| wwox 101-414 |
| ID: | 1496830392 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 314 (291) | ||
| Sequences: | 7310 (5042) | ||
| Seq/Len: | 25.120 | ||
| Nf(neff/√len): | 295.6 |
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: 25.120).
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 |
| 133_H | 301_S | 3.355 | 1.00 |
| 27_V | 106_V | 3.117 | 1.00 |
| 58_M | 62_S | 3.053 | 1.00 |
| 206_E | 210_R | 2.830 | 1.00 |
| 206_E | 295_R | 2.592 | 1.00 |
| 133_H | 200_N | 2.572 | 1.00 |
| 208_H | 272_G | 2.547 | 1.00 |
| 65_V | 69_L | 2.536 | 1.00 |
| 40_T | 259_T | 2.457 | 1.00 |
| 34_S | 230_N | 2.439 | 1.00 |
| 80_M | 93_F | 2.400 | 1.00 |
| 39_E | 42_K | 2.398 | 1.00 |
| 80_M | 96_A | 2.385 | 1.00 |
| 38_F | 67_R | 2.335 | 1.00 |
| 121_T | 130_Q | 2.286 | 1.00 |
| 132_N | 196_S | 2.185 | 1.00 |
| 157_V | 204_S | 2.168 | 1.00 |
| 33_N | 55_C | 2.152 | 1.00 |
| 208_H | 212_S | 2.144 | 1.00 |
| 97_F | 104_L | 2.142 | 1.00 |
| 204_S | 220_A | 2.127 | 1.00 |
| 86_L | 123_D | 2.091 | 1.00 |
| 109_C | 140_V | 2.078 | 1.00 |
| 61_A | 79_A | 2.070 | 1.00 |
| 91_Q | 142_L | 2.067 | 1.00 |
| 50_H | 76_K | 2.064 | 1.00 |
| 109_C | 157_V | 2.058 | 1.00 |
| 54_A | 82_L | 2.055 | 1.00 |
| 295_R | 299_A | 2.036 | 1.00 |
| 26_V | 52_I | 1.937 | 1.00 |
| 38_F | 64_A | 1.935 | 1.00 |
| 50_H | 78_E | 1.905 | 1.00 |
| 206_E | 209_R | 1.864 | 1.00 |
| 98_K | 146_V | 1.861 | 1.00 |
| 28_V | 104_L | 1.855 | 1.00 |
| 38_F | 42_K | 1.821 | 1.00 |
| 55_C | 61_A | 1.817 | 1.00 |
| 86_L | 122_K | 1.807 | 1.00 |
| 65_V | 79_A | 1.807 | 1.00 |
| 32_A | 53_L | 1.799 | 1.00 |
| 58_M | 79_A | 1.789 | 1.00 |
| 78_E | 100_K | 1.785 | 1.00 |
| 202_L | 294_A | 1.775 | 1.00 |
| 300_L | 303_R | 1.770 | 1.00 |
| 94_A | 142_L | 1.753 | 1.00 |
| 80_M | 100_K | 1.733 | 1.00 |
| 261_Y | 265_V | 1.721 | 1.00 |
| 57_N | 60_R | 1.720 | 1.00 |
| 157_V | 218_S | 1.717 | 1.00 |
| 204_S | 218_S | 1.691 | 1.00 |
| 86_L | 89_S | 1.659 | 1.00 |
| 58_M | 81_T | 1.650 | 1.00 |
| 96_A | 100_K | 1.606 | 1.00 |
| 88_R | 122_K | 1.589 | 1.00 |
| 40_T | 108_V | 1.587 | 1.00 |
| 28_V | 93_F | 1.584 | 1.00 |
| 158_V | 259_T | 1.572 | 1.00 |
| 138_Y | 142_L | 1.559 | 1.00 |
| 29_V | 41_A | 1.544 | 1.00 |
| 41_A | 53_L | 1.539 | 1.00 |
| 93_F | 139_L | 1.524 | 1.00 |
| 27_V | 49_A | 1.520 | 1.00 |
| 93_F | 97_F | 1.509 | 1.00 |
| 33_N | 64_A | 1.507 | 1.00 |
| 62_S | 66_S | 1.492 | 1.00 |
| 163_H | 285_S | 1.486 | 1.00 |
| 87_L | 90_V | 1.481 | 1.00 |
| 205_N | 291_E | 1.469 | 1.00 |
| 106_V | 263_A | 1.462 | 1.00 |
| 55_C | 79_A | 1.443 | 1.00 |
| 205_N | 288_A | 1.438 | 1.00 |
| 26_V | 50_H | 1.424 | 1.00 |
| 29_V | 51_V | 1.423 | 1.00 |
| 42_K | 71_E | 1.407 | 0.99 |
| 140_V | 155_V | 1.403 | 0.99 |
| 299_A | 303_R | 1.403 | 0.99 |
| 92_H | 96_A | 1.392 | 0.99 |
| 39_E | 253_Q | 1.379 | 0.99 |
| 125_L | 134_L | 1.377 | 0.99 |
| 158_V | 221_V | 1.376 | 0.99 |
| 125_L | 130_Q | 1.369 | 0.99 |
| 109_C | 136_H | 1.364 | 0.99 |
