| BMV_1aC 120-390 |
| ID: | 1489304005 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 271 (267) | ||
| Sequences: | 4924 (3133) | ||
| Seq/Len: | 18.442 | ||
| Nf(neff/√len): | 191.7 |
HHblits Results: (2016_02)
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: 18.442).
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 |
| 235_D | 264_K | 4.316 | 1.00 |
| 27_E | 74_H | 3.645 | 1.00 |
| 235_D | 265_K | 3.578 | 1.00 |
| 148_V | 261_T | 3.192 | 1.00 |
| 236_N | 266_S | 3.084 | 1.00 |
| 227_H | 255_Y | 2.882 | 1.00 |
| 193_T | 234_V | 2.728 | 1.00 |
| 142_Q | 146_A | 2.624 | 1.00 |
| 191_N | 235_D | 2.607 | 1.00 |
| 19_I | 77_L | 2.399 | 1.00 |
| 58_V | 73_C | 2.395 | 1.00 |
| 137_T | 140_C | 2.373 | 1.00 |
| 29_L | 73_C | 2.238 | 1.00 |
| 23_F | 30_I | 2.235 | 1.00 |
| 196_T | 202_K | 2.235 | 1.00 |
| 193_T | 237_V | 2.190 | 1.00 |
| 83_L | 230_Q | 2.132 | 1.00 |
| 239_L | 259_A | 2.091 | 1.00 |
| 229_A | 234_V | 2.081 | 1.00 |
| 106_D | 109_Q | 2.049 | 1.00 |
| 195_L | 229_A | 2.029 | 1.00 |
| 32_T | 38_A | 2.008 | 1.00 |
| 21_D | 25_M | 2.008 | 1.00 |
| 146_A | 150_L | 1.983 | 1.00 |
| 32_T | 37_S | 1.945 | 1.00 |
| 60_R | 65_A | 1.903 | 1.00 |
| 40_D | 44_A | 1.900 | 1.00 |
| 222_H | 232_I | 1.839 | 1.00 |
| 22_A | 102_L | 1.838 | 1.00 |
| 222_H | 234_V | 1.770 | 1.00 |
| 239_L | 267_F | 1.760 | 1.00 |
| 234_V | 237_V | 1.750 | 1.00 |
| 30_I | 41_V | 1.747 | 1.00 |
| 224_K | 228_E | 1.743 | 1.00 |
| 205_L | 223_I | 1.674 | 1.00 |
| 75_R | 102_L | 1.651 | 1.00 |
| 21_D | 24_R | 1.651 | 1.00 |
| 19_I | 104_F | 1.646 | 1.00 |
| 238_T | 268_E | 1.643 | 1.00 |
| 17_T | 44_A | 1.642 | 1.00 |
| 198_T | 201_D | 1.571 | 1.00 |
| 236_N | 268_E | 1.565 | 1.00 |
| 9_G | 13_C | 1.542 | 1.00 |
| 137_T | 145_I | 1.523 | 1.00 |
| 39_E | 42_R | 1.514 | 1.00 |
| 75_R | 100_Q | 1.508 | 1.00 |
| 226_V | 259_A | 1.506 | 1.00 |
| 17_T | 21_D | 1.500 | 1.00 |
| 74_H | 99_S | 1.484 | 1.00 |
| 10_V | 13_C | 1.482 | 1.00 |
| 224_K | 229_A | 1.472 | 1.00 |
| 147_A | 151_L | 1.467 | 1.00 |
| 8_D | 107_T | 1.431 | 1.00 |
| 85_H | 88_Q | 1.428 | 1.00 |
| 31_V | 65_A | 1.417 | 1.00 |
| 229_A | 237_V | 1.395 | 0.99 |
| 29_L | 76_L | 1.386 | 0.99 |
| 81_A | 103_A | 1.380 | 0.99 |
| 5_S | 102_L | 1.376 | 0.99 |
| 5_S | 132_D | 1.349 | 0.99 |
| 22_A | 77_L | 1.347 | 0.99 |
| 140_C | 145_I | 1.327 | 0.99 |
| 9_G | 14_G | 1.288 | 0.99 |
| 111_S | 230_Q | 1.286 | 0.99 |
| 195_L | 226_V | 1.275 | 0.99 |
| 20_K | 44_A | 1.270 | 0.99 |
| 199_Q | 225_T | 1.266 | 0.99 |
