| bub3 |
| ID: | 1436441757 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 328 (304) | ||
| Sequences: | 8798 (7166.6) | ||
| Seq/Len: | 28.941 | ||
| Nf(neff/√len): | 411.0 |
Jackhmmer Results: (2015_01_07)
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: 28.941).
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 |
| 95_H | 113_T | 3.666 | 1.00 |
| 55_H | 72_S | 3.587 | 1.00 |
| 61_D | 73_G | 3.539 | 1.00 |
| 32_V | 42_Y | 3.316 | 1.00 |
| 71_W | 81_M | 3.098 | 1.00 |
| 113_T | 123_W | 3.018 | 1.00 |
| 101_C | 114_G | 2.822 | 1.00 |
| 72_S | 82_H | 2.808 | 1.00 |
| 31_L | 70_A | 2.704 | 1.00 |
| 19_S | 33_S | 2.680 | 1.00 |
| 13_P | 32_V | 2.677 | 1.00 |
| 31_L | 64_F | 2.584 | 1.00 |
| 196_L | 206_E | 2.530 | 1.00 |
| 251_T | 261_W | 2.509 | 1.00 |
| 79_L | 113_T | 2.405 | 1.00 |
| 71_W | 104_Y | 2.397 | 1.00 |
| 184_C | 197_S | 2.366 | 1.00 |
| 142_T | 153_G | 2.334 | 1.00 |
| 152_V | 162_W | 2.325 | 1.00 |
| 71_W | 111_M | 2.256 | 1.00 |
| 112_V | 122_L | 2.227 | 1.00 |
| 114_G | 140_V | 2.193 | 1.00 |
| 31_L | 41_L | 2.080 | 1.00 |
| 178_L | 196_L | 2.060 | 1.00 |
| 112_V | 145_V | 2.058 | 1.00 |
| 39_V | 72_S | 2.002 | 1.00 |
| 195_V | 205_V | 2.000 | 1.00 |
| 115_S | 119_T | 1.934 | 1.00 |
| 151_I | 161_V | 1.920 | 1.00 |
| 43_D | 46_A | 1.886 | 1.00 |
| 239_A | 252_G | 1.854 | 1.00 |
| 124_D | 127_T | 1.820 | 1.00 |
| 31_L | 62_C | 1.804 | 1.00 |
| 233_Q | 251_T | 1.797 | 1.00 |
| 262_D | 265_N | 1.776 | 1.00 |
| 136_Q | 152_V | 1.751 | 1.00 |
| 62_C | 72_S | 1.733 | 1.00 |
| 250_A | 260_I | 1.726 | 1.00 |
| 121_K | 130_N | 1.725 | 1.00 |
| 80_K | 89_E | 1.650 | 1.00 |
| 25_N | 28_Q | 1.643 | 1.00 |
| 23_S | 64_F | 1.618 | 1.00 |
| 95_H | 117_D | 1.612 | 1.00 |
| 60_L | 75_L | 1.608 | 1.00 |
| 80_K | 91_L | 1.601 | 1.00 |
| 34_S | 38_S | 1.594 | 1.00 |
| 33_S | 59_V | 1.572 | 1.00 |
| 55_H | 74_G | 1.563 | 1.00 |
| 153_G | 157_R | 1.542 | 1.00 |
| 195_V | 242_F | 1.536 | 1.00 |
| 100_R | 116_W | 1.527 | 1.00 |
| 21_K | 63_A | 1.519 | 1.00 |
| 63_A | 103_E | 1.515 | 1.00 |
| 74_G | 78_Q | 1.511 | 1.00 |
| 73_G | 99_I | 1.505 | 1.00 |
| 197_S | 201_G | 1.487 | 1.00 |
| 112_V | 150_L | 1.478 | 1.00 |
| 23_S | 28_Q | 1.477 | 1.00 |
| 95_H | 115_S | 1.465 | 1.00 |
| 76_D | 80_K | 1.458 | 1.00 |
| 18_S | 35_W | 1.437 | 1.00 |
| 105_C | 145_V | 1.425 | 1.00 |
| 20_V | 32_V | 1.419 | 1.00 |
| 83_D | 86_T | 1.417 | 1.00 |
| 55_H | 59_V | 1.415 | 1.00 |
| 103_E | 144_S | 1.412 | 1.00 |
| 117_D | 121_K | 1.395 | 0.99 |
| 33_S | 37_T | 1.383 | 0.99 |
| 13_P | 34_S | 1.381 | 0.99 |
| 55_H | 76_D | 1.372 | 0.99 |
| 241_S | 250_A | 1.358 | 0.99 |
| 33_S | 62_C | 1.355 | 0.99 |
| 187_A | 208_L | 1.328 | 0.99 |
| 65_Y | 71_W | 1.327 | 0.99 |
| 163_D | 166_N | 1.320 | 0.99 |
| 154_T | 158_R | 1.305 | 0.99 |
| 207_Y | 210_P | 1.300 | 0.99 |
| 102_V | 113_T | 1.272 | 0.99 |
| 65_Y | 104_Y | 1.270 | 0.99 |
| 72_S | 80_K | 1.268 | 0.99 |
| 178_L | 198_S | 1.263 | 0.99 |
| 39_V | 62_C | 1.261 | 0.99 |