| 141_Q | 302_E | 1.361 | 0.99 |
| 36_I | 259_T | 1.355 | 0.99 |
| 229_S | 252_M | 1.355 | 0.99 |
| 130_Q | 135_G | 1.349 | 0.99 |
| 66_S | 70_E | 1.347 | 0.99 |
| 95_E | 99_A | 1.346 | 0.99 |
| 52_I | 101_N | 1.333 | 0.99 |
| 193_Y | 197_K | 1.316 | 0.99 |
| 129_F | 134_L | 1.314 | 0.99 |
| 45_A | 68_I | 1.310 | 0.99 |
| 290_S | 293_T | 1.296 | 0.99 |
| 251_S | 254_Q | 1.294 | 0.99 |
| 81_T | 92_H | 1.284 | 0.99 |
| 43_S | 47_H | 1.283 | 0.99 |
| 201_I | 220_A | 1.278 | 0.99 |
| 43_S | 46_L | 1.273 | 0.99 |
| 133_H | 203_F | 1.266 | 0.99 |
| 156_I | 219_N | 1.264 | 0.99 |
| 119_S | 127_T | 1.263 | 0.99 |
| 59_A | 63_E | 1.251 | 0.99 |
| 28_V | 97_F | 1.246 | 0.98 |
| 80_M | 97_F | 1.224 | 0.98 |
| 219_N | 268_L | 1.204 | 0.98 |
| 82_L | 93_F | 1.199 | 0.98 |
| 24_G | 49_A | 1.191 | 0.98 |
| 59_A | 62_S | 1.183 | 0.98 |
| 54_A | 93_F | 1.183 | 0.98 |
| 52_I | 97_F | 1.181 | 0.98 |
| 137_F | 301_S | 1.181 | 0.98 |
| 219_N | 271_L | 1.180 | 0.98 |
| 137_F | 203_F | 1.178 | 0.98 |
| 127_T | 131_V | 1.170 | 0.97 |
| 63_E | 67_R | 1.165 | 0.97 |
| 22_F | 27_V | 1.164 | 0.97 |
| 39_E | 43_S | 1.163 | 0.97 |
| 300_L | 304_L | 1.163 | 0.97 |
| 50_H | 101_N | 1.155 | 0.97 |
| 42_K | 46_L | 1.154 | 0.97 |
| 98_K | 142_L | 1.152 | 0.97 |
| 91_Q | 138_Y | 1.148 | 0.97 |
| 134_L | 301_S | 1.143 | 0.97 |
| 123_D | 130_Q | 1.143 | 0.97 |
| 225_N | 249_T | 1.142 | 0.97 |
| 230_N | 233_R | 1.141 | 0.97 |
| 94_A | 139_L | 1.139 | 0.97 |
| 36_I | 226_M | 1.137 | 0.97 |
| 108_V | 263_A | 1.136 | 0.97 |
| 256_A | 260_V | 1.135 | 0.97 |
| 141_Q | 309_L | 1.128 | 0.97 |
| 78_E | 101_N | 1.128 | 0.97 |
| 211_L | 216_V | 1.115 | 0.96 |
| 179_R | 182_P | 1.113 | 0.96 |
| 22_F | 264_A | 1.112 | 0.96 |
| 159_S | 201_I | 1.102 | 0.96 |
| 85_A | 127_T | 1.100 | 0.96 |
| 87_L | 138_Y | 1.099 | 0.96 |
| 199_C | 297_L | 1.092 | 0.96 |
| 108_V | 158_V | 1.091 | 0.96 |
| 203_F | 301_S | 1.076 | 0.95 |
| 262_C | 276_F | 1.073 | 0.95 |
| 221_V | 259_T | 1.071 | 0.95 |
| 27_V | 44_F | 1.064 | 0.95 |
| 147_L | 155_V | 1.058 | 0.95 |
| 301_S | 305_I | 1.051 | 0.94 |
| 88_R | 92_H | 1.050 | 0.94 |
| 161_E | 164_R | 1.042 | 0.94 |
| 22_F | 25_K | 1.027 | 0.94 |
| 66_S | 69_L | 1.026 | 0.94 |
| 92_H | 95_E | 1.025 | 0.93 |
| 177_F | 296_T | 1.009 | 0.93 |
| 159_S | 220_A | 1.009 | 0.93 |
| 142_L | 146_V | 1.006 | 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 | |
| 3rd5A | 1 | 0.8248 | 100 | 0.397 | Contact Map |
| 3sc4A | 2 | 0.8408 | 100 | 0.427 | Contact Map |
| 2qq5A | 1 | 0.7261 | 100 | 0.429 | Contact Map |
| 3kvoA | 2 | 0.8217 | 100 | 0.429 | Contact Map |
| 4z0tA | 1 | 0 | 100 | 0.433 | Contact Map |
| 3h7aA | 4 | 0.6688 | 100 | 0.435 | Contact Map |
| 3rkuA | 4 | 0.8217 | 100 | 0.435 | Contact Map |
| 3e03A | 3 | 0.8185 | 100 | 0.436 | Contact Map |
| 1w6uA | 4 | 0.8822 | 100 | 0.436 | Contact Map |
| 4is2A | 1 | 0.0478 | 100 | 0.437 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)