| Hs-A1 |
| ID: | 1403686971 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 349 (286) | ||
| Sequences: | 1427 (1040.8) | ||
| Seq/Len: | 4.990 | ||
| Nf(neff/√len): | 61.5 |
HHblits Results: (2013_03)
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: 4.990).
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 |
| 115_D | 250_C | 6.055 | 1.00 |
| 68_Q | 101_G | 2.946 | 1.00 |
| 241_S | 254_V | 2.833 | 1.00 |
| 40_L | 176_L | 2.801 | 1.00 |
| 266_C | 286_P | 2.690 | 1.00 |
| 248_G | 252_R | 2.575 | 1.00 |
| 93_I | 225_T | 2.495 | 1.00 |
| 40_L | 172_I | 2.366 | 1.00 |
| 242_A | 251_R | 2.347 | 1.00 |
| 230_P | 296_E | 2.316 | 1.00 |
| 246_L | 254_V | 2.305 | 1.00 |
| 109_S | 253_T | 2.222 | 1.00 |
| 52_K | 56_W | 2.206 | 1.00 |
| 72_M | 233_G | 2.080 | 1.00 |
| 109_S | 114_G | 2.071 | 1.00 |
| 239_V | 243_L | 1.957 | 1.00 |
| 98_C | 137_L | 1.950 | 1.00 |
| 101_G | 123_T | 1.912 | 1.00 |
| 69_Y | 133_M | 1.902 | 1.00 |
| 155_P | 158_G | 1.856 | 1.00 |
| 108_F | 256_M | 1.835 | 1.00 |
| 99_S | 266_C | 1.797 | 1.00 |
| 101_G | 106_N | 1.776 | 1.00 |
| 227_S | 292_F | 1.738 | 1.00 |
| 164_V | 168_I | 1.700 | 1.00 |
| 238_Y | 251_R | 1.642 | 0.99 |
| 68_Q | 123_T | 1.590 | 0.99 |
| 227_S | 296_E | 1.583 | 0.99 |
| 80_G | 90_A | 1.574 | 0.99 |
| 74_L | 78_V | 1.569 | 0.99 |
| 77_F | 81_K | 1.548 | 0.99 |
| 76_A | 97_G | 1.547 | 0.99 |
| 238_Y | 252_R | 1.504 | 0.99 |
| 251_R | 255_S | 1.476 | 0.98 |
| 79_L | 228_L | 1.471 | 0.98 |
| 68_Q | 119_S | 1.470 | 0.98 |
| 177_K | 185_R | 1.453 | 0.98 |
| 292_F | 296_E | 1.453 | 0.98 |
| 63_I | 254_V | 1.423 | 0.98 |
| 101_G | 122_M | 1.414 | 0.98 |
| 105_S | 119_S | 1.405 | 0.97 |
| 66_V | 70_G | 1.392 | 0.97 |
| 102_G | 257_E | 1.385 | 0.97 |
| 300_L | 304_F | 1.377 | 0.97 |
| 247_N | 250_C | 1.376 | 0.97 |
| 235_L | 239_V | 1.372 | 0.97 |
| 101_G | 127_T | 1.363 | 0.97 |
| 96_C | 289_Y | 1.343 | 0.96 |
| 105_S | 261_Q | 1.327 | 0.96 |
| 190_G | 193_I | 1.327 | 0.96 |
| 69_Y | 126_S | 1.320 | 0.96 |
| 72_M | 97_G | 1.300 | 0.95 |
| 67_A | 71_I | 1.295 | 0.95 |
| 68_Q | 257_E | 1.292 | 0.95 |
| 106_N | 123_T | 1.290 | 0.95 |
| 238_Y | 248_G | 1.286 | 0.95 |
| 278_V | 281_P | 1.285 | 0.95 |
| 130_A | 134_M | 1.281 | 0.95 |
| 49_S | 53_A | 1.276 | 0.95 |
| 102_G | 290_M | 1.272 | 0.95 |
| 238_Y | 255_S | 1.269 | 0.95 |
| 92_A | 169_P | 1.266 | 0.95 |
| 102_G | 105_S | 1.259 | 0.94 |
| 95_V | 270_L | 1.250 | 0.94 |
| 121_V | 124_T | 1.248 | 0.94 |
| 180_R | 183_Y | 1.222 | 0.93 |
| 98_C | 127_T | 1.203 | 0.92 |
| 68_Q | 106_N | 1.198 | 0.92 |
| 29_V | 33_F | 1.196 | 0.92 |
