| test5 |
| ID: | 1478103305 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (97) | ||
| Sequences: | 3949 (3234.4) | ||
| Seq/Len: | 40.711 | ||
| Nf(neff/√len): | 328.4 |
Jackhmmer Results: (2016_04)
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: 40.711).
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_Q | 47_Y | 1.562 | 1.00 |
| 21_M | 33_Q | 1.416 | 1.00 |
| 93_D | 96_L | 1.288 | 0.99 |
| 76_P | 88_P | 1.279 | 0.99 |
| 20_M | 26_Q | 1.266 | 0.99 |
| 34_H | 68_P | 1.258 | 0.99 |
| 35_H | 38_N | 1.252 | 0.99 |
| 16_P | 22_P | 1.249 | 0.99 |
| 38_N | 41_P | 1.239 | 0.98 |
| 19_P | 54_P | 1.204 | 0.98 |
| 24_P | 36_Q | 1.187 | 0.98 |
| 79_P | 91_L | 1.174 | 0.98 |
| 66_V | 78_L | 1.172 | 0.98 |
| 3_H | 6_P | 1.172 | 0.98 |
| 23_V | 29_M | 1.170 | 0.97 |
| 14_V | 32_I | 1.164 | 0.97 |
| 51_P | 86_P | 1.155 | 0.97 |
| 36_Q | 48_Q | 1.155 | 0.97 |
| 47_Y | 52_V | 1.139 | 0.97 |
| 28_S | 34_H | 1.137 | 0.97 |
| 73_P | 85_Q | 1.131 | 0.97 |
| 20_M | 38_N | 1.130 | 0.97 |
| 64_P | 82_F | 1.130 | 0.97 |
| 21_M | 55_Q | 1.111 | 0.96 |
| 32_I | 38_N | 1.102 | 0.96 |
| 50_Q | 61_Q | 1.102 | 0.96 |
| 12_Q | 30_T | 1.101 | 0.96 |
| 64_P | 70_Q | 1.098 | 0.96 |
| 13_P | 19_P | 1.096 | 0.96 |
| 18_Q | 30_T | 1.095 | 0.96 |
| 90_M | 93_D | 1.087 | 0.96 |
| 32_I | 66_V | 1.081 | 0.95 |
| 42_P | 53_Q | 1.070 | 0.95 |
| 72_L | 78_L | 1.055 | 0.95 |
| 26_Q | 32_I | 1.053 | 0.95 |
| 37_P | 71_P | 1.051 | 0.94 |
| 26_Q | 38_N | 1.046 | 0.94 |
| 70_Q | 82_F | 1.044 | 0.94 |
| 58_Q | 70_Q | 1.044 | 0.94 |
| 55_Q | 58_Q | 1.041 | 0.94 |
| 45_Q | 79_P | 1.041 | 0.94 |
| 64_P | 76_P | 1.034 | 0.94 |
| 26_Q | 60_M | 1.034 | 0.94 |
| 48_Q | 58_Q | 1.031 | 0.94 |
| 55_Q | 67_H | 1.028 | 0.94 |
| 14_V | 20_M | 1.026 | 0.94 |
| 73_P | 79_P | 1.022 | 0.93 |
| 32_I | 44_Q | 1.021 | 0.93 |
| 28_S | 62_P | 1.019 | 0.93 |
| 38_N | 72_L | 1.013 | 0.93 |
| 42_P | 45_Q | 1.012 | 0.93 |
| 62_P | 68_P | 1.010 | 0.93 |
| 75_Q | 87_L | 1.010 | 0.93 |
| 47_Y | 57_H | 1.008 | 0.93 |
| 19_P | 31_P | 1.005 | 0.93 |
| 39_L | 73_P | 1.005 | 0.93 |
| 60_M | 66_V | 1.002 | 0.92 |
| 20_M | 44_Q | 1.001 | 0.92 |
| 26_Q | 44_Q | 1.000 | 0.92 |
| 78_L | 84_M | 1.000 | 0.92 |
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 | |
| 3mlqE | 4 | 0.12 | 0.8 | 0.907 | Contact Map |
| 3izxD | 2 | 0 | 0.4 | 0.929 | Contact Map |
| 1mvhA | 1 | 0.63 | 0.3 | 0.932 | Contact Map |
| 4p7tA | 6 | 0.1 | 0.3 | 0.934 | Contact Map |
| 4rg9S | 1 | 0.23 | 0.3 | 0.937 | Contact Map |
| 3nekA | 2 | 0.45 | 0.3 | 0.937 | Contact Map |
| 2pkhA | 8 | 0.44 | 0.3 | 0.938 | Contact Map |
| 2p19A | 3 | 0.49 | 0.3 | 0.938 | Contact Map |
| 4rdqA | 5 | 0 | 0.3 | 0.939 | Contact Map |
| 2nzcA | 4 | 0.27 | 0.3 | 0.939 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)