| oxa-23 |
| ID: | 1421955994 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 273 (235) | ||
| Sequences: | 5110 (3550.9) | ||
| Seq/Len: | 21.745 | ||
| Nf(neff/√len): | 231.6 |
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: 21.745).
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 |
| 55_I | 244_F | 3.293 | 1.00 |
| 215_G | 230_L | 3.135 | 1.00 |
| 231_T | 245_A | 2.955 | 1.00 |
| 200_K | 233_W | 2.918 | 1.00 |
| 178_V | 245_A | 2.831 | 1.00 |
| 91_E | 195_V | 2.566 | 1.00 |
| 120_G | 205_L | 2.523 | 1.00 |
| 92_N | 142_L | 2.506 | 1.00 |
| 53_L | 266_S | 2.448 | 1.00 |
| 204_L | 212_K | 2.392 | 1.00 |
| 55_I | 266_S | 2.344 | 1.00 |
| 214_F | 236_Q | 2.319 | 1.00 |
| 88_I | 146_E | 2.301 | 1.00 |
| 100_I | 116_D | 2.300 | 1.00 |
| 117_M | 127_A | 2.276 | 1.00 |
| 122_A | 130_V | 2.254 | 1.00 |
| 57_T | 60_K | 2.248 | 1.00 |
| 56_Q | 178_V | 2.216 | 1.00 |
| 58_D | 243_A | 2.129 | 1.00 |
| 145_K | 149_R | 2.119 | 1.00 |
| 87_L | 195_V | 2.093 | 1.00 |
| 84_L | 180_F | 2.074 | 1.00 |
| 91_E | 192_S | 2.016 | 1.00 |
| 121_E | 125_L | 1.977 | 1.00 |
| 99_E | 137_R | 1.970 | 1.00 |
| 57_T | 62_N | 1.927 | 1.00 |
| 263_L | 267_L | 1.917 | 1.00 |
| 124_K | 205_L | 1.898 | 1.00 |
| 95_T | 119_L | 1.858 | 1.00 |
| 96_D | 99_E | 1.847 | 1.00 |
| 120_G | 201_N | 1.824 | 1.00 |
| 192_S | 195_V | 1.810 | 1.00 |
| 184_L | 199_V | 1.766 | 1.00 |
| 81_F | 147_V | 1.763 | 1.00 |
| 264_M | 268_K | 1.747 | 1.00 |
| 121_E | 124_K | 1.744 | 1.00 |
| 182_S | 243_A | 1.721 | 1.00 |
| 89_G | 134_L | 1.713 | 1.00 |
| 55_I | 242_V | 1.690 | 1.00 |
| 87_L | 191_F | 1.683 | 1.00 |
| 191_F | 196_Q | 1.678 | 1.00 |
| 118_T | 121_E | 1.669 | 1.00 |
| 174_P | 245_A | 1.588 | 1.00 |
| 86_A | 131_Y | 1.569 | 1.00 |
| 117_M | 121_E | 1.540 | 1.00 |
| 181_V | 203_L | 1.534 | 1.00 |
| 189_L | 193_E | 1.498 | 1.00 |
| 80_T | 177_E | 1.496 | 1.00 |
| 83_M | 184_L | 1.494 | 1.00 |
| 64_Y | 242_V | 1.491 | 1.00 |
| 257_S | 261_E | 1.484 | 1.00 |
| 181_V | 231_T | 1.471 | 1.00 |
| 114_E | 127_A | 1.468 | 1.00 |
| 50_S | 250_M | 1.466 | 1.00 |
| 144_Q | 148_K | 1.444 | 1.00 |
| 232_G | 267_L | 1.427 | 1.00 |
| 193_E | 197_A | 1.423 | 1.00 |
| 150_I | 191_F | 1.402 | 0.99 |
| 90_L | 202_M | 1.383 | 0.99 |
| 57_T | 241_I | 1.382 | 0.99 |
| 135_A | 143_M | 1.379 | 0.99 |
| 53_L | 246_L | 1.365 | 0.99 |
| 92_N | 146_E | 1.359 | 0.99 |
| 97_I | 202_M | 1.356 | 0.99 |
| 232_G | 263_L | 1.351 | 0.99 |
| 54_V | 175_I | 1.349 | 0.99 |
| 246_L | 263_L | 1.343 | 0.99 |
| 152_F | 172_V | 1.337 | 0.99 |
| 103_W | 127_A | 1.326 | 0.99 |
| 214_F | 233_W | 1.323 | 0.99 |
