| T0811 |
| ID: | 1402339849 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 255 (246) | ||
| Sequences: | 2387 (1661.8) | ||
| Seq/Len: | 9.703 | ||
| Nf(neff/√len): | 106.0 |
HHblits Results: (2013_03)
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: 9.703).
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 |
| 189_D | 228_H | 3.836 | 1.00 |
| 44_I | 65_G | 3.636 | 1.00 |
| 138_E | 181_I | 3.380 | 1.00 |
| 142_A | 191_R | 3.112 | 1.00 |
| 109_D | 148_R | 2.623 | 1.00 |
| 15_N | 74_A | 2.556 | 1.00 |
| 141_E | 144_T | 2.549 | 1.00 |
| 47_F | 81_I | 2.501 | 1.00 |
| 146_L | 191_R | 2.294 | 1.00 |
| 86_L | 91_L | 2.280 | 1.00 |
| 116_T | 128_I | 2.201 | 1.00 |
| 119_A | 124_L | 2.178 | 1.00 |
| 240_D | 243_G | 2.170 | 1.00 |
| 158_E | 162_R | 2.124 | 1.00 |
| 215_V | 232_L | 2.053 | 1.00 |
| 136_Q | 141_E | 1.995 | 1.00 |
| 9_G | 127_L | 1.979 | 1.00 |
| 77_W | 104_H | 1.959 | 1.00 |
| 151_E | 198_V | 1.958 | 1.00 |
| 134_L | 138_E | 1.905 | 1.00 |
| 217_P | 243_G | 1.865 | 1.00 |
| 48_T | 81_I | 1.855 | 1.00 |
| 128_I | 153_A | 1.854 | 1.00 |
| 7_W | 167_L | 1.850 | 1.00 |
| 16_K | 20_E | 1.835 | 1.00 |
| 136_Q | 145_V | 1.833 | 1.00 |
| 130_I | 146_L | 1.832 | 1.00 |
| 134_L | 181_I | 1.815 | 1.00 |
| 69_M | 119_A | 1.758 | 1.00 |
| 143_D | 194_L | 1.727 | 1.00 |
| 112_V | 128_I | 1.710 | 1.00 |
| 69_M | 83_P | 1.708 | 1.00 |
| 57_L | 64_V | 1.690 | 1.00 |
| 44_I | 95_E | 1.684 | 1.00 |
| 186_D | 226_Q | 1.673 | 1.00 |
| 94_V | 119_A | 1.616 | 1.00 |
| 8_V | 224_I | 1.615 | 1.00 |
| 95_E | 127_L | 1.593 | 1.00 |
| 147_K | 194_L | 1.591 | 1.00 |
| 193_R | 197_E | 1.590 | 1.00 |
| 40_Q | 208_P | 1.586 | 1.00 |
| 143_D | 190_A | 1.573 | 1.00 |
| 9_G | 42_F | 1.564 | 1.00 |
| 41_R | 248_L | 1.561 | 1.00 |
| 188_A | 223_L | 1.552 | 1.00 |
| 7_W | 42_F | 1.547 | 1.00 |
| 120_V | 166_V | 1.546 | 1.00 |
| 72_D | 114_L | 1.545 | 1.00 |
| 196_G | 209_V | 1.541 | 1.00 |
| 109_D | 152_G | 1.528 | 1.00 |
| 54_K | 64_V | 1.509 | 1.00 |
| 63_K | 92_D | 1.509 | 1.00 |
| 68_N | 105_F | 1.495 | 1.00 |
| 24_F | 241_V | 1.492 | 1.00 |
| 133_T | 173_V | 1.485 | 1.00 |
| 188_A | 226_Q | 1.478 | 1.00 |
| 45_P | 67_Q | 1.462 | 1.00 |
| 73_D | 121_K | 1.460 | 1.00 |
| 71_W | 114_L | 1.452 | 1.00 |
| 66_A | 86_L | 1.432 | 1.00 |
| 25_A | 53_V | 1.432 | 1.00 |
| 108_T | 111_T | 1.432 | 1.00 |
| 185_A | 222_E | 1.421 | 1.00 |
| 188_A | 229_I | 1.418 | 0.99 |
| 133_T | 136_Q | 1.417 | 0.99 |
| 220_C | 224_I | 1.414 | 0.99 |
| 215_V | 224_I | 1.412 | 0.99 |
| 136_Q | 148_R | 1.406 | 0.99 |
| 130_I | 173_V | 1.403 | 0.99 |
| 21_A | 49_A | 1.389 | 0.99 |
| 199_A | 207_V | 1.374 | 0.99 |
| 118_A | 121_K | 1.371 | 0.99 |
| 50_A | 66_A | 1.362 | 0.99 |
