| T0825 |
| ID: | 1404799818 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 205 (203) | ||
| Sequences: | 1170 (1116.7) | ||
| Seq/Len: | 5.764 | ||
| Nf(neff/√len): | 78.4 |
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: 5.764).
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 |
| 75_L | 116_L | 2.112 | 1.00 |
| 116_L | 157_L | 1.978 | 1.00 |
| 77_Q | 118_Q | 1.970 | 1.00 |
| 75_L | 157_L | 1.891 | 1.00 |
| 115_Q | 156_Q | 1.869 | 1.00 |
| 50_F | 91_F | 1.800 | 1.00 |
| 118_Q | 159_Q | 1.800 | 1.00 |
| 74_Q | 115_Q | 1.709 | 1.00 |
| 49_A | 90_A | 1.684 | 1.00 |
| 71_R | 112_R | 1.650 | 1.00 |
| 116_L | 198_L | 1.629 | 0.99 |
| 97_T | 138_T | 1.626 | 0.99 |
| 56_T | 138_T | 1.611 | 0.99 |
| 132_F | 173_F | 1.609 | 0.99 |
| 157_L | 198_L | 1.608 | 0.99 |
| 96_Q | 137_Q | 1.601 | 0.99 |
| 149_K | 160_T | 1.592 | 0.99 |
| 76_L | 158_L | 1.584 | 0.99 |
| 72_N | 113_N | 1.583 | 0.99 |
| 55_Q | 96_Q | 1.580 | 0.99 |
| 67_K | 78_T | 1.564 | 0.99 |
| 56_T | 97_T | 1.546 | 0.99 |
| 91_F | 132_F | 1.535 | 0.99 |
| 124_S | 165_S | 1.529 | 0.99 |
| 121_T | 162_T | 1.525 | 0.99 |
| 83_S | 124_S | 1.525 | 0.99 |
| 9_F | 50_F | 1.522 | 0.99 |
| 50_F | 132_F | 1.508 | 0.99 |
| 112_R | 153_R | 1.507 | 0.99 |
| 66_V | 100_S | 1.504 | 0.99 |
| 148_V | 182_S | 1.497 | 0.99 |
| 190_K | 201_T | 1.487 | 0.99 |
| 90_A | 131_A | 1.483 | 0.99 |
| 34_L | 75_L | 1.458 | 0.99 |
| 117_L | 158_L | 1.437 | 0.98 |
| 113_N | 154_N | 1.435 | 0.98 |
| 108_K | 119_T | 1.432 | 0.98 |
| 156_Q | 197_Q | 1.421 | 0.98 |
| 123_H | 141_S | 1.409 | 0.98 |
| 29_N | 70_N | 1.385 | 0.98 |
| 76_L | 117_L | 1.379 | 0.98 |
| 8_A | 172_A | 1.374 | 0.98 |
| 71_R | 153_R | 1.371 | 0.98 |
| 154_N | 195_N | 1.358 | 0.98 |
| 140_A | 173_F | 1.355 | 0.97 |
| 33_Q | 74_Q | 1.344 | 0.97 |
| 80_T | 121_T | 1.344 | 0.97 |
| 36_Q | 77_Q | 1.333 | 0.97 |
| 131_A | 172_A | 1.323 | 0.97 |
| 55_Q | 178_Q | 1.317 | 0.97 |
| 17_A | 57_I | 1.304 | 0.97 |
| 152_N | 193_N | 1.303 | 0.97 |
| 80_T | 162_T | 1.296 | 0.96 |
| 68_L | 109_L | 1.295 | 0.96 |
| 14_Q | 55_Q | 1.294 | 0.96 |
| 55_Q | 137_Q | 1.293 | 0.96 |
| 31_N | 72_N | 1.292 | 0.96 |
| 137_Q | 178_Q | 1.282 | 0.96 |
| 42_S | 83_S | 1.279 | 0.96 |
| 97_T | 179_T | 1.278 | 0.96 |
| 14_Q | 137_Q | 1.273 | 0.96 |
| 72_N | 154_N | 1.271 | 0.96 |
| 11_P | 54_G | 1.266 | 0.96 |
| 15_T | 97_T | 1.266 | 0.96 |
| 30_R | 71_R | 1.261 | 0.96 |
| 82_H | 104_D | 1.256 | 0.96 |
| 96_Q | 178_Q | 1.255 | 0.96 |
| 25_V | 59_S | 1.236 | 0.95 |
| 66_V | 107_V | 1.223 | 0.95 |
| 105_K | 146_K | 1.220 | 0.95 |
