| DHH |
| ID: | 1518200821 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 300 (292) | ||
| Sequences: | 1111 (783.9) | ||
| Seq/Len: | 3.805 | ||
| Nf(neff/√len): | 45.9 |
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: 3.805).
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 |
| 145_C | 155_H | 4.788 | 1.00 |
| 131_C | 141_H | 3.331 | 1.00 |
| 145_C | 162_C | 3.115 | 1.00 |
| 155_H | 162_C | 2.979 | 1.00 |
| 141_H | 148_C | 2.807 | 1.00 |
| 131_C | 148_C | 2.632 | 1.00 |
| 142_C | 145_C | 2.613 | 1.00 |
| 168_Y | 231_H | 2.608 | 1.00 |
| 264_S | 268_R | 2.486 | 1.00 |
| 272_G | 278_W | 2.472 | 1.00 |
| 267_W | 271_F | 2.395 | 1.00 |
| 141_H | 145_C | 2.246 | 1.00 |
| 235_V | 267_W | 2.223 | 1.00 |
| 159_V | 163_V | 2.201 | 1.00 |
| 169_K | 173_L | 2.178 | 1.00 |
| 142_C | 162_C | 2.159 | 1.00 |
| 142_C | 155_H | 2.140 | 1.00 |
| 172_L | 235_V | 2.019 | 1.00 |
| 172_L | 232_C | 2.009 | 1.00 |
| 131_C | 145_C | 1.982 | 1.00 |
| 164_G | 167_N | 1.977 | 1.00 |
| 76_S | 147_S | 1.948 | 1.00 |
| 153_D | 156_C | 1.926 | 1.00 |
| 148_C | 155_H | 1.858 | 1.00 |
| 135_K | 140_H | 1.827 | 1.00 |
| 141_H | 155_H | 1.767 | 0.99 |
| 72_T | 159_V | 1.767 | 0.99 |
| 231_H | 241_T | 1.757 | 0.99 |
| 131_C | 155_H | 1.742 | 0.99 |
| 278_W | 281_P | 1.733 | 0.99 |
| 128_C | 131_C | 1.726 | 0.99 |
| 289_G | 292_F | 1.622 | 0.99 |
| 238_N | 269_Q | 1.593 | 0.98 |
| 151_K | 168_Y | 1.588 | 0.98 |
| 212_F | 215_F | 1.540 | 0.98 |
| 272_G | 281_P | 1.534 | 0.98 |
| 128_C | 141_H | 1.522 | 0.98 |
| 145_C | 148_C | 1.508 | 0.97 |
| 30_Y | 59_H | 1.498 | 0.97 |
| 128_C | 140_H | 1.479 | 0.97 |
| 34_V | 59_H | 1.468 | 0.97 |
| 120_S | 123_K | 1.466 | 0.97 |
| 231_H | 234_L | 1.456 | 0.97 |
| 230_Y | 234_L | 1.454 | 0.97 |
| 208_F | 212_F | 1.434 | 0.96 |
| 126_R | 135_K | 1.428 | 0.96 |
| 32_A | 62_F | 1.420 | 0.96 |
| 128_C | 138_R | 1.391 | 0.95 |
| 60_L | 64_M | 1.386 | 0.95 |
| 67_W | 71_M | 1.372 | 0.95 |
| 233_W | 237_K | 1.365 | 0.95 |
| 260_S | 266_N | 1.355 | 0.94 |
| 151_K | 270_V | 1.352 | 0.94 |
| 126_R | 137_D | 1.350 | 0.94 |
| 170_F | 173_L | 1.348 | 0.94 |
| 176_L | 228_F | 1.348 | 0.94 |
| 262_G | 266_N | 1.348 | 0.94 |
| 268_R | 273_D | 1.335 | 0.94 |
| 140_H | 152_M | 1.316 | 0.93 |
| 179_L | 225_L | 1.309 | 0.93 |
| 71_M | 170_F | 1.299 | 0.93 |
| 30_Y | 34_V | 1.297 | 0.92 |
| 77_P | 164_G | 1.295 | 0.92 |
| 17_V | 21_F | 1.280 | 0.92 |
| 62_F | 181_Y | 1.277 | 0.92 |
| 140_H | 154_H | 1.273 | 0.92 |
| 225_L | 229_S | 1.272 | 0.91 |
| 152_M | 158_W | 1.270 | 0.91 |
| 173_L | 277_Y | 1.247 | 0.90 |
| 156_C | 171_F | 1.239 | 0.90 |
| 288_D | 291_S | 1.238 | 0.90 |
| 224_V | 229_S | 1.235 | 0.90 |
| 148_C | 154_H | 1.234 | 0.90 |
| 138_R | 156_C | 1.229 | 0.90 |
| 131_C | 135_K | 1.226 | 0.89 |
| 236_G | 263_C | 1.223 | 0.89 |
| 138_R | 141_H | 1.222 | 0.89 |
