| 71-4 |
| ID: | 1470650283 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 249 (241) | ||
| Sequences: | 3403 (2289.3) | ||
| Seq/Len: | 14.120 | ||
| Nf(neff/√len): | 147.5 |
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: 14.120).
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 |
| 12_V | 86_L | 4.711 | 1.00 |
| 153_T | 218_V | 3.555 | 1.00 |
| 67_K | 90_D | 2.852 | 1.00 |
| 163_C | 228_C | 2.609 | 1.00 |
| 18_V | 121_V | 2.467 | 1.00 |
| 13_K | 16_A | 2.404 | 1.00 |
| 26_G | 32_T | 2.214 | 1.00 |
| 22_C | 96_C | 2.207 | 1.00 |
| 201_R | 222_D | 2.162 | 1.00 |
| 79_A | 211_F | 2.094 | 1.00 |
| 167_Q | 171_T | 2.039 | 1.00 |
| 28_N | 32_T | 1.999 | 1.00 |
| 36_W | 81_L | 1.955 | 1.00 |
| 17_S | 84_S | 1.841 | 1.00 |
| 19_K | 82_H | 1.741 | 1.00 |
| 165_A | 173_V | 1.695 | 1.00 |
| 34_V | 173_V | 1.693 | 1.00 |
| 19_K | 80_Y | 1.677 | 1.00 |
| 162_T | 212_T | 1.635 | 1.00 |
| 20_L | 161_I | 1.631 | 1.00 |
| 163_C | 175_W | 1.573 | 1.00 |
| 153_T | 159_V | 1.573 | 1.00 |
| 20_L | 121_V | 1.563 | 1.00 |
| 62_P | 65_Q | 1.554 | 1.00 |
| 24_A | 165_A | 1.547 | 1.00 |
| 173_V | 211_F | 1.521 | 1.00 |
| 87_T | 219_Q | 1.505 | 1.00 |
| 89_E | 221_E | 1.496 | 1.00 |
| 177_Q | 226_Y | 1.476 | 1.00 |
| 176_Y | 227_F | 1.463 | 1.00 |
| 10_E | 151_M | 1.460 | 1.00 |
| 230_Q | 237_T | 1.439 | 1.00 |
| 177_Q | 224_A | 1.434 | 1.00 |
| 38_K | 92_A | 1.430 | 1.00 |
| 18_V | 159_V | 1.414 | 1.00 |
| 176_Y | 229_L | 1.405 | 0.99 |
| 222_D | 226_Y | 1.401 | 0.99 |
| 24_A | 34_V | 1.380 | 0.99 |
| 86_L | 218_V | 1.376 | 0.99 |
| 98_R | 230_Q | 1.365 | 0.99 |
| 129_G | 132_G | 1.363 | 0.99 |
| 177_Q | 180_P | 1.362 | 0.99 |
| 37_V | 176_Y | 1.362 | 0.99 |
| 231_H | 236_L | 1.361 | 0.99 |
| 161_I | 175_W | 1.361 | 0.99 |
| 28_N | 100_F | 1.353 | 0.99 |
| 21_S | 78_T | 1.350 | 0.99 |
| 127_G | 131_G | 1.347 | 0.99 |
| 159_V | 244_L | 1.338 | 0.99 |
| 239_G | 242_T | 1.331 | 0.99 |
| 100_F | 103_Y | 1.299 | 0.99 |
| 213_L | 226_Y | 1.298 | 0.99 |
| 160_S | 214_T | 1.292 | 0.99 |
| 69_T | 82_H | 1.291 | 0.99 |
| 81_L | 213_L | 1.289 | 0.99 |
| 128_G | 131_G | 1.286 | 0.99 |
| 35_H | 97_A | 1.275 | 0.99 |
| 151_M | 159_V | 1.274 | 0.99 |
| 85_S | 217_N | 1.270 | 0.99 |
| 127_G | 132_G | 1.269 | 0.99 |
| 37_V | 95_Y | 1.264 | 0.99 |
| 81_L | 175_W | 1.262 | 0.99 |
| 19_K | 160_S | 1.257 | 0.99 |
