| T0848 1-170 |
| ID: | 1404966313 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 170 (156) | ||
| Sequences: | 546 (511.1) | ||
| Seq/Len: | 3.500 | ||
| Nf(neff/√len): | 40.9 |
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: 3.500).
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 |
| 76_K | 121_S | 3.895 | 1.00 |
| 66_Q | 129_V | 3.262 | 1.00 |
| 65_D | 129_V | 2.363 | 1.00 |
| 74_A | 123_E | 2.339 | 1.00 |
| 3_Q | 7_Y | 2.304 | 1.00 |
| 48_K | 74_A | 2.096 | 1.00 |
| 72_N | 125_N | 2.060 | 1.00 |
| 67_L | 133_G | 1.995 | 1.00 |
| 44_Q | 76_K | 1.838 | 0.99 |
| 74_A | 121_S | 1.748 | 0.99 |
| 19_T | 22_C | 1.720 | 0.99 |
| 92_L | 138_L | 1.711 | 0.99 |
| 154_T | 157_I | 1.683 | 0.99 |
| 82_P | 115_T | 1.604 | 0.98 |
| 117_N | 120_K | 1.536 | 0.97 |
| 64_D | 129_V | 1.532 | 0.97 |
| 52_Y | 69_L | 1.526 | 0.97 |
| 3_Q | 9_V | 1.503 | 0.97 |
| 98_K | 128_F | 1.502 | 0.97 |
| 68_V | 127_F | 1.417 | 0.95 |
| 3_Q | 8_A | 1.414 | 0.95 |
| 65_D | 116_I | 1.405 | 0.95 |
| 94_Q | 97_T | 1.402 | 0.95 |
| 85_V | 90_F | 1.394 | 0.95 |
| 62_T | 65_D | 1.365 | 0.94 |
| 93_Y | 137_E | 1.356 | 0.93 |
| 49_D | 106_D | 1.355 | 0.93 |
| 15_L | 26_K | 1.339 | 0.93 |
| 48_K | 72_N | 1.321 | 0.92 |
| 86_D | 112_Q | 1.315 | 0.92 |
| 8_A | 12_I | 1.292 | 0.91 |
| 8_A | 13_L | 1.274 | 0.90 |
| 20_A | 23_S | 1.273 | 0.90 |
| 93_Y | 97_T | 1.267 | 0.90 |
| 14_L | 35_E | 1.252 | 0.89 |
| 70_K | 125_N | 1.251 | 0.89 |
| 32_K | 36_T | 1.245 | 0.89 |
| 89_D | 140_Y | 1.240 | 0.89 |
| 44_Q | 78_T | 1.229 | 0.88 |
| 5_K | 11_L | 1.229 | 0.88 |
| 3_Q | 22_C | 1.226 | 0.88 |
| 91_T | 98_K | 1.224 | 0.88 |
| 97_T | 100_S | 1.224 | 0.88 |
| 73_V | 92_L | 1.185 | 0.85 |
| 13_L | 22_C | 1.180 | 0.85 |
| 90_F | 140_Y | 1.180 | 0.85 |
| 86_D | 89_D | 1.152 | 0.83 |
| 73_V | 126_L | 1.149 | 0.83 |
| 62_T | 129_V | 1.142 | 0.82 |
| 66_Q | 117_N | 1.135 | 0.82 |
| 93_Y | 98_K | 1.133 | 0.82 |
| 35_E | 43_A | 1.123 | 0.81 |
| 135_Q | 142_P | 1.122 | 0.81 |
| 103_D | 133_G | 1.117 | 0.81 |
| 143_E | 146_G | 1.101 | 0.79 |
| 111_L | 124_G | 1.092 | 0.78 |
| 86_D | 113_G | 1.082 | 0.78 |
| 6_T | 10_F | 1.074 | 0.77 |
| 23_S | 26_K | 1.073 | 0.77 |
| 96_D | 100_S | 1.068 | 0.76 |
| 28_S | 34_S | 1.063 | 0.76 |
| 82_P | 117_N | 1.054 | 0.75 |
| 89_D | 142_P | 1.051 | 0.75 |
| 10_F | 14_L | 1.045 | 0.74 |
| 16_M | 133_G | 1.041 | 0.74 |
| 66_Q | 120_K | 1.040 | 0.73 |
| 68_V | 129_V | 1.034 | 0.73 |
| 70_K | 127_F | 1.030 | 0.72 |
| 4_K | 20_A | 1.028 | 0.72 |
| 86_D | 115_T | 1.021 | 0.72 |
| 67_L | 85_V | 1.020 | 0.71 |
| 3_Q | 6_T | 1.019 | 0.71 |
| 15_L | 22_C | 1.018 | 0.71 |
| 117_N | 129_V | 1.007 | 0.70 |
| 88_M | 140_Y | 1.006 | 0.70 |
| 14_L | 22_C | 1.000 | 0.69 |
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 | |
| 3cfuA | 2 | 0.7706 | 99.6 | 0.551 | Contact Map |
| 4lesA | 1 | 0.7059 | 99.4 | 0.605 | Contact Map |
| 2llgA | 1 | 0.7647 | 98.3 | 0.741 | Contact Map |
| 3qfgA | 2 | 0.6765 | 98.2 | 0.751 | Contact Map |
| 2x3cA | 1 | 0.5882 | 96.9 | 0.807 | Contact Map |
| 3ucpA | 1 | 0.7176 | 94.8 | 0.838 | Contact Map |
| 3nrfA | 2 | 0.6118 | 94.7 | 0.839 | Contact Map |
| 4lmhA | 4 | 0.7118 | 94.1 | 0.844 | Contact Map |
| 3pmqA | 1 | 0.6176 | 91.6 | 0.856 | Contact Map |
| 3o0lA | 2 | 0.6471 | 83 | 0.875 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)