| bub3 |
| ID: | 1407249026 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 320 (299) | ||
| Sequences: | 9644 (7921.3) | ||
| Seq/Len: | 32.254 | ||
| Nf(neff/√len): | 458.1 |
Jackhmmer Results: (2014_04_16)
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: 32.254).
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 |
| 54_L | 71_V | 3.914 | 1.00 |
| 94_H | 112_S | 3.874 | 1.00 |
| 11_S | 30_A | 3.708 | 1.00 |
| 100_C | 113_G | 3.132 | 1.00 |
| 60_S | 72_G | 3.107 | 1.00 |
| 112_S | 122_W | 3.090 | 1.00 |
| 30_A | 40_Y | 2.984 | 1.00 |
| 195_S | 205_E | 2.824 | 1.00 |
| 78_V | 112_S | 2.762 | 1.00 |
| 250_T | 260_W | 2.725 | 1.00 |
| 151_L | 161_Y | 2.713 | 1.00 |
| 70_L | 80_T | 2.712 | 1.00 |
| 29_I | 69_A | 2.690 | 1.00 |
| 29_I | 63_Y | 2.592 | 1.00 |
| 17_S | 31_G | 2.481 | 1.00 |
| 71_V | 81_L | 2.478 | 1.00 |
| 70_L | 110_F | 2.366 | 1.00 |
| 70_L | 103_K | 2.339 | 1.00 |
| 232_I | 250_T | 2.338 | 1.00 |
| 111_I | 121_V | 2.235 | 1.00 |
| 194_V | 204_V | 2.115 | 1.00 |
| 183_S | 196_S | 2.079 | 1.00 |
| 29_I | 39_H | 2.073 | 1.00 |
| 114_S | 118_S | 2.055 | 1.00 |
| 141_A | 152_G | 2.024 | 1.00 |
| 37_L | 71_V | 2.016 | 1.00 |
| 113_G | 139_I | 1.985 | 1.00 |
| 177_F | 195_S | 1.895 | 1.00 |
| 238_D | 251_A | 1.892 | 1.00 |
| 54_L | 58_I | 1.827 | 1.00 |
| 123_D | 126_V | 1.746 | 1.00 |
| 150_V | 160_V | 1.723 | 1.00 |
| 94_H | 116_D | 1.715 | 1.00 |
| 249_A | 283_F | 1.672 | 1.00 |
| 82_D | 85_T | 1.656 | 1.00 |
| 196_S | 200_G | 1.651 | 1.00 |
| 162_D | 165_N | 1.648 | 1.00 |
| 16_S | 33_W | 1.648 | 1.00 |
| 111_I | 144_S | 1.646 | 1.00 |
| 194_V | 241_F | 1.643 | 1.00 |
| 111_I | 149_L | 1.640 | 1.00 |
| 38_L | 47_E | 1.628 | 1.00 |
| 34_D | 38_L | 1.613 | 1.00 |
| 29_I | 61_L | 1.589 | 1.00 |
| 23_S | 26_N | 1.588 | 1.00 |
| 79_T | 90_F | 1.585 | 1.00 |
| 293_A | 297_Q | 1.583 | 1.00 |
| 261_D | 264_V | 1.573 | 1.00 |
| 73_N | 76_G | 1.564 | 1.00 |
| 79_T | 88_H | 1.547 | 1.00 |
| 72_G | 101_I | 1.534 | 1.00 |
| 152_G | 156_R | 1.510 | 1.00 |
| 94_H | 114_S | 1.507 | 1.00 |
| 19_I | 62_E | 1.499 | 1.00 |
| 18_V | 30_A | 1.488 | 1.00 |
| 54_L | 73_N | 1.488 | 1.00 |
| 54_L | 75_D | 1.481 | 1.00 |
| 112_S | 120_R | 1.474 | 1.00 |
| 30_A | 38_L | 1.469 | 1.00 |
| 59_L | 74_L | 1.464 | 1.00 |
| 62_E | 102_S | 1.460 | 1.00 |
| 32_C | 36_S | 1.449 | 1.00 |
| 20_F | 28_L | 1.445 | 1.00 |
| 120_R | 129_P | 1.444 | 1.00 |
| 11_S | 34_D | 1.441 | 1.00 |
| 72_G | 98_V | 1.436 | 1.00 |
| 249_A | 259_F | 1.430 | 1.00 |
| 61_L | 71_V | 1.420 | 1.00 |
| 119_F | 151_L | 1.405 | 0.99 |
| 21_S | 26_N | 1.403 | 0.99 |
| 73_N | 77_T | 1.396 | 0.99 |
| 31_G | 58_I | 1.389 | 0.99 |
| 11_S | 32_C | 1.383 | 0.99 |
| 93_N | 122_W | 1.378 | 0.99 |
| 135_I | 151_L | 1.373 | 0.99 |
| 72_G | 76_G | 1.360 | 0.99 |
| 19_I | 61_L | 1.354 | 0.99 |
| 32_C | 35_G | 1.351 | 0.99 |
| 41_Q | 44_E | 1.341 | 0.99 |