| 240_V | 243_K | 1.261 | 0.99 |
| 7_V | 102_L | 1.253 | 0.99 |
| 194_Y | 205_L | 1.252 | 0.99 |
| 8_D | 131_R | 1.247 | 0.99 |
| 259_A | 262_R | 1.241 | 0.98 |
| 231_G | 262_R | 1.240 | 0.98 |
| 140_C | 144_V | 1.237 | 0.98 |
| 86_Y | 90_L | 1.223 | 0.98 |
| 12_G | 15_K | 1.222 | 0.98 |
| 195_L | 259_A | 1.219 | 0.98 |
| 193_T | 229_A | 1.218 | 0.98 |
| 202_K | 206_Q | 1.215 | 0.98 |
| 82_G | 230_Q | 1.209 | 0.98 |
| 21_D | 48_D | 1.199 | 0.98 |
| 230_Q | 257_L | 1.197 | 0.98 |
| 153_R | 157_N | 1.192 | 0.98 |
| 35_R | 39_E | 1.173 | 0.98 |
| 194_Y | 238_T | 1.167 | 0.97 |
| 9_G | 15_K | 1.161 | 0.97 |
| 173_R | 176_T | 1.155 | 0.97 |
| 89_L | 93_A | 1.154 | 0.97 |
| 237_V | 263_H | 1.136 | 0.97 |
| 80_E | 109_Q | 1.133 | 0.97 |
| 78_V | 103_A | 1.125 | 0.97 |
| 207_T | 210_K | 1.125 | 0.97 |
| 36_K | 228_E | 1.124 | 0.97 |
| 230_Q | 258_V | 1.122 | 0.97 |
| 36_K | 232_I | 1.114 | 0.96 |
| 80_E | 258_V | 1.111 | 0.96 |
| 19_I | 30_I | 1.106 | 0.96 |
| 61_T | 64_S | 1.097 | 0.96 |
| 20_K | 41_V | 1.090 | 0.96 |
| 197_M | 226_V | 1.088 | 0.96 |
| 205_L | 240_V | 1.087 | 0.96 |
| 81_A | 105_G | 1.085 | 0.96 |
| 194_Y | 223_I | 1.076 | 0.95 |
| 6_M | 103_A | 1.073 | 0.95 |
| 87_G | 90_L | 1.067 | 0.95 |
| 208_R | 212_F | 1.059 | 0.95 |
| 236_N | 265_K | 1.050 | 0.94 |
| 33_A | 230_Q | 1.046 | 0.94 |
| 33_A | 83_L | 1.041 | 0.94 |
| 260_L | 267_F | 1.036 | 0.94 |
| 187_T | 190_P | 1.034 | 0.94 |
| 258_V | 262_R | 1.033 | 0.94 |
| 105_G | 109_Q | 1.032 | 0.94 |
| 53_K | 56_L | 1.031 | 0.94 |
| 37_S | 40_D | 1.031 | 0.94 |
| 78_V | 88_Q | 1.026 | 0.94 |
| 204_A | 208_R | 1.025 | 0.93 |
| 256_C | 260_L | 1.024 | 0.93 |
| 13_C | 134_V | 1.019 | 0.93 |
| 12_G | 16_T | 1.009 | 0.93 |
| 132_D | 136_K | 1.006 | 0.93 |
| 108_E | 158_R | 1.005 | 0.93 |
| 35_R | 38_A | 1.003 | 0.93 |
| 197_M | 252_H | 1.001 | 0.92 |
| 83_L | 111_S | 1.000 | 0.92 |
| 144_V | 263_H | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3vkwA | 1 | 0.9262 | 100 | 0.241 | Contact Map |
| 2xzlA | 1 | 0.9963 | 100 | 0.267 | Contact Map |
| 4b3fX | 1 | 0.9742 | 100 | 0.283 | Contact Map |
| 4pj3A | 1 | 1 | 100 | 0.288 | Contact Map |
| 2gk6A | 2 | 0.9852 | 100 | 0.289 | Contact Map |
| 2wjyA | 1 | 0.9963 | 100 | 0.29 | Contact Map |
| 3upuA | 3 | 0.952 | 100 | 0.351 | Contact Map |
| 4c2tA | 4 | 0.9852 | 100 | 0.353 | Contact Map |
| 4c2uA | 2 | 0.9926 | 100 | 0.362 | Contact Map |
| 1pjrA | 1 | 0.9889 | 100 | 0.364 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)