| 220_C | 247_I | 1.352 | 0.99 |
| 69_M | 96_L | 1.343 | 0.99 |
| 164_A | 206_K | 1.320 | 0.99 |
| 147_K | 151_E | 1.316 | 0.99 |
| 113_G | 117_A | 1.313 | 0.99 |
| 46_P | 49_A | 1.312 | 0.99 |
| 45_P | 53_V | 1.310 | 0.99 |
| 44_I | 127_L | 1.310 | 0.99 |
| 66_A | 94_V | 1.308 | 0.99 |
| 137_R | 187_Y | 1.290 | 0.99 |
| 218_Q | 243_G | 1.289 | 0.99 |
| 68_N | 80_E | 1.278 | 0.99 |
| 185_A | 188_A | 1.275 | 0.99 |
| 200_E | 205_V | 1.272 | 0.99 |
| 92_D | 125_V | 1.267 | 0.99 |
| 70_H | 105_F | 1.265 | 0.99 |
| 16_K | 21_A | 1.264 | 0.99 |
| 145_V | 173_V | 1.262 | 0.99 |
| 94_V | 124_L | 1.254 | 0.98 |
| 5_G | 40_Q | 1.254 | 0.98 |
| 72_D | 77_W | 1.213 | 0.98 |
| 223_L | 229_I | 1.211 | 0.98 |
| 130_I | 150_V | 1.207 | 0.98 |
| 189_D | 227_P | 1.207 | 0.98 |
| 71_W | 105_F | 1.196 | 0.98 |
| 113_G | 156_F | 1.186 | 0.98 |
| 215_V | 234_I | 1.174 | 0.97 |
| 93_I | 125_V | 1.172 | 0.97 |
| 182_P | 223_L | 1.165 | 0.97 |
| 187_Y | 190_A | 1.159 | 0.97 |
| 27_G | 242_G | 1.144 | 0.97 |
| 42_F | 93_I | 1.137 | 0.97 |
| 73_D | 122_H | 1.121 | 0.96 |
| 158_E | 161_A | 1.121 | 0.96 |
| 4_S | 230_D | 1.114 | 0.96 |
| 125_V | 165_P | 1.113 | 0.96 |
| 71_W | 111_T | 1.111 | 0.96 |
| 17_T | 49_A | 1.105 | 0.96 |
| 186_D | 190_A | 1.105 | 0.96 |
| 21_A | 53_V | 1.094 | 0.96 |
| 51_R | 55_E | 1.092 | 0.96 |
| 70_H | 118_A | 1.090 | 0.95 |
| 6_L | 224_I | 1.080 | 0.95 |
| 103_E | 133_T | 1.078 | 0.95 |
| 137_R | 190_A | 1.076 | 0.95 |
| 151_E | 202_A | 1.076 | 0.95 |
| 226_Q | 229_I | 1.075 | 0.95 |
| 17_T | 20_E | 1.071 | 0.95 |
| 83_P | 118_A | 1.068 | 0.95 |
| 144_T | 147_K | 1.053 | 0.94 |
| 54_K | 57_L | 1.052 | 0.94 |
| 159_G | 204_G | 1.050 | 0.94 |
| 6_L | 208_P | 1.048 | 0.94 |
| 80_E | 105_F | 1.047 | 0.94 |
| 23_V | 27_G | 1.047 | 0.94 |
| 69_M | 94_V | 1.038 | 0.94 |
| 133_T | 145_V | 1.038 | 0.94 |
| 7_W | 210_L | 1.038 | 0.94 |
| 57_L | 62_V | 1.032 | 0.93 |
| 52_Q | 55_E | 1.022 | 0.93 |
| 117_A | 121_K | 1.010 | 0.92 |
| 118_A | 122_H | 1.010 | 0.92 |
| 197_E | 201_R | 1.009 | 0.92 |
| 28_L | 241_V | 1.006 | 0.92 |
| 162_R | 165_P | 1.003 | 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 | |
| 2j27A | 2 | 0.9608 | 100 | 0.024 | Contact Map |
| 4mvaA | 2 | 0.9804 | 100 | 0.024 | Contact Map |
| 3ta6A | 2 | 0.9765 | 100 | 0.027 | Contact Map |
| 4g1kA | 4 | 0.9725 | 100 | 0.027 | Contact Map |
| 1m6jA | 2 | 0.9843 | 100 | 0.027 | Contact Map |
| 1aw2A | 8 | 0.9765 | 100 | 0.027 | Contact Map |
| 1yyaA | 2 | 0.9647 | 100 | 0.028 | Contact Map |
| 3m9yA | 2 | 0.9686 | 100 | 0.028 | Contact Map |
| 2btmA | 2 | 0.9647 | 100 | 0.029 | Contact Map |
| 1b9bA | 2 | 0.9804 | 100 | 0.029 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)