| d2wztb_ |
| ID: | 1447593029 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 258 (256) | ||
| Sequences: | 13680 (8894.5) | ||
| Seq/Len: | 53.438 | ||
| Nf(neff/√len): | 555.9 |
HHblits Results: (2015_06)
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: 53.438).
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 |
| 89_R | 130_I | 2.900 | 1.00 |
| 33_A | 236_A | 2.650 | 1.00 |
| 59_A | 96_G | 2.479 | 1.00 |
| 88_A | 125_V | 2.464 | 1.00 |
| 247_T | 250_E | 2.418 | 1.00 |
| 85_Q | 128_D | 2.352 | 1.00 |
| 206_H | 250_E | 2.261 | 1.00 |
| 85_Q | 124_K | 2.223 | 1.00 |
| 70_V | 97_L | 2.209 | 1.00 |
| 28_E | 56_R | 2.110 | 1.00 |
| 90_A | 94_R | 2.109 | 1.00 |
| 232_P | 236_A | 2.087 | 1.00 |
| 33_A | 37_A | 2.076 | 1.00 |
| 124_K | 128_D | 2.031 | 1.00 |
| 99_Y | 132_R | 2.020 | 1.00 |
| 220_Q | 251_M | 2.006 | 1.00 |
| 205_A | 250_E | 1.945 | 1.00 |
| 33_A | 232_P | 1.897 | 1.00 |
| 28_E | 60_A | 1.854 | 1.00 |
| 201_A | 253_T | 1.793 | 1.00 |
| 248_A | 252_E | 1.758 | 1.00 |
| 221_L | 255_N | 1.757 | 1.00 |
| 181_V | 224_V | 1.751 | 1.00 |
| 174_V | 178_Y | 1.734 | 1.00 |
| 72_T | 100_V | 1.733 | 1.00 |
| 52_A | 94_R | 1.731 | 1.00 |
| 72_T | 91_S | 1.729 | 1.00 |
| 175_N | 182_T | 1.717 | 1.00 |
| 145_E | 149_S | 1.707 | 1.00 |
| 5_T | 11_T | 1.701 | 1.00 |
| 33_A | 36_E | 1.696 | 1.00 |
| 127_E | 152_Y | 1.694 | 1.00 |
| 145_E | 174_V | 1.694 | 1.00 |
| 81_F | 124_K | 1.686 | 1.00 |
| 71_T | 104_L | 1.673 | 1.00 |
| 85_Q | 89_R | 1.661 | 1.00 |
| 121_G | 124_K | 1.650 | 1.00 |
| 200_T | 204_E | 1.617 | 1.00 |
| 100_V | 131_A | 1.616 | 1.00 |
| 37_A | 236_A | 1.580 | 1.00 |
| 133_S | 156_A | 1.570 | 1.00 |
| 209_T | 237_S | 1.549 | 1.00 |
| 252_E | 256_G | 1.527 | 1.00 |
| 74_L | 103_Y | 1.519 | 1.00 |
| 34_A | 39_Y | 1.516 | 1.00 |
| 173_E | 177_G | 1.510 | 1.00 |
| 16_G | 41_L | 1.508 | 1.00 |
| 216_R | 244_F | 1.489 | 1.00 |
| 89_R | 93_E | 1.488 | 1.00 |
| 205_A | 253_T | 1.486 | 1.00 |
| 28_E | 57_A | 1.483 | 1.00 |
| 126_K | 156_A | 1.481 | 1.00 |
| 81_F | 85_Q | 1.480 | 1.00 |
| 208_R | 212_Q | 1.460 | 1.00 |
| 202_I | 213_V | 1.456 | 1.00 |
| 85_Q | 121_G | 1.441 | 1.00 |
| 28_E | 32_S | 1.436 | 1.00 |
| 140_G | 143_D | 1.434 | 1.00 |
| 125_V | 131_A | 1.422 | 1.00 |
| 64_P | 67_E | 1.417 | 1.00 |
| 32_S | 60_A | 1.415 | 1.00 |
| 236_A | 240_D | 1.407 | 0.99 |
| 229_S | 235_I | 1.388 | 0.99 |
| 148_V | 178_Y | 1.387 | 0.99 |
| 69_Y | 102_L | 1.376 | 0.99 |
| 208_R | 213_V | 1.372 | 0.99 |
| 88_A | 103_Y | 1.364 | 0.99 |
| 160_I | 182_T | 1.361 | 0.99 |
| 31_V | 57_A | 1.360 | 0.99 |
| 86_A | 90_A | 1.351 | 0.99 |
| 104_L | 157_V | 1.348 | 0.99 |
| 42_I | 54_V | 1.340 | 0.99 |
| 165_L | 196_H | 1.318 | 0.99 |
| 10_N | 133_S | 1.315 | 0.99 |
| 216_R | 220_Q | 1.314 | 0.99 |
| 126_K | 153_F | 1.309 | 0.99 |
| 26_E | 29_R | 1.309 | 0.99 |
| 81_F | 121_G | 1.301 | 0.99 |