| 64_A | 261_Q | 1.196 | 0.92 |
| 49_S | 52_K | 1.191 | 0.92 |
| 133_M | 136_L | 1.188 | 0.92 |
| 234_F | 268_T | 1.183 | 0.91 |
| 157_K | 161_I | 1.181 | 0.91 |
| 171_T | 175_V | 1.178 | 0.91 |
| 106_N | 257_E | 1.177 | 0.91 |
| 39_M | 43_G | 1.172 | 0.91 |
| 257_E | 261_Q | 1.166 | 0.91 |
| 231_F | 235_L | 1.163 | 0.91 |
| 203_T | 207_A | 1.157 | 0.90 |
| 119_S | 123_T | 1.157 | 0.90 |
| 68_Q | 122_M | 1.156 | 0.90 |
| 123_T | 257_E | 1.155 | 0.90 |
| 79_L | 93_I | 1.146 | 0.90 |
| 241_S | 251_R | 1.145 | 0.90 |
| 112_M | 301_I | 1.141 | 0.89 |
| 281_P | 285_F | 1.137 | 0.89 |
| 120_I | 170_C | 1.135 | 0.89 |
| 199_S | 203_T | 1.134 | 0.89 |
| 174_I | 178_S | 1.132 | 0.89 |
| 289_Y | 294_L | 1.124 | 0.88 |
| 119_S | 257_E | 1.120 | 0.88 |
| 37_F | 299_L | 1.118 | 0.88 |
| 127_T | 269_I | 1.114 | 0.88 |
| 252_R | 304_F | 1.099 | 0.87 |
| 78_V | 81_K | 1.098 | 0.87 |
| 64_A | 253_T | 1.094 | 0.87 |
| 57_K | 115_D | 1.093 | 0.87 |
| 96_C | 263_V | 1.092 | 0.86 |
| 33_F | 36_F | 1.091 | 0.86 |
| 101_G | 119_S | 1.089 | 0.86 |
| 93_I | 98_C | 1.085 | 0.86 |
| 196_L | 207_A | 1.080 | 0.86 |
| 102_G | 106_N | 1.076 | 0.85 |
| 230_P | 265_L | 1.075 | 0.85 |
| 69_Y | 97_G | 1.066 | 0.85 |
| 290_M | 294_L | 1.057 | 0.84 |
| 60_G | 118_L | 1.053 | 0.84 |
| 137_L | 141_Y | 1.052 | 0.84 |
| 154_V | 189_K | 1.051 | 0.83 |
| 102_G | 262_N | 1.048 | 0.83 |
| 218_M | 222_L | 1.047 | 0.83 |
| 50_K | 117_N | 1.046 | 0.83 |
| 215_M | 269_I | 1.046 | 0.83 |
| 139_Y | 143_R | 1.039 | 0.82 |
| 119_S | 261_Q | 1.038 | 0.82 |
| 276_P | 279_I | 1.036 | 0.82 |
| 82_V | 242_A | 1.036 | 0.82 |
| 263_V | 297_G | 1.036 | 0.82 |
| 104_L | 234_F | 1.034 | 0.82 |
| 301_I | 304_F | 1.031 | 0.82 |
| 129_C | 133_M | 1.027 | 0.81 |
| 183_Y | 186_Y | 1.027 | 0.81 |
| 229_M | 289_Y | 1.022 | 0.81 |
| 67_A | 240_L | 1.022 | 0.81 |
| 184_M | 244_F | 1.021 | 0.81 |
| 75_T | 232_I | 1.015 | 0.80 |
| 60_G | 250_C | 1.010 | 0.80 |
| 97_G | 229_M | 1.008 | 0.80 |
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 | |
| 3zuxA | 1 | 0.8223 | 100 | 0.481 | Contact Map |
| 4n7wA | 2 | 0.851 | 100 | 0.49 | Contact Map |
| 4bwzA | 1 | 0.8367 | 95.2 | 0.93 | Contact Map |
| 1zcdA | 2 | 0.8481 | 82.3 | 0.947 | Contact Map |
| 4px7A | 1 | 0.5645 | 23 | 0.965 | Contact Map |
| 2kluA | 1 | 0.1633 | 22.7 | 0.965 | Contact Map |
| 4pypA | 1 | 0.7937 | 22.3 | 0.965 | Contact Map |
| 2nq2A | 2 | 0.7736 | 14 | 0.968 | Contact Map |
| 4g1uA | 2 | 0.7335 | 12.9 | 0.969 | Contact Map |
| 2jlnA | 1 | 0.6991 | 11.2 | 0.97 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)