| 3fbw |
| ID: | 1470718281 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 290 (274) | ||
| Sequences: | 37491 (24951.2) | ||
| Seq/Len: | 136.828 | ||
| Nf(neff/√len): | 1507.4 |
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: 136.828).
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 |
| 23_D | 57_R | 4.303 | 1.00 |
| 98_V | 122_G | 4.250 | 1.00 |
| 64_I | 84_Y | 3.889 | 1.00 |
| 86_D | 112_W | 3.085 | 1.00 |
| 239_T | 265_G | 3.034 | 1.00 |
| 234_L | 286_W | 2.995 | 1.00 |
| 48_I | 280_G | 2.922 | 1.00 |
| 262_V | 282_E | 2.919 | 1.00 |
| 264_I | 282_E | 2.670 | 1.00 |
| 226_L | 231_V | 2.661 | 1.00 |
| 275_N | 278_L | 2.585 | 1.00 |
| 126_M | 279_I | 2.491 | 1.00 |
| 98_V | 121_K | 2.480 | 1.00 |
| 96_E | 121_K | 2.353 | 1.00 |
| 86_D | 116_N | 2.276 | 1.00 |
| 127_E | 241_G | 2.218 | 1.00 |
| 89_I | 97_V | 2.218 | 1.00 |
| 239_T | 263_D | 2.196 | 1.00 |
| 106_S | 128_F | 2.190 | 1.00 |
| 90_E | 119_R | 2.157 | 1.00 |
| 113_A | 123_I | 2.144 | 1.00 |
| 18_R | 70_D | 2.142 | 1.00 |
| 86_D | 90_E | 2.129 | 1.00 |
| 99_L | 109_G | 2.087 | 1.00 |
| 112_W | 116_N | 2.064 | 1.00 |
| 253_A | 259_C | 2.048 | 1.00 |
| 20_H | 68_K | 2.007 | 1.00 |
| 111_H | 115_R | 1.969 | 1.00 |
| 55_S | 284_A | 1.956 | 1.00 |
| 246_P | 263_D | 1.944 | 1.00 |
| 86_D | 119_R | 1.893 | 1.00 |
| 109_G | 123_I | 1.882 | 1.00 |
| 98_V | 287_L | 1.873 | 1.00 |
| 83_R | 115_R | 1.862 | 1.00 |
| 31_P | 57_R | 1.841 | 1.00 |
| 31_P | 59_I | 1.838 | 1.00 |
| 260_K | 289_A | 1.796 | 1.00 |
| 98_V | 124_A | 1.772 | 1.00 |
| 22_V | 42_S | 1.752 | 1.00 |
| 51_H | 280_G | 1.746 | 1.00 |
| 21_Y | 88_F | 1.740 | 1.00 |
| 267_G | 275_N | 1.707 | 1.00 |
| 61_P | 85_L | 1.694 | 1.00 |
| 251_R | 255_S | 1.685 | 1.00 |
| 124_A | 283_I | 1.682 | 1.00 |
| 35_L | 85_L | 1.674 | 1.00 |
| 282_E | 285_R | 1.650 | 1.00 |
| 36_H | 66_M | 1.648 | 1.00 |
| 35_L | 63_L | 1.617 | 1.00 |
| 82_V | 111_H | 1.616 | 1.00 |
| 23_D | 59_I | 1.592 | 1.00 |
| 125_C | 128_F | 1.588 | 1.00 |
| 30_T | 98_V | 1.553 | 1.00 |
| 233_K | 256_L | 1.548 | 1.00 |
| 24_V | 60_A | 1.546 | 1.00 |
| 234_L | 262_V | 1.546 | 1.00 |
| 79_D | 115_R | 1.536 | 1.00 |
| 36_H | 63_L | 1.525 | 1.00 |
| 49_I | 60_A | 1.514 | 1.00 |
| 278_L | 282_E | 1.477 | 1.00 |
| 281_S | 285_R | 1.471 | 1.00 |
| 85_L | 112_W | 1.464 | 1.00 |
| 111_H | 114_K | 1.452 | 1.00 |
| 228_Q | 231_V | 1.448 | 1.00 |
| 30_T | 121_K | 1.439 | 1.00 |
| 63_L | 108_L | 1.416 | 1.00 |
| 35_L | 109_G | 1.409 | 1.00 |
| 124_A | 234_L | 1.409 | 1.00 |
| 221_A | 225_W | 1.404 | 0.99 |
| 77_F | 80_D | 1.401 | 0.99 |
| 237_W | 249_A | 1.399 | 0.99 |
| 264_I | 267_G | 1.391 | 0.99 |
| 90_E | 116_N | 1.381 | 0.99 |
| 40_T | 44_L | 1.381 | 0.99 |
| 59_I | 88_F | 1.365 | 0.99 |
| 250_A | 254_E | 1.352 | 0.99 |
| 116_N | 119_R | 1.349 | 0.99 |
| 62_D | 67_G | 1.347 | 0.99 |
| 37_G | 103_D | 1.346 | 0.99 |
| 34_F | 100_V | 1.342 | 0.99 |
| 246_P | 250_A | 1.341 | 0.99 |