| 187_T | 200_K | 1.319 | 0.99 |
| 177_E | 231_T | 1.309 | 0.99 |
| 59_K | 238_D | 1.304 | 0.99 |
| 187_T | 193_E | 1.286 | 0.99 |
| 59_K | 241_I | 1.282 | 0.99 |
| 127_A | 130_V | 1.276 | 0.99 |
| 234_V | 267_L | 1.271 | 0.99 |
| 141_D | 145_K | 1.264 | 0.99 |
| 142_L | 145_K | 1.263 | 0.99 |
| 222_D | 249_E | 1.254 | 0.99 |
| 201_N | 204_L | 1.254 | 0.99 |
| 256_A | 260_N | 1.250 | 0.99 |
| 112_A | 127_A | 1.245 | 0.98 |
| 207_E | 215_G | 1.231 | 0.98 |
| 54_V | 178_V | 1.224 | 0.98 |
| 146_E | 150_I | 1.221 | 0.98 |
| 53_L | 244_F | 1.217 | 0.98 |
| 42_Q | 46_E | 1.216 | 0.98 |
| 87_L | 150_I | 1.210 | 0.98 |
| 83_M | 123_M | 1.207 | 0.98 |
| 185_A | 233_W | 1.205 | 0.98 |
| 212_K | 237_P | 1.203 | 0.98 |
| 58_D | 182_S | 1.195 | 0.98 |
| 77_P | 172_V | 1.187 | 0.98 |
| 102_K | 116_D | 1.187 | 0.98 |
| 56_Q | 182_S | 1.181 | 0.98 |
| 58_D | 242_V | 1.178 | 0.98 |
| 95_T | 137_R | 1.172 | 0.98 |
| 187_T | 197_A | 1.165 | 0.97 |
| 97_I | 198_N | 1.164 | 0.97 |
| 56_Q | 243_A | 1.158 | 0.97 |
| 129_P | 133_E | 1.155 | 0.97 |
| 139_G | 142_L | 1.145 | 0.97 |
| 146_E | 149_R | 1.142 | 0.97 |
| 200_K | 214_F | 1.130 | 0.97 |
| 133_E | 137_R | 1.124 | 0.97 |
| 75_Y | 227_V | 1.118 | 0.96 |
| 91_E | 146_E | 1.083 | 0.96 |
| 200_K | 203_L | 1.079 | 0.95 |
| 83_M | 181_V | 1.074 | 0.95 |
| 178_V | 231_T | 1.067 | 0.95 |
| 41_H | 45_D | 1.057 | 0.95 |
| 54_V | 174_P | 1.056 | 0.95 |
| 172_V | 177_E | 1.050 | 0.94 |
| 207_E | 230_L | 1.049 | 0.94 |
| 235_E | 239_G | 1.047 | 0.94 |
| 57_T | 64_Y | 1.042 | 0.94 |
| 123_M | 203_L | 1.041 | 0.94 |
| 255_P | 260_N | 1.038 | 0.94 |
| 207_E | 213_I | 1.032 | 0.94 |
| 87_L | 196_Q | 1.031 | 0.94 |
| 92_N | 138_I | 1.028 | 0.94 |
| 39_V | 42_Q | 1.021 | 0.93 |
| 194_K | 198_N | 1.016 | 0.93 |
| 174_P | 178_V | 1.014 | 0.93 |
| 86_A | 119_L | 1.007 | 0.93 |
| 242_V | 270_L | 1.003 | 0.93 |
| 123_M | 202_M | 1.002 | 0.92 |
| 90_L | 198_N | 1.002 | 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
- 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 | |
| 2iwbA | 1 | 0.8901 | 100 | 0.311 | Contact Map |
| 3hbrA | 4 | 0.8718 | 100 | 0.317 | Contact Map |
| 1k38A | 2 | 0.8498 | 100 | 0.331 | Contact Map |
| 4f7yA | 4 | 0.8681 | 100 | 0.332 | Contact Map |
| 4oh0A | 1 | 0.8718 | 100 | 0.336 | Contact Map |
| 4ovdA | 1 | 0.9634 | 100 | 0.34 | Contact Map |
| 3pbtA | 1 | 0.989 | 100 | 0.346 | Contact Map |
| 3zntA | 1 | 0.8901 | 100 | 0.348 | Contact Map |
| 3ue3A | 1 | 0.9744 | 100 | 0.348 | Contact Map |
| 4jf5A | 1 | 0.8828 | 100 | 0.351 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)