| T0783 240-411 -force run |
| ID: | 1400649167 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 172 (172) | ||
| Sequences: | 59 (43.5) | ||
| Seq/Len: | 0.343 | ||
| Nf(neff/√len): | 3.3 |
Jackhmmer Results: (2014_04_16)
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: 0.343).
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 |
| 1_R | 58_N | 1.840 | 0.68 |
| 11_D | 118_F | 1.785 | 0.65 |
| 5_E | 26_V | 1.600 | 0.52 |
| 89_P | 133_L | 1.598 | 0.52 |
| 92_V | 97_F | 1.581 | 0.51 |
| 16_N | 106_S | 1.551 | 0.49 |
| 22_L | 70_Q | 1.535 | 0.48 |
| 4_Q | 23_L | 1.519 | 0.47 |
| 161_R | 167_G | 1.514 | 0.46 |
| 161_R | 168_Q | 1.514 | 0.46 |
| 76_L | 92_V | 1.490 | 0.45 |
| 51_I | 94_S | 1.475 | 0.43 |
| 76_L | 97_F | 1.460 | 0.42 |
| 1_R | 86_I | 1.443 | 0.41 |
| 146_S | 160_E | 1.436 | 0.41 |
| 75_L | 127_I | 1.393 | 0.38 |
| 85_C | 94_S | 1.392 | 0.38 |
| 5_E | 105_P | 1.376 | 0.37 |
| 157_L | 161_R | 1.369 | 0.36 |
| 10_M | 58_N | 1.356 | 0.36 |
| 66_T | 130_Y | 1.348 | 0.35 |
| 93_V | 127_I | 1.347 | 0.35 |
| 154_I | 157_L | 1.339 | 0.35 |
| 102_L | 106_S | 1.330 | 0.34 |
| 25_E | 73_Q | 1.311 | 0.33 |
| 25_E | 71_E | 1.305 | 0.32 |
| 64_V | 96_H | 1.293 | 0.32 |
| 72_T | 109_M | 1.289 | 0.31 |
| 107_Q | 138_Q | 1.289 | 0.31 |
| 20_G | 35_K | 1.288 | 0.31 |
| 58_N | 164_G | 1.286 | 0.31 |
| 63_N | 132_L | 1.260 | 0.30 |
| 45_G | 93_V | 1.256 | 0.29 |
| 71_E | 120_K | 1.244 | 0.29 |
| 34_V | 89_P | 1.235 | 0.28 |
| 10_M | 29_S | 1.235 | 0.28 |
| 142_K | 153_I | 1.230 | 0.28 |
| 20_G | 38_S | 1.222 | 0.28 |
| 32_N | 101_K | 1.212 | 0.27 |
| 44_A | 64_V | 1.200 | 0.26 |
| 157_L | 168_Q | 1.179 | 0.25 |
| 157_L | 167_G | 1.179 | 0.25 |
| 63_N | 112_L | 1.174 | 0.25 |
| 157_L | 165_L | 1.157 | 0.24 |
| 34_V | 43_H | 1.157 | 0.24 |
| 106_S | 130_Y | 1.147 | 0.24 |
| 101_K | 106_S | 1.146 | 0.24 |
| 58_N | 163_S | 1.140 | 0.23 |
| 8_V | 134_I | 1.125 | 0.22 |
| 51_I | 118_F | 1.122 | 0.22 |
| 20_G | 63_N | 1.113 | 0.22 |
| 103_V | 122_V | 1.109 | 0.22 |
| 154_I | 165_L | 1.108 | 0.22 |
| 43_H | 104_P | 1.103 | 0.21 |
| 74_K | 96_H | 1.103 | 0.21 |
| 151_A | 170_L | 1.102 | 0.21 |
| 34_V | 39_E | 1.093 | 0.21 |
| 41_L | 71_E | 1.088 | 0.21 |
| 87_L | 90_V | 1.081 | 0.20 |
| 140_D | 159_K | 1.080 | 0.20 |
| 145_E | 154_I | 1.077 | 0.20 |
| 15_D | 67_S | 1.076 | 0.20 |
| 4_Q | 22_L | 1.071 | 0.20 |
| 5_E | 21_H | 1.070 | 0.20 |
| 118_F | 130_Y | 1.069 | 0.20 |
| 13_E | 23_L | 1.069 | 0.20 |
| 8_V | 70_Q | 1.062 | 0.20 |
| 46_R | 101_K | 1.061 | 0.20 |
| 1_R | 10_M | 1.054 | 0.19 |
| 26_V | 105_P | 1.050 | 0.19 |
| 26_V | 106_S | 1.048 | 0.19 |
| 146_S | 164_G | 1.048 | 0.19 |
| 50_Q | 129_L | 1.047 | 0.19 |
| 58_N | 166_I | 1.046 | 0.19 |
| 8_V | 115_I | 1.042 | 0.19 |
| 15_D | 166_I | 1.041 | 0.19 |
| 4_Q | 13_E | 1.034 | 0.18 |
| 149_Q | 155_A | 1.034 | 0.18 |
| 8_V | 16_N | 1.026 | 0.18 |
| 158_I | 162_N | 1.020 | 0.18 |
| 154_I | 161_R | 1.017 | 0.18 |
| 104_P | 130_Y | 1.016 | 0.18 |
| 101_K | 118_F | 1.013 | 0.18 |
| 74_K | 129_L | 1.013 | 0.18 |
| 37_T | 146_S | 1.012 | 0.17 |
| 8_V | 150_G | 1.008 | 0.17 |
| 142_K | 161_R | 1.006 | 0.17 |
| 8_V | 60_V | 1.005 | 0.17 |
| 1_R | 97_F | 1.002 | 0.17 |
| 15_D | 25_E | 1.002 | 0.17 |
| 63_N | 73_Q | 1.001 | 0.17 |
| 35_K | 53_L | 1.000 | 0.17 |
| 50_Q | 60_V | 1.000 | 0.17 |
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 | |
| 2qgqA | 8 | 0.936 | 14.3 | 0.966 | Contact Map |
| 3qmlC | 2 | 0.5291 | 12.9 | 0.967 | Contact Map |
| 3ktbA | 4 | 0.5058 | 11.4 | 0.967 | Contact Map |
| 3kgkA | 2 | 0.5174 | 7.6 | 0.97 | Contact Map |
| 3cu2A | 2 | 0.8372 | 6.9 | 0.97 | Contact Map |
| 4jc0A | 2 | 0.9477 | 6.5 | 0.971 | Contact Map |
| 1tqjA | 6 | 0.6047 | 6.3 | 0.971 | Contact Map |
| 3oziA | 2 | 0.814 | 6.1 | 0.971 | Contact Map |
| 3w6gA | 20 | 0.6047 | 6 | 0.971 | Contact Map |
| 3n89A | 2 | 0.3547 | 4.7 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)