| 125_V | 130_I | 1.301 | 0.99 |
| 198_A | 201_A | 1.294 | 0.99 |
| 32_S | 36_E | 1.290 | 0.99 |
| 83_S | 86_A | 1.289 | 0.99 |
| 102_L | 157_V | 1.286 | 0.99 |
| 82_T | 86_A | 1.282 | 0.99 |
| 209_T | 212_Q | 1.279 | 0.99 |
| 90_A | 93_E | 1.256 | 0.99 |
| 37_A | 239_L | 1.250 | 0.99 |
| 104_L | 183_E | 1.239 | 0.98 |
| 74_L | 84_S | 1.238 | 0.98 |
| 167_N | 258_D | 1.237 | 0.98 |
| 208_R | 244_F | 1.236 | 0.98 |
| 117_D | 120_G | 1.236 | 0.98 |
| 229_S | 234_R | 1.232 | 0.98 |
| 35_L | 68_I | 1.222 | 0.98 |
| 41_L | 71_T | 1.220 | 0.98 |
| 145_E | 178_Y | 1.218 | 0.98 |
| 124_K | 127_E | 1.216 | 0.98 |
| 7_N | 156_A | 1.212 | 0.98 |
| 55_G | 96_G | 1.199 | 0.98 |
| 199_V | 210_A | 1.195 | 0.98 |
| 51_E | 91_S | 1.194 | 0.98 |
| 131_A | 134_I | 1.186 | 0.98 |
| 30_S | 235_I | 1.186 | 0.98 |
| 101_D | 132_R | 1.185 | 0.98 |
| 80_G | 83_S | 1.180 | 0.98 |
| 162_L | 221_L | 1.179 | 0.98 |
| 88_A | 100_V | 1.175 | 0.98 |
| 19_V | 42_I | 1.175 | 0.98 |
| 95_L | 100_V | 1.174 | 0.98 |
| 172_R | 176_A | 1.170 | 0.97 |
| 32_S | 57_A | 1.170 | 0.97 |
| 46_A | 87_A | 1.157 | 0.97 |
| 29_R | 33_A | 1.142 | 0.97 |
| 157_V | 183_E | 1.123 | 0.97 |
| 201_A | 204_E | 1.117 | 0.96 |
| 233_E | 236_A | 1.117 | 0.96 |
| 141_A | 145_E | 1.111 | 0.96 |
| 8_D | 133_S | 1.108 | 0.96 |
| 125_V | 128_D | 1.102 | 0.96 |
| 123_M | 127_E | 1.088 | 0.96 |
| 253_T | 256_G | 1.082 | 0.96 |
| 41_L | 183_E | 1.076 | 0.95 |
| 216_R | 241_V | 1.073 | 0.95 |
| 198_A | 253_T | 1.069 | 0.95 |
| 51_E | 94_R | 1.068 | 0.95 |
| 123_M | 152_Y | 1.058 | 0.95 |
| 40_R | 69_Y | 1.054 | 0.95 |
| 136_V | 144_L | 1.054 | 0.95 |
| 71_T | 183_E | 1.045 | 0.94 |
| 141_A | 174_V | 1.045 | 0.94 |
| 122_L | 134_I | 1.045 | 0.94 |
| 123_M | 153_F | 1.042 | 0.94 |
| 148_V | 174_V | 1.041 | 0.94 |
| 13_P | 40_R | 1.035 | 0.94 |
| 183_E | 224_V | 1.033 | 0.94 |
| 252_E | 255_N | 1.030 | 0.94 |
| 116_V | 146_T | 1.030 | 0.94 |
| 240_D | 243_G | 1.028 | 0.94 |
| 71_T | 102_L | 1.027 | 0.94 |
| 217_W | 255_N | 1.023 | 0.93 |
| 89_R | 128_D | 1.021 | 0.93 |
| 31_V | 42_I | 1.019 | 0.93 |
| 52_A | 56_R | 1.019 | 0.93 |
| 81_F | 120_G | 1.017 | 0.93 |
| 173_E | 176_A | 1.016 | 0.93 |
| 105_I | 122_L | 1.008 | 0.93 |
| 235_I | 239_L | 1.006 | 0.93 |
| 145_E | 177_G | 1.003 | 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 | |
| 3o0kA | 4 | 1 | 100 | 0.005 | Contact Map |
| 4otkA | 1 | 1 | 100 | 0.008 | Contact Map |
| 1hw6A | 1 | 0.9806 | 100 | 0.012 | Contact Map |
| 2wzmA | 2 | 1 | 100 | 0.012 | Contact Map |
| 4q3mA | 6 | 0.9922 | 100 | 0.017 | Contact Map |
| 3f7jA | 2 | 0.9922 | 100 | 0.021 | Contact Map |
| 1vbjA | 2 | 0.9922 | 100 | 0.023 | Contact Map |
| 1mi3A | 4 | 1 | 100 | 0.023 | Contact Map |
| 3wbwA | 2 | 0.9845 | 100 | 0.023 | Contact Map |
| 3b3dA | 3 | 0.9922 | 100 | 0.024 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)