| 83_L | 215_I | 1.255 | 0.99 |
| 21_S | 80_Y | 1.253 | 0.99 |
| 160_S | 212_T | 1.248 | 0.99 |
| 17_S | 85_S | 1.246 | 0.98 |
| 16_A | 157_D | 1.245 | 0.98 |
| 14_P | 88_S | 1.240 | 0.98 |
| 165_A | 230_Q | 1.238 | 0.98 |
| 130_S | 133_G | 1.233 | 0.98 |
| 68_A | 83_L | 1.230 | 0.98 |
| 17_S | 82_H | 1.230 | 0.98 |
| 238_F | 241_G | 1.226 | 0.98 |
| 14_P | 155_V | 1.211 | 0.98 |
| 34_V | 79_A | 1.209 | 0.98 |
| 100_F | 232_R | 1.195 | 0.98 |
| 76_S | 208_G | 1.194 | 0.98 |
| 131_G | 134_G | 1.191 | 0.98 |
| 177_Q | 223_L | 1.187 | 0.98 |
| 77_S | 209_T | 1.183 | 0.98 |
| 36_W | 175_W | 1.182 | 0.98 |
| 69_T | 84_S | 1.179 | 0.98 |
| 93_V | 120_T | 1.158 | 0.97 |
| 238_F | 242_T | 1.158 | 0.97 |
| 154_S | 157_D | 1.156 | 0.97 |
| 171_T | 232_R | 1.147 | 0.97 |
| 126_G | 131_G | 1.145 | 0.97 |
| 35_H | 174_A | 1.130 | 0.97 |
| 12_V | 16_A | 1.126 | 0.97 |
| 201_R | 215_I | 1.109 | 0.96 |
| 22_C | 163_C | 1.106 | 0.96 |
| 215_I | 219_Q | 1.099 | 0.96 |
| 95_Y | 118_G | 1.092 | 0.96 |
| 93_V | 225_D | 1.084 | 0.96 |
| 23_T | 78_T | 1.082 | 0.96 |
| 68_A | 81_L | 1.075 | 0.95 |
| 12_V | 18_V | 1.067 | 0.95 |
| 223_L | 226_Y | 1.064 | 0.95 |
| 10_E | 18_V | 1.056 | 0.95 |
| 22_C | 228_C | 1.055 | 0.95 |
| 23_T | 164_K | 1.053 | 0.95 |
| 17_S | 86_L | 1.052 | 0.95 |
| 92_A | 224_A | 1.051 | 0.94 |
| 129_G | 133_G | 1.043 | 0.94 |
| 130_S | 134_G | 1.040 | 0.94 |
| 37_V | 97_A | 1.039 | 0.94 |
| 31_S | 170_R | 1.036 | 0.94 |
| 189_Y | 194_R | 1.032 | 0.94 |
| 169_V | 232_R | 1.024 | 0.93 |
| 38_K | 46_E | 1.016 | 0.93 |
| 38_K | 90_D | 1.015 | 0.93 |
| 158_R | 214_T | 1.011 | 0.93 |
| 23_T | 80_Y | 1.008 | 0.93 |
| 171_T | 230_Q | 1.003 | 0.93 |
| 63_N | 197_G | 1.002 | 0.92 |
| 32_T | 98_R | 1.001 | 0.92 |
| 14_P | 91_T | 1.001 | 0.92 |
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 | |
| 3umtA | 1 | 0.9116 | 100 | 0.225 | Contact Map |
| 2ghwB | 2 | 0.9197 | 100 | 0.236 | Contact Map |
| 1nqbA | 2 | 0.9116 | 100 | 0.237 | Contact Map |
| 1f3rB | 1 | 0.988 | 100 | 0.24 | Contact Map |
| 4buhA | 2 | 0.9317 | 100 | 0.244 | Contact Map |
| 3uzqA | 1 | 0.9237 | 100 | 0.244 | Contact Map |
| 4nikB | 1 | 0.8996 | 100 | 0.244 | Contact Map |
| 3gkzA | 1 | 0.9317 | 100 | 0.249 | Contact Map |
| 5a2jH | 1 | 0 | 100 | 0.249 | Contact Map |
| 2gkiA | 2 | 0.9277 | 100 | 0.252 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)