| 58_A | 98_I | 1.210 | 0.94 |
| 64_K | 105_K | 1.208 | 0.94 |
| 83_S | 165_S | 1.204 | 0.94 |
| 50_F | 173_F | 1.203 | 0.94 |
| 74_Q | 156_Q | 1.199 | 0.94 |
| 57_I | 98_I | 1.198 | 0.94 |
| 31_N | 154_N | 1.194 | 0.94 |
| 15_T | 56_T | 1.190 | 0.94 |
| 150_L | 191_L | 1.188 | 0.94 |
| 140_A | 180_I | 1.181 | 0.93 |
| 75_L | 198_L | 1.175 | 0.93 |
| 26_K | 37_T | 1.175 | 0.93 |
| 164_H | 186_D | 1.173 | 0.93 |
| 56_T | 179_T | 1.163 | 0.93 |
| 39_T | 80_T | 1.159 | 0.92 |
| 164_H | 182_S | 1.159 | 0.92 |
| 93_P | 134_P | 1.156 | 0.92 |
| 18_S | 22_D | 1.154 | 0.92 |
| 139_I | 180_I | 1.144 | 0.92 |
| 134_P | 177_G | 1.142 | 0.92 |
| 77_Q | 159_Q | 1.139 | 0.91 |
| 15_T | 138_T | 1.138 | 0.91 |
| 39_T | 121_T | 1.136 | 0.91 |
| 109_L | 150_L | 1.134 | 0.91 |
| 153_R | 194_R | 1.122 | 0.91 |
| 70_N | 111_N | 1.117 | 0.90 |
| 74_Q | 197_Q | 1.114 | 0.90 |
| 34_L | 116_L | 1.114 | 0.90 |
| 138_T | 179_T | 1.105 | 0.90 |
| 112_R | 194_R | 1.099 | 0.89 |
| 184_S | 188_T | 1.095 | 0.89 |
| 14_Q | 178_Q | 1.092 | 0.89 |
| 36_Q | 159_Q | 1.092 | 0.89 |
| 35_L | 76_L | 1.089 | 0.89 |
| 90_A | 172_A | 1.088 | 0.89 |
| 31_N | 113_N | 1.085 | 0.89 |
| 41_H | 63_D | 1.081 | 0.88 |
| 78_T | 119_T | 1.073 | 0.88 |
| 8_A | 131_A | 1.071 | 0.88 |
| 98_I | 139_I | 1.070 | 0.88 |
| 41_H | 59_S | 1.066 | 0.87 |
| 109_L | 191_L | 1.059 | 0.87 |
| 72_N | 195_N | 1.057 | 0.87 |
| 33_Q | 115_Q | 1.056 | 0.87 |
| 119_T | 160_T | 1.056 | 0.87 |
| 8_A | 49_A | 1.052 | 0.87 |
| 125_S | 166_S | 1.050 | 0.86 |
| 71_R | 194_R | 1.045 | 0.86 |
| 91_F | 173_F | 1.043 | 0.86 |
| 42_S | 124_S | 1.030 | 0.85 |
| 52_P | 93_P | 1.029 | 0.85 |
| 67_K | 149_K | 1.026 | 0.85 |
| 16_I | 98_I | 1.024 | 0.84 |
| 61_S | 65_T | 1.022 | 0.84 |
| 39_T | 162_T | 1.018 | 0.84 |
| 23_K | 64_K | 1.017 | 0.84 |
| 111_N | 152_N | 1.014 | 0.84 |
| 113_N | 195_N | 1.014 | 0.84 |
| 67_K | 108_K | 1.009 | 0.83 |
| 41_H | 61_S | 1.003 | 0.83 |
| 16_I | 139_I | 1.000 | 0.83 |
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 | |
| 1nr0A | 1 | 0.9951 | 100 | 0.31 | Contact Map |
| 2ymuA | 2 | 1 | 100 | 0.314 | Contact Map |
| 1vyhC | 10 | 1 | 100 | 0.319 | Contact Map |
| 3sfzA | 1 | 0.9756 | 100 | 0.322 | Contact Map |
| 3w15A | 1 | 0.9854 | 100 | 0.328 | Contact Map |
| 3f3fA | 4 | 0.9951 | 100 | 0.331 | Contact Map |
| 4lg9A | 1 | 1 | 100 | 0.351 | Contact Map |
| 3mkqA | 3 | 1 | 100 | 0.357 | Contact Map |
| 3j65q | 1 | 0.9951 | 100 | 0.361 | Contact Map |
| 3zwlB | 2 | 0.9951 | 100 | 0.362 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)