| sub_bpn_mat |
| ID: | 1494278083 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 275 (273) | ||
| Sequences: | 16787 (11456) | ||
| Seq/Len: | 61.491 | ||
| Nf(neff/√len): | 693.3 |
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: 61.491).
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 |
| 22_T | 87_S | 2.915 | 1.00 |
| 230_A | 270_V | 2.819 | 1.00 |
| 178_G | 199_M | 2.728 | 1.00 |
| 96_L | 102_G | 2.674 | 1.00 |
| 209_L | 215_G | 2.644 | 1.00 |
| 28_V | 72_V | 2.501 | 1.00 |
| 123_N | 224_S | 2.412 | 1.00 |
| 67_H | 222_M | 2.356 | 1.00 |
| 230_A | 268_I | 2.238 | 1.00 |
| 61_D | 98_D | 2.216 | 1.00 |
| 255_T | 269_N | 2.210 | 1.00 |
| 24_S | 87_S | 2.195 | 1.00 |
| 27_K | 89_A | 2.163 | 1.00 |
| 67_H | 207_S | 2.158 | 1.00 |
| 179_A | 189_F | 2.120 | 1.00 |
| 179_A | 187_A | 2.119 | 1.00 |
| 187_A | 203_V | 2.117 | 1.00 |
| 189_F | 203_V | 2.079 | 1.00 |
| 179_A | 202_G | 1.994 | 1.00 |
| 93_V | 113_W | 1.981 | 1.00 |
| 70_G | 207_S | 1.975 | 1.00 |
| 70_G | 208_T | 1.954 | 1.00 |
| 27_K | 91_Y | 1.911 | 1.00 |
| 71_T | 226_H | 1.909 | 1.00 |
| 93_V | 110_G | 1.883 | 1.00 |
| 112_E | 141_K | 1.866 | 1.00 |
| 68_V | 225_P | 1.856 | 1.00 |
| 242_T | 245_Q | 1.848 | 1.00 |
| 140_D | 173_S | 1.836 | 1.00 |
| 68_V | 123_N | 1.835 | 1.00 |
| 148_V | 231_A | 1.823 | 1.00 |
| 209_L | 217_Y | 1.806 | 1.00 |
| 253_T | 273_A | 1.788 | 1.00 |
| 169_G | 176_A | 1.781 | 1.00 |
| 60_D | 63_S | 1.780 | 1.00 |
| 30_V | 72_V | 1.774 | 1.00 |
| 123_N | 228_A | 1.736 | 1.00 |
| 120_D | 235_L | 1.736 | 1.00 |
| 7_G | 226_H | 1.691 | 1.00 |
| 133_A | 137_A | 1.680 | 1.00 |
| 231_A | 246_V | 1.654 | 1.00 |
| 217_Y | 222_M | 1.644 | 1.00 |
| 248_S | 252_N | 1.640 | 1.00 |
| 21_Y | 236_S | 1.639 | 1.00 |
| 73_A | 90_L | 1.631 | 1.00 |
| 224_S | 228_A | 1.620 | 1.00 |
| 150_V | 231_A | 1.616 | 1.00 |
| 28_V | 232_A | 1.610 | 1.00 |
| 178_G | 190_S | 1.601 | 1.00 |
| 10_Q | 184_N | 1.576 | 1.00 |
| 235_L | 246_V | 1.575 | 1.00 |
| 91_Y | 119_M | 1.572 | 1.00 |
| 29_A | 114_A | 1.560 | 1.00 |
| 238_H | 241_W | 1.549 | 1.00 |
| 150_V | 224_S | 1.548 | 1.00 |
| 84_V | 229_G | 1.540 | 1.00 |
| 31_I | 95_V | 1.533 | 1.00 |
| 115_I | 142_A | 1.509 | 1.00 |
| 184_N | 267_L | 1.507 | 1.00 |
| 113_W | 117_N | 1.495 | 1.00 |
| 67_H | 217_Y | 1.480 | 1.00 |
| 181_D | 203_V | 1.476 | 1.00 |
| 29_A | 119_M | 1.475 | 1.00 |
| 30_V | 68_V | 1.473 | 1.00 |
| 112_E | 116_A | 1.470 | 1.00 |
| 148_V | 175_I | 1.464 | 1.00 |
| 234_I | 273_A | 1.457 | 1.00 |
| 150_V | 227_V | 1.457 | 1.00 |
| 35_I | 92_A | 1.436 | 1.00 |
| 103_Q | 106_W | 1.426 | 1.00 |
| 74_A | 208_T | 1.421 | 1.00 |
| 22_T | 236_S | 1.420 | 1.00 |
| 121_V | 228_A | 1.416 | 1.00 |
| 140_D | 144_A | 1.415 | 1.00 |
| 69_A | 90_L | 1.406 | 0.99 |
| 247_R | 251_Q | 1.394 | 0.99 |
| 181_D | 185_Q | 1.368 | 0.99 |