| 65_Y | 69_H | 1.261 | 0.99 |
| 64_F | 70_A | 1.257 | 0.99 |
| 120_V | 152_V | 1.256 | 0.99 |
| 103_E | 143_L | 1.254 | 0.99 |
| 20_V | 30_L | 1.251 | 0.99 |
| 197_S | 237_V | 1.246 | 0.98 |
| 13_P | 42_Y | 1.243 | 0.98 |
| 121_K | 133_T | 1.239 | 0.98 |
| 105_C | 110_V | 1.232 | 0.98 |
| 149_R | 153_G | 1.229 | 0.98 |
| 21_K | 62_C | 1.213 | 0.98 |
| 154_T | 157_R | 1.213 | 0.98 |
| 167_M | 170_V | 1.210 | 0.98 |
| 233_Q | 237_V | 1.202 | 0.98 |
| 69_H | 81_M | 1.191 | 0.98 |
| 253_G | 259_N | 1.185 | 0.98 |
| 98_P | 116_W | 1.183 | 0.98 |
| 146_S | 187_A | 1.180 | 0.98 |
| 99_I | 113_T | 1.180 | 0.98 |
| 95_H | 123_W | 1.166 | 0.97 |
| 285_S | 288_G | 1.163 | 0.97 |
| 113_T | 121_K | 1.155 | 0.97 |
| 34_S | 37_T | 1.154 | 0.97 |
| 186_R | 195_V | 1.145 | 0.97 |
| 106_P | 145_V | 1.140 | 0.97 |
| 32_V | 40_R | 1.138 | 0.97 |
| 186_R | 241_S | 1.133 | 0.97 |
| 24_P | 67_P | 1.132 | 0.97 |
| 73_G | 102_V | 1.123 | 0.97 |
| 166_N | 170_V | 1.122 | 0.97 |
| 154_T | 160_L | 1.119 | 0.96 |
| 211_S | 214_V | 1.118 | 0.96 |
| 207_Y | 211_S | 1.113 | 0.96 |
| 250_A | 284_F | 1.108 | 0.96 |
| 94_T | 123_W | 1.103 | 0.96 |
| 156_G | 160_L | 1.099 | 0.96 |
| 188_F | 191_K | 1.098 | 0.96 |
| 71_W | 102_V | 1.095 | 0.96 |
| 163_D | 170_V | 1.094 | 0.96 |
| 136_Q | 140_V | 1.094 | 0.96 |
| 82_H | 89_E | 1.093 | 0.96 |
| 63_A | 102_V | 1.084 | 0.96 |
| 115_S | 121_K | 1.077 | 0.95 |
| 104_Y | 111_M | 1.076 | 0.95 |
| 74_G | 77_H | 1.076 | 0.95 |
| 293_I | 302_D | 1.073 | 0.95 |
| 285_S | 289_T | 1.071 | 0.95 |
| 62_C | 70_A | 1.070 | 0.95 |
| 243_H | 247_N | 1.050 | 0.94 |
| 187_A | 194_Y | 1.049 | 0.94 |
| 196_L | 204_A | 1.046 | 0.94 |
| 197_S | 240_I | 1.043 | 0.94 |
| 13_P | 36_D | 1.040 | 0.94 |
| 299_Y | 302_D | 1.039 | 0.94 |
| 297_Y | 300_E | 1.035 | 0.94 |
| 112_V | 143_L | 1.032 | 0.94 |
| 23_S | 29_F | 1.030 | 0.94 |
| 151_I | 187_A | 1.027 | 0.94 |
| 33_S | 72_S | 1.024 | 0.93 |
| 59_V | 72_S | 1.022 | 0.93 |
| 163_D | 167_M | 1.020 | 0.93 |
| 95_H | 99_I | 1.018 | 0.93 |
| 65_Y | 68_T | 1.018 | 0.93 |
| 152_V | 156_G | 1.015 | 0.93 |
| 259_N | 268_R | 1.013 | 0.93 |
| 22_F | 30_L | 1.013 | 0.93 |
| 34_S | 40_R | 1.012 | 0.93 |
| 285_S | 292_A | 1.010 | 0.93 |
| 61_D | 102_V | 1.010 | 0.93 |
| 36_D | 40_R | 1.008 | 0.93 |
| 40_R | 51_L | 1.005 | 0.93 |
| 243_H | 248_T | 1.004 | 0.93 |
| 300_E | 303_D | 1.001 | 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 | |
| 1vyhC | 10 | 0.875 | 100 | 0.211 | Contact Map |
| 4wjsA | 1 | 0.8841 | 100 | 0.221 | Contact Map |
| 4j87A | 1 | 0.8841 | 100 | 0.235 | Contact Map |
| 4wjuA | 2 | 0.8872 | 100 | 0.247 | Contact Map |
| 4j73A | 1 | 0.8659 | 100 | 0.251 | Contact Map |
| 1gotB | 1 | 0.878 | 100 | 0.252 | Contact Map |
| 4lg9A | 1 | 0.8628 | 100 | 0.256 | Contact Map |
| 3dm0A | 1 | 0.875 | 100 | 0.261 | Contact Map |
| 3j80g | 1 | 0.8811 | 100 | 0.271 | Contact Map |
| 3sfzA | 1 | 0.8811 | 100 | 0.272 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)