| 21_S | 63_Y | 1.339 | 0.99 |
| 145_R | 186_C | 1.332 | 0.99 |
| 53_D | 81_L | 1.315 | 0.99 |
| 94_H | 98_V | 1.312 | 0.99 |
| 242_H | 246_Q | 1.302 | 0.99 |
| 120_R | 132_G | 1.282 | 0.99 |
| 11_S | 40_Y | 1.282 | 0.99 |
| 150_V | 186_C | 1.280 | 0.99 |
| 61_L | 69_A | 1.272 | 0.99 |
| 280_S | 293_A | 1.258 | 0.99 |
| 186_C | 193_F | 1.256 | 0.99 |
| 101_I | 112_S | 1.254 | 0.99 |
| 196_S | 236_V | 1.253 | 0.99 |
| 206_Y | 209_P | 1.253 | 0.99 |
| 103_K | 110_F | 1.234 | 0.98 |
| 54_L | 81_L | 1.230 | 0.98 |
| 194_V | 248_L | 1.230 | 0.98 |
| 71_V | 79_T | 1.228 | 0.98 |
| 232_I | 236_V | 1.220 | 0.98 |
| 64_T | 68_T | 1.216 | 0.98 |
| 184_V | 193_F | 1.212 | 0.98 |
| 152_G | 181_T | 1.196 | 0.98 |
| 64_T | 70_L | 1.194 | 0.98 |
| 99_S | 115_W | 1.193 | 0.98 |
| 281_I | 290_L | 1.190 | 0.98 |
| 21_S | 27_E | 1.169 | 0.97 |
| 31_G | 35_G | 1.168 | 0.97 |
| 146_D | 186_C | 1.165 | 0.97 |
| 38_L | 50_G | 1.164 | 0.97 |
| 94_H | 122_W | 1.162 | 0.97 |
| 28_L | 42_I | 1.159 | 0.97 |
| 111_I | 142_S | 1.155 | 0.97 |
| 102_S | 143_S | 1.155 | 0.97 |
| 251_A | 255_G | 1.154 | 0.97 |
| 18_V | 28_L | 1.148 | 0.97 |
| 64_T | 103_K | 1.146 | 0.97 |
| 75_D | 79_T | 1.145 | 0.97 |
| 116_D | 120_R | 1.145 | 0.97 |
| 54_L | 79_T | 1.136 | 0.97 |
| 63_Y | 69_A | 1.135 | 0.97 |
| 62_E | 101_I | 1.132 | 0.97 |
| 47_E | 50_G | 1.127 | 0.97 |
| 104_L | 144_S | 1.124 | 0.97 |
| 284_N | 288_S | 1.120 | 0.96 |
| 22_P | 67_K | 1.113 | 0.96 |
| 196_S | 239_L | 1.102 | 0.96 |
| 284_N | 289_M | 1.098 | 0.96 |
| 153_C | 159_L | 1.097 | 0.96 |
| 70_L | 101_I | 1.097 | 0.96 |
| 31_G | 61_L | 1.096 | 0.96 |
| 187_N | 190_F | 1.088 | 0.96 |
| 105_R | 144_S | 1.086 | 0.96 |
| 232_I | 252_G | 1.085 | 0.96 |
| 41_Q | 48_L | 1.083 | 0.96 |
| 177_F | 197_S | 1.071 | 0.95 |
| 274_S | 292_I | 1.068 | 0.95 |
| 188_Q | 245_H | 1.063 | 0.95 |
| 240_K | 249_A | 1.063 | 0.95 |
| 284_N | 287_G | 1.062 | 0.95 |
| 195_S | 203_S | 1.055 | 0.95 |
| 108_N | 125_R | 1.050 | 0.94 |
| 260_W | 267_R | 1.050 | 0.94 |
| 32_C | 38_L | 1.048 | 0.94 |
| 151_L | 159_L | 1.047 | 0.94 |
| 155_E | 159_L | 1.041 | 0.94 |
| 292_I | 302_G | 1.037 | 0.94 |
| 194_V | 239_L | 1.034 | 0.94 |
| 73_N | 79_T | 1.028 | 0.94 |
| 22_P | 63_Y | 1.020 | 0.93 |
| 129_P | 132_G | 1.010 | 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 | |
| 1vyhC | 10 | 0.8969 | 100 | 0.154 | Contact Map |
| 3j65q | 1 | 0.9094 | 100 | 0.186 | Contact Map |
| 3sfzA | 1 | 0.9031 | 100 | 0.198 | Contact Map |
| 1nr0A | 1 | 0.9156 | 100 | 0.214 | Contact Map |
| 4lg9A | 1 | 0.8812 | 100 | 0.218 | Contact Map |
| 1gotB | 1 | 0.9 | 100 | 0.219 | Contact Map |
| 3jroA | 1 | 0.8219 | 100 | 0.227 | Contact Map |
| 2pbiB | 2 | 0.9031 | 100 | 0.229 | Contact Map |
| 1erjA | 3 | 0.9031 | 100 | 0.231 | Contact Map |
| 4nsxA | 1 | 0.9469 | 100 | 0.231 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)