| 152_A | 224_S | 1.348 | 0.99 |
| 269_N | 272_A | 1.348 | 0.99 |
| 26_V | 235_L | 1.347 | 0.99 |
| 142_A | 149_V | 1.344 | 0.99 |
| 231_A | 250_L | 1.337 | 0.99 |
| 256_K | 260_S | 1.327 | 0.99 |
| 136_K | 140_D | 1.321 | 0.99 |
| 179_A | 203_V | 1.316 | 0.99 |
| 115_I | 147_V | 1.306 | 0.99 |
| 153_A | 176_A | 1.300 | 0.99 |
| 85_A | 232_A | 1.299 | 0.99 |
| 178_G | 196_L | 1.295 | 0.99 |
| 136_K | 170_K | 1.288 | 0.99 |
| 164_T | 195_E | 1.273 | 0.99 |
| 111_I | 142_A | 1.270 | 0.99 |
| 28_V | 88_S | 1.268 | 0.99 |
| 241_W | 249_S | 1.267 | 0.99 |
| 71_T | 222_M | 1.265 | 0.99 |
| 238_H | 249_S | 1.263 | 0.99 |
| 206_Q | 216_A | 1.245 | 0.98 |
| 186_R | 199_M | 1.240 | 0.98 |
| 180_V | 199_M | 1.235 | 0.98 |
| 186_R | 190_S | 1.234 | 0.98 |
| 36_D | 210_P | 1.233 | 0.98 |
| 198_V | 250_L | 1.218 | 0.98 |
| 85_A | 88_S | 1.204 | 0.98 |
| 124_M | 151_A | 1.199 | 0.98 |
| 69_A | 92_A | 1.199 | 0.98 |
| 108_I | 138_A | 1.195 | 0.98 |
| 26_V | 232_A | 1.193 | 0.98 |
| 157_G | 186_R | 1.181 | 0.98 |
| 203_V | 218_N | 1.180 | 0.98 |
| 122_I | 147_V | 1.173 | 0.98 |
| 156_E | 191_S | 1.173 | 0.98 |
| 192_V | 262_Y | 1.166 | 0.97 |
| 227_V | 268_I | 1.166 | 0.97 |
| 45_A | 89_A | 1.165 | 0.97 |
| 107_I | 126_L | 1.155 | 0.97 |
| 67_H | 71_T | 1.155 | 0.97 |
| 200_A | 227_V | 1.149 | 0.97 |
| 39_H | 214_Y | 1.139 | 0.97 |
| 175_I | 247_R | 1.136 | 0.97 |
| 141_K | 144_A | 1.134 | 0.97 |
| 177_V | 198_V | 1.124 | 0.97 |
| 32_D | 64_H | 1.120 | 0.96 |
| 68_V | 222_M | 1.110 | 0.96 |
| 148_V | 246_V | 1.109 | 0.96 |
| 271_Q | 275_Q | 1.109 | 0.96 |
| 143_V | 173_S | 1.102 | 0.96 |
| 151_A | 174_V | 1.093 | 0.96 |
| 124_M | 149_V | 1.091 | 0.96 |
| 64_H | 221_S | 1.088 | 0.96 |
| 180_V | 267_L | 1.072 | 0.95 |
| 73_A | 88_S | 1.070 | 0.95 |
| 95_V | 126_L | 1.066 | 0.95 |
| 12_K | 269_N | 1.061 | 0.95 |
| 116_A | 141_K | 1.042 | 0.94 |
| 125_S | 225_P | 1.040 | 0.94 |
| 12_K | 15_A | 1.033 | 0.94 |
| 111_I | 124_M | 1.033 | 0.94 |
| 108_I | 134_A | 1.033 | 0.94 |
| 234_I | 241_W | 1.031 | 0.94 |
| 249_S | 253_T | 1.024 | 0.93 |
| 222_M | 225_P | 1.018 | 0.93 |
| 45_A | 91_Y | 1.010 | 0.93 |
| 141_K | 145_S | 1.007 | 0.93 |
| 255_T | 267_L | 1.005 | 0.93 |
| 95_V | 110_G | 1.004 | 0.93 |
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 | |
| 1to2E | 1 | 1 | 100 | 0.052 | Contact Map |
| 3whiA | 2 | 1 | 100 | 0.058 | Contact Map |
| 1r0rE | 1 | 0.9964 | 100 | 0.062 | Contact Map |
| 1gciA | 1 | 0.9782 | 100 | 0.068 | Contact Map |
| 4j94A | 1 | 0.9927 | 100 | 0.122 | Contact Map |
| 2x8jA | 5 | 0.9782 | 100 | 0.122 | Contact Map |
| 1r6vA | 1 | 0.9855 | 100 | 0.127 | Contact Map |
| 1dbiA | 1 | 0.9418 | 100 | 0.131 | Contact Map |
| 4kg7A | 1 | 0.9782 | 100 | 0.134 | Contact Map |
| 4tr2A | 2 | 0.9964 | 100 | 0.135 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)