| 178_S | 224_V | 1.214 | 0.89 |
| 152_M | 242_I | 1.212 | 0.89 |
| 61_F | 184_F | 1.209 | 0.88 |
| 153_D | 171_F | 1.207 | 0.88 |
| 64_M | 68_S | 1.193 | 0.88 |
| 131_C | 140_H | 1.190 | 0.87 |
| 67_W | 231_H | 1.180 | 0.87 |
| 172_L | 184_F | 1.168 | 0.86 |
| 123_K | 137_D | 1.166 | 0.86 |
| 179_L | 228_F | 1.158 | 0.85 |
| 136_P | 145_C | 1.155 | 0.85 |
| 168_Y | 241_T | 1.149 | 0.85 |
| 128_C | 154_H | 1.148 | 0.85 |
| 190_L | 194_I | 1.142 | 0.84 |
| 14_V | 17_V | 1.139 | 0.84 |
| 78_A | 164_G | 1.138 | 0.84 |
| 17_V | 22_I | 1.138 | 0.84 |
| 232_C | 236_G | 1.123 | 0.83 |
| 149_I | 152_M | 1.116 | 0.82 |
| 259_F | 266_N | 1.112 | 0.82 |
| 21_F | 24_F | 1.109 | 0.82 |
| 70_W | 74_F | 1.106 | 0.82 |
| 148_C | 153_D | 1.105 | 0.82 |
| 128_C | 135_K | 1.098 | 0.81 |
| 185_V | 188_T | 1.095 | 0.81 |
| 78_A | 166_S | 1.095 | 0.81 |
| 168_Y | 270_V | 1.092 | 0.80 |
| 152_M | 157_P | 1.090 | 0.80 |
| 238_N | 266_N | 1.090 | 0.80 |
| 240_T | 243_E | 1.087 | 0.80 |
| 154_H | 157_P | 1.084 | 0.80 |
| 81_S | 84_F | 1.076 | 0.79 |
| 28_W | 31_Y | 1.072 | 0.79 |
| 26_V | 65_F | 1.068 | 0.78 |
| 98_F | 101_E | 1.067 | 0.78 |
| 152_M | 164_G | 1.067 | 0.78 |
| 7_W | 10_C | 1.067 | 0.78 |
| 173_L | 177_Y | 1.066 | 0.78 |
| 158_W | 163_V | 1.060 | 0.78 |
| 176_L | 180_L | 1.058 | 0.78 |
| 262_G | 265_K | 1.058 | 0.78 |
| 135_K | 141_H | 1.057 | 0.77 |
| 269_Q | 293_P | 1.053 | 0.77 |
| 128_C | 148_C | 1.048 | 0.77 |
| 57_A | 184_F | 1.047 | 0.76 |
| 32_A | 37_L | 1.047 | 0.76 |
| 7_W | 11_Q | 1.045 | 0.76 |
| 69_Y | 159_V | 1.039 | 0.76 |
| 69_Y | 174_F | 1.037 | 0.76 |
| 138_R | 154_H | 1.036 | 0.75 |
| 61_F | 177_Y | 1.033 | 0.75 |
| 80_P | 139_A | 1.030 | 0.75 |
| 148_C | 156_C | 1.029 | 0.75 |
| 15_G | 18_P | 1.027 | 0.75 |
| 119_T | 123_K | 1.026 | 0.74 |
| 163_V | 242_I | 1.026 | 0.74 |
| 142_C | 243_E | 1.025 | 0.74 |
| 158_W | 161_N | 1.024 | 0.74 |
| 50_K | 54_Y | 1.021 | 0.74 |
| 140_H | 153_D | 1.018 | 0.74 |
| 64_M | 67_W | 1.016 | 0.73 |
| 231_H | 271_F | 1.010 | 0.73 |
| 261_L | 265_K | 1.009 | 0.73 |
| 173_L | 271_F | 1.008 | 0.73 |
| 174_F | 230_Y | 1.007 | 0.72 |
| 19_V | 30_Y | 1.006 | 0.72 |
| 61_F | 181_Y | 1.001 | 0.72 |
| 141_H | 154_H | 1.001 | 0.72 |
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 | |
| 2rowA | 1 | 0.2467 | 13.8 | 0.967 | Contact Map |
| 4c7rA | 3 | 0.3533 | 12 | 0.968 | Contact Map |
| 2fnfX | 1 | 0.1767 | 11.2 | 0.968 | Contact Map |
| 3j21g | 1 | 0.15 | 6.6 | 0.971 | Contact Map |
| 4xp4A | 1 | 0 | 6.2 | 0.972 | Contact Map |
| 1wflA | 1 | 0.2267 | 6.1 | 0.972 | Contact Map |
| 1qleD | 1 | 0.1433 | 5.6 | 0.972 | Contact Map |
| 4ujrZ | 1 | 0.1633 | 5.4 | 0.972 | Contact Map |
| 1faqA | 1 | 0.1567 | 4.5 | 0.973 | Contact Map |
| 3uejA | 2 | 0.19 | 4.5 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)