| BMRR -force run |
| ID: | 1420825649 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 278 (268) | ||
| Sequences: | 62 (58) | ||
| Seq/Len: | 0.231 | ||
| Nf(neff/√len): | 3.5 |
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: 0.231).
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 |
| 124_V | 218_A | 2.238 | 0.78 |
| 17_V | 84_Y | 2.160 | 0.74 |
| 12_S | 16_N | 2.102 | 0.71 |
| 175_S | 251_V | 2.038 | 0.68 |
| 171_G | 195_L | 1.850 | 0.57 |
| 132_I | 273_K | 1.811 | 0.54 |
| 218_A | 240_I | 1.651 | 0.44 |
| 29_D | 32_K | 1.650 | 0.44 |
| 8_I | 53_L | 1.618 | 0.42 |
| 78_E | 91_I | 1.541 | 0.38 |
| 8_I | 23_R | 1.488 | 0.35 |
| 66_L | 69_M | 1.459 | 0.33 |
| 6_Y | 9_G | 1.452 | 0.33 |
| 67_E | 95_L | 1.428 | 0.31 |
| 19_I | 57_K | 1.421 | 0.31 |
| 126_V | 221_A | 1.386 | 0.29 |
| 51_I | 55_L | 1.384 | 0.29 |
| 134_I | 239_Y | 1.378 | 0.29 |
| 124_V | 129_E | 1.377 | 0.29 |
| 8_I | 11_V | 1.361 | 0.28 |
| 36_V | 245_L | 1.350 | 0.27 |
| 21_A | 258_I | 1.335 | 0.26 |
| 67_E | 272_M | 1.329 | 0.26 |
| 8_I | 19_I | 1.329 | 0.26 |
| 12_S | 29_D | 1.326 | 0.26 |
| 153_S | 170_Y | 1.322 | 0.26 |
| 235_K | 244_Q | 1.319 | 0.26 |
| 65_P | 80_L | 1.317 | 0.26 |
| 8_I | 132_I | 1.312 | 0.25 |
| 27_K | 193_P | 1.301 | 0.25 |
| 149_N | 195_L | 1.300 | 0.25 |
| 135_I | 236_L | 1.281 | 0.24 |
| 34_A | 218_A | 1.276 | 0.24 |
| 26_D | 30_L | 1.275 | 0.24 |
| 34_A | 46_T | 1.274 | 0.24 |
| 58_S | 199_Q | 1.273 | 0.24 |
| 89_R | 93_E | 1.265 | 0.23 |
| 69_M | 76_E | 1.263 | 0.23 |
| 28_I | 59_L | 1.259 | 0.23 |
| 11_V | 132_I | 1.258 | 0.23 |
| 91_I | 244_Q | 1.256 | 0.23 |
| 102_E | 135_I | 1.255 | 0.23 |
| 60_K | 73_Q | 1.247 | 0.22 |
| 65_P | 213_P | 1.246 | 0.22 |
| 14_L | 199_Q | 1.237 | 0.22 |
| 182_I | 212_I | 1.234 | 0.22 |
| 11_V | 19_I | 1.234 | 0.22 |
| 19_I | 255_I | 1.227 | 0.21 |
| 256_I | 266_E | 1.223 | 0.21 |
| 81_F | 96_D | 1.218 | 0.21 |
| 12_S | 214_K | 1.216 | 0.21 |
| 8_I | 254_L | 1.212 | 0.21 |
| 8_I | 275_R | 1.209 | 0.21 |
| 32_K | 134_I | 1.209 | 0.21 |
| 15_A | 68_E | 1.201 | 0.20 |
| 124_V | 240_I | 1.197 | 0.20 |
| 8_I | 273_K | 1.188 | 0.20 |
| 94_K | 97_F | 1.187 | 0.20 |
| 108_V | 258_I | 1.186 | 0.20 |
| 10_E | 19_I | 1.184 | 0.20 |
| 40_T | 212_I | 1.182 | 0.20 |
| 9_G | 253_E | 1.181 | 0.20 |
| 62_I | 115_Q | 1.180 | 0.20 |
| 11_V | 255_I | 1.179 | 0.20 |
| 9_G | 233_L | 1.177 | 0.19 |
| 58_S | 168_N | 1.177 | 0.19 |
| 10_E | 14_L | 1.176 | 0.19 |
| 124_V | 235_K | 1.174 | 0.19 |
| 12_S | 32_K | 1.173 | 0.19 |
| 24_Y | 64_T | 1.166 | 0.19 |
| 240_I | 247_V | 1.161 | 0.19 |
| 67_E | 105_I | 1.161 | 0.19 |
| 7_S | 234_Q | 1.149 | 0.18 |
| 94_K | 229_Y | 1.141 | 0.18 |
| 60_K | 262_P | 1.138 | 0.18 |
| 44_Y | 98_L | 1.138 | 0.18 |
| 95_L | 102_E | 1.137 | 0.18 |
| 6_Y | 168_N | 1.135 | 0.18 |
| 8_I | 40_T | 1.131 | 0.18 |
| 15_A | 269_R | 1.129 | 0.18 |
| 113_K | 196_T | 1.125 | 0.17 |
