9244 | 99.7 | 0.37 | Contact Map |
| 2j0vA | 4 | 0.8151 | 99.7 | 0.37 | Contact Map |
| 1x3sA | 1 | 0.8571 | 99.7 | 0.372 | Contact Map |
| 2bovA | 1 | 0.8487 | 99.7 | 0.374 | Contact Map |
| 3ihwA | 1 | 0.8151 | 99.7 | 0.375 | Contact Map |
| 2yc2C | 2 | 0.8403 | 99.6 | 0.381 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)