| qstr |
| ID: | 1412713837 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 214 (190) | ||
| Sequences: | 121858 (86648.5) | ||
| Seq/Len: | 641.358 | ||
| Nf(neff/√len): | 6286.1 |
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: 641.358).
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_E | 63_G | 2.968 | 1.00 |
| 57_L | 68_Q | 2.679 | 1.00 |
| 41_E | 63_G | 2.536 | 1.00 |
| 14_T | 43_L | 2.348 | 1.00 |
| 40_P | 64_L | 2.323 | 1.00 |
| 21_H | 36_P | 2.225 | 1.00 |
| 10_I | 34_P | 2.166 | 1.00 |
| 59_H | 83_L | 2.148 | 1.00 |
| 83_L | 101_L | 2.074 | 1.00 |
| 39_E | 42_R | 2.059 | 1.00 |
| 25_Q | 29_E | 2.050 | 1.00 |
| 25_Q | 36_P | 2.039 | 1.00 |
| 69_L | 81_T | 2.019 | 1.00 |
| 57_L | 69_L | 1.893 | 1.00 |
| 71_P | 74_L | 1.874 | 1.00 |
| 44_L | 68_Q | 1.833 | 1.00 |
| 64_L | 71_P | 1.817 | 1.00 |
| 60_A | 87_E | 1.781 | 1.00 |
| 103_G | 117_G | 1.769 | 1.00 |
| 21_H | 38_I | 1.768 | 1.00 |
| 36_P | 52_H | 1.748 | 1.00 |
| 73_K | 102_K | 1.748 | 1.00 |
| 15_T | 21_H | 1.731 | 1.00 |
| 38_I | 42_R | 1.677 | 1.00 |
| 184_F | 187_K | 1.676 | 1.00 |
| 40_P | 68_Q | 1.672 | 1.00 |
| 21_H | 37_V | 1.619 | 1.00 |
| 69_L | 83_L | 1.601 | 1.00 |
| 48_Q | 75_T | 1.599 | 1.00 |
| 171_S | 175_I | 1.566 | 1.00 |
| 47_Y | 72_L | 1.548 | 1.00 |
| 27_A | 111_T | 1.535 | 1.00 |
| 70_G | 95_L | 1.522 | 1.00 |
| 189_H | 192_Q | 1.495 | 1.00 |
| 12_L | 43_L | 1.477 | 1.00 |
| 158_R | 161_Q | 1.444 | 1.00 |
| 14_T | 61_E | 1.434 | 1.00 |
| 54_I | 118_L | 1.421 | 1.00 |
| 10_I | 52_H | 1.418 | 1.00 |
| 44_L | 71_P | 1.411 | 1.00 |
| 55_L | 79_F | 1.410 | 1.00 |
| 32_N | 35_V | 1.402 | 0.99 |
| 41_E | 45_R | 1.399 | 0.99 |
| 57_L | 81_T | 1.399 | 0.99 |
| 64_L | 67_Q | 1.385 | 0.99 |
| 93_E | 113_F | 1.371 | 0.99 |
| 31_L | 115_A | 1.366 | 0.99 |
| 171_S | 174_Q | 1.363 | 0.99 |
| 37_V | 46_E | 1.361 | 0.99 |
| 44_L | 64_L | 1.340 | 0.99 |
| 172_N | 187_K | 1.332 | 0.99 |
| 16_Q | 58_D | 1.330 | 0.99 |
| 89_R | 92_T | 1.325 | 0.99 |
| 46_E | 52_H | 1.317 | 0.99 |
| 45_R | 49_S | 1.292 | 0.99 |
| 67_Q | 71_P | 1.265 | 0.99 |
| 18_K | 21_H | 1.261 | 0.99 |
| 9_T | 122_I | 1.259 | 0.99 |
| 67_Q | 70_G | 1.256 | 0.99 |
| 82_I | 121_I | 1.251 | 0.99 |
| 15_T | 61_E | 1.248 | 0.99 |
| 159_E | 196_K | 1.246 | 0.98 |
| 83_L | 96_L | 1.233 | 0.98 |
| 28_I | 118_L | 1.204 | 0.98 |
| 14_T | 55_L | 1.204 | 0.98 |
| 11_Y | 33_L | 1.197 | 0.98 |
| 87_E | 92_T | 1.197 | 0.98 |
| 12_L | 52_H | 1.192 | 0.98 |
| 47_Y | 76_S | 1.191 | 0.98 |
| 76_S | 79_F | 1.169 | 0.97 |
| 12_L | 37_V | 1.164 | 0.97 |
| 31_L | 35_V | 1.163 | 0.97 |
| 10_I | 50_D | 1.159 | 0.97 |
| 40_P | 44_L | 1.157 | 0.97 |
| 176_A | 179_L | 1.144 | 0.97 |
| 90_L | 110_D | 1.143 | 0.97 |
| 17_P | 20_L | 1.139 | 0.97 |
| 113_F | 117_G | 1.130 | 0.97 |
| 82_I | 117_G | 1.128 | 0.97 |
| 43_L | 47_Y | 1.127 | 0.97 |
| 90_L | 94_D | 1.116 | 0.96 |
| 41_E | 64_L | 1.108 | 0.96 |
| 24_I | 84_F | 1.106 | 0.96 |
| 102_K | 121_I | 1.105 | 0.96 |
| 55_L | 72_L | 1.102 | 0.96 |
| 24_I | 114_I | 1.101 | 0.96 |
| 46_E | 50_D | 1.099 | 0.96 |
| 60_A | 86_V | 1.087 | 0.96 |
| 13_L | 24_I | 1.072 | 0.95 |
| 46_E | 49_S | 1.059 | 0.95 |
| 42_R | 46_E | 1.058 | 0.95 |
| 175_I | 179_L | 1.051 | 0.94 |
| 47_Y | 79_F | 1.044 | 0.94 |
| 190_L | 194_F | 1.042 | 0.94 |
| 69_L | 99_G | 1.041 | 0.94 |
| 56_L | 84_F | 1.031 | 0.94 |
| 9_T | 33_L | 1.030 | 0.94 |
| 172_N | 175_I | 1.023 | 0.93 |
| 54_I | 122_I | 1.021 | 0.93 |
| 10_I | 53_K | 1.012 | 0.93 |
| 42_R | 45_R | 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 | |
| 3kloA | 4 | 0.9813 | 100 | 0.2 | Contact Map |
| 3c3wA | 2 | 0.9579 | 100 | 0.209 | Contact Map |
| 1a04A | 2 | 0.9346 | 100 | 0.218 | Contact Map |
| 4gvpA | 4 | 0.9439 | 100 | 0.224 | Contact Map |
| 4hyeA | 2 | 0.9112 | 100 | 0.237 | Contact Map |
| 4ldzA | 2 | 0.8972 | 100 | 0.266 | Contact Map |
| 1yioA | 1 | 0.9159 | 100 | 0.284 | Contact Map |
| 1ys7A | 2 | 0.9626 | 100 | 0.297 | Contact Map |
| 1kgsA | 1 | 0.9673 | 100 | 0.3 | Contact Map |
| 4b09A | 12 | 0.8925 | 100 | 0.305 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)