| 56_H | 98_V | 1.341 | 0.99 |
| 112_W | 120_V | 1.334 | 0.99 |
| 20_H | 42_S | 1.332 | 0.99 |
| 51_H | 284_A | 1.315 | 0.99 |
| 31_P | 94_L | 1.315 | 0.99 |
| 33_L | 89_I | 1.306 | 0.99 |
| 250_A | 263_D | 1.306 | 0.99 |
| 103_D | 269_H | 1.305 | 0.99 |
| 110_F | 125_C | 1.291 | 0.99 |
| 237_W | 263_D | 1.289 | 0.99 |
| 11_Y | 18_R | 1.270 | 0.99 |
| 30_T | 56_H | 1.267 | 0.99 |
| 56_H | 288_P | 1.259 | 0.99 |
| 34_F | 58_C | 1.252 | 0.99 |
| 100_V | 126_M | 1.246 | 0.98 |
| 260_K | 282_E | 1.224 | 0.98 |
| 32_V | 56_H | 1.210 | 0.98 |
| 237_W | 246_P | 1.207 | 0.98 |
| 284_A | 288_P | 1.203 | 0.98 |
| 279_I | 283_I | 1.192 | 0.98 |
| 123_I | 233_K | 1.182 | 0.98 |
| 42_S | 62_D | 1.176 | 0.98 |
| 14_V | 87_A | 1.175 | 0.98 |
| 102_H | 272_Q | 1.172 | 0.98 |
| 79_D | 111_H | 1.171 | 0.98 |
| 256_L | 259_C | 1.169 | 0.97 |
| 236_F | 264_I | 1.162 | 0.97 |
| 86_D | 115_R | 1.152 | 0.97 |
| 249_A | 261_T | 1.142 | 0.97 |
| 15_L | 87_A | 1.138 | 0.97 |
| 224_N | 255_S | 1.138 | 0.97 |
| 51_H | 54_P | 1.134 | 0.97 |
| 97_V | 120_V | 1.132 | 0.97 |
| 236_F | 282_E | 1.129 | 0.97 |
| 82_V | 108_L | 1.127 | 0.97 |
| 19_M | 84_Y | 1.126 | 0.97 |
| 112_W | 119_R | 1.122 | 0.97 |
| 253_A | 261_T | 1.120 | 0.96 |
| 17_E | 64_I | 1.115 | 0.96 |
| 101_I | 109_G | 1.111 | 0.96 |
| 13_E | 18_R | 1.103 | 0.96 |
| 239_T | 266_P | 1.103 | 0.96 |
| 236_F | 279_I | 1.101 | 0.96 |
| 122_G | 286_W | 1.100 | 0.96 |
| 251_R | 254_E | 1.094 | 0.96 |
| 267_G | 271_L | 1.093 | 0.96 |
| 278_L | 281_S | 1.093 | 0.96 |
| 94_L | 97_V | 1.091 | 0.96 |
| 56_H | 287_L | 1.089 | 0.96 |
| 61_P | 88_F | 1.084 | 0.96 |
| 240_P | 266_P | 1.081 | 0.95 |
| 122_G | 232_P | 1.079 | 0.95 |
| 51_H | 277_D | 1.079 | 0.95 |
| 30_T | 96_E | 1.077 | 0.95 |
| 100_V | 283_I | 1.077 | 0.95 |
| 250_A | 261_T | 1.070 | 0.95 |
| 39_P | 66_M | 1.065 | 0.95 |
| 114_K | 221_A | 1.063 | 0.95 |
| 42_S | 68_K | 1.062 | 0.95 |
| 264_I | 278_L | 1.050 | 0.94 |
| 20_H | 62_D | 1.049 | 0.94 |
| 49_I | 58_C | 1.047 | 0.94 |
| 126_M | 271_L | 1.045 | 0.94 |
| 21_Y | 92_L | 1.041 | 0.94 |
| 75_D | 80_D | 1.029 | 0.94 |
| 19_M | 69_S | 1.026 | 0.94 |
| 262_V | 278_L | 1.022 | 0.93 |
| 268_L | 274_D | 1.020 | 0.93 |
| 237_W | 261_T | 1.015 | 0.93 |
| 250_A | 253_A | 1.015 | 0.93 |
| 239_T | 246_P | 1.007 | 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
- 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 | |
| 1ehyA | 4 | 0.9276 | 100 | 0.07 | Contact Map |
| 4psuA | 1 | 0.9414 | 100 | 0.079 | Contact Map |
| 4inzA | 2 | 0.9483 | 100 | 0.081 | Contact Map |
| 3om8A | 2 | 0.9138 | 100 | 0.088 | Contact Map |
| 2xuaA | 2 | 0.8931 | 100 | 0.105 | Contact Map |
| 2pujA | 1 | 0.931 | 100 | 0.108 | Contact Map |
| 1iupA | 1 | 0.9207 | 100 | 0.108 | Contact Map |
| 3oosA | 1 | 0.9138 | 100 | 0.109 | Contact Map |
| 2wueA | 2 | 0.9448 | 100 | 0.11 | Contact Map |
| 3g9xA | 1 | 0.9862 | 100 | 0.112 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)