| 34_A | 64_T | 1.123 | 0.17 |
| 30_L | 252_Y | 1.118 | 0.17 |
| 92_R | 102_E | 1.117 | 0.17 |
| 53_L | 84_Y | 1.113 | 0.17 |
| 127_L | 267_E | 1.111 | 0.17 |
| 102_E | 254_L | 1.111 | 0.17 |
| 62_I | 258_I | 1.109 | 0.17 |
| 174_F | 235_K | 1.106 | 0.17 |
| 6_Y | 101_L | 1.104 | 0.17 |
| 83_F | 95_L | 1.102 | 0.17 |
| 30_L | 189_H | 1.102 | 0.17 |
| 60_K | 63_G | 1.101 | 0.17 |
| 63_G | 276_I | 1.099 | 0.17 |
| 53_L | 219_C | 1.097 | 0.17 |
| 74_D | 86_E | 1.093 | 0.16 |
| 168_N | 199_Q | 1.092 | 0.16 |
| 218_A | 227_E | 1.091 | 0.16 |
| 27_K | 217_Y | 1.087 | 0.16 |
| 10_E | 253_E | 1.082 | 0.16 |
| 16_N | 217_Y | 1.082 | 0.16 |
| 97_F | 263_K | 1.079 | 0.16 |
| 8_I | 212_I | 1.079 | 0.16 |
| 109_K | 247_V | 1.077 | 0.16 |
| 53_L | 212_I | 1.075 | 0.16 |
| 50_L | 149_N | 1.075 | 0.16 |
| 96_D | 239_Y | 1.075 | 0.16 |
| 31_F | 102_E | 1.074 | 0.16 |
| 214_K | 244_Q | 1.073 | 0.16 |
| 17_V | 55_L | 1.073 | 0.16 |
| 73_Q | 191_F | 1.072 | 0.16 |
| 17_V | 264_K | 1.068 | 0.16 |
| 149_N | 153_S | 1.068 | 0.16 |
| 37_D | 272_M | 1.068 | 0.16 |
| 218_A | 247_V | 1.064 | 0.15 |
| 50_L | 262_P | 1.064 | 0.15 |
| 108_V | 260_Y | 1.061 | 0.15 |
| 60_K | 107_L | 1.061 | 0.15 |
| 148_L | 171_G | 1.060 | 0.15 |
| 169_S | 232_N | 1.057 | 0.15 |
| 32_K | 195_L | 1.055 | 0.15 |
| 60_K | 214_K | 1.055 | 0.15 |
| 19_I | 23_R | 1.054 | 0.15 |
| 66_L | 74_D | 1.054 | 0.15 |
| 36_V | 170_Y | 1.054 | 0.15 |
| 56_I | 270_V | 1.051 | 0.15 |
| 40_T | 73_Q | 1.051 | 0.15 |
| 48_S | 274_I | 1.050 | 0.15 |
| 93_E | 210_T | 1.046 | 0.15 |
| 91_I | 156_K | 1.046 | 0.15 |
| 176_F | 183_D | 1.043 | 0.15 |
| 132_I | 212_I | 1.039 | 0.15 |
| 89_R | 180_T | 1.037 | 0.15 |
| 36_V | 273_K | 1.034 | 0.14 |
| 105_I | 234_Q | 1.032 | 0.14 |
| 96_D | 196_T | 1.027 | 0.14 |
| 22_L | 30_L | 1.027 | 0.14 |
| 40_T | 94_K | 1.025 | 0.14 |
| 148_L | 172_A | 1.025 | 0.14 |
| 76_E | 182_I | 1.025 | 0.14 |
| 41_S | 76_E | 1.020 | 0.14 |
| 224_F | 270_V | 1.020 | 0.14 |
| 12_S | 41_S | 1.018 | 0.14 |
| 2_K | 181_S | 1.017 | 0.14 |
| 89_R | 183_D | 1.014 | 0.14 |
| 222_Y | 232_N | 1.011 | 0.14 |
| 233_L | 253_E | 1.007 | 0.14 |
| 60_K | 234_Q | 1.007 | 0.14 |
| 41_S | 66_L | 1.006 | 0.14 |
| 232_N | 255_I | 1.004 | 0.14 |
| 39_D | 77_M | 1.003 | 0.14 |
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 | |
| 1r8eA | 1 | 0.9892 | 100 | 0.491 | Contact Map |
| 1d5yA | 4 | 0.9209 | 99.9 | 0.732 | Contact Map |
| 3gpvA | 2 | 0.3957 | 99.9 | 0.746 | Contact Map |
| 3gp4A | 2 | 0.4532 | 99.9 | 0.749 | Contact Map |
| 3hh0A | 4 | 0.4712 | 99.9 | 0.756 | Contact Map |
| 2zhgA | 1 | 0.4281 | 99.9 | 0.757 | Contact Map |
| 1r8dA | 2 | 0.3921 | 99.9 | 0.758 | Contact Map |
| 1q06A | 2 | 0.4353 | 99.9 | 0.758 | Contact Map |
| 3qaoA | 1 | 0.4568 | 99.9 | 0.763 | Contact Map |
| 2vz4A | 1 | 0.3597 | 99.9 | 0.766 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)