| rfah-new |
| ID: | 1510164662 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 243 (172) | ||
| Sequences: | 3875 (2234.9) | ||
| Seq/Len: | 22.529 | ||
| Nf(neff/√len): | 170.4 |
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: 22.529).
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 |
| 92_K | 96_E | 4.209 | 1.00 |
| 110_E | 141_H | 3.745 | 1.00 |
| 117_E | 128_V | 3.366 | 1.00 |
| 220_V | 240_V | 3.201 | 1.00 |
| 197_S | 241_K | 3.188 | 1.00 |
| 174_D | 178_R | 3.123 | 1.00 |
| 117_E | 130_Q | 2.799 | 1.00 |
| 76_M | 141_H | 2.461 | 1.00 |
| 100_E | 105_E | 2.402 | 1.00 |
| 200_A | 239_D | 2.144 | 1.00 |
| 120_E | 131_R | 2.131 | 1.00 |
| 195_V | 207_V | 2.085 | 1.00 |
| 194_D | 242_K | 2.070 | 1.00 |
| 212_K | 221_T | 2.036 | 1.00 |
| 83_T | 88_E | 1.962 | 1.00 |
| 197_S | 207_V | 1.933 | 1.00 |
| 115_T | 130_Q | 1.884 | 1.00 |
| 98_A | 156_T | 1.734 | 1.00 |
| 89_N | 115_T | 1.714 | 1.00 |
| 91_V | 159_V | 1.700 | 1.00 |
| 119_V | 126_N | 1.684 | 1.00 |
| 118_V | 131_R | 1.658 | 1.00 |
| 121_D | 126_N | 1.635 | 1.00 |
| 109_L | 141_H | 1.630 | 1.00 |
| 214_D | 217_R | 1.600 | 1.00 |
| 173_T | 176_E | 1.556 | 1.00 |
| 219_T | 234_E | 1.522 | 1.00 |
| 119_V | 128_V | 1.506 | 1.00 |
| 141_H | 174_D | 1.486 | 1.00 |
| 196_I | 208_G | 1.477 | 1.00 |
| 93_A | 97_K | 1.467 | 1.00 |
| 82_H | 161_G | 1.460 | 1.00 |
| 191_A | 194_D | 1.457 | 1.00 |
| 87_Y | 90_K | 1.454 | 1.00 |
| 107_E | 145_D | 1.443 | 1.00 |
| 116_Q | 131_R | 1.441 | 1.00 |
| 220_V | 237_F | 1.433 | 1.00 |
| 211_Q | 223_S | 1.432 | 1.00 |
| 208_G | 222_I | 1.420 | 1.00 |
| 134_F | 180_L | 1.416 | 1.00 |
| 196_I | 222_I | 1.416 | 1.00 |
| 81_V | 159_V | 1.378 | 0.99 |
| 75_G | 143_D | 1.367 | 0.99 |
| 225_E | 230_E | 1.347 | 0.99 |
| 236_N | 239_D | 1.342 | 0.99 |
| 190_F | 210_V | 1.341 | 0.99 |
| 76_M | 109_L | 1.332 | 0.99 |
| 198_V | 235_I | 1.318 | 0.99 |
| 199_T | 241_K | 1.303 | 0.99 |
| 223_S | 230_E | 1.295 | 0.99 |
| 82_H | 160_T | 1.283 | 0.99 |
| 87_Y | 158_G | 1.281 | 0.99 |
| 95_I | 99_I | 1.263 | 0.99 |
| 84_Y | 87_Y | 1.245 | 0.98 |
| 81_V | 153_V | 1.231 | 0.98 |
| 209_T | 223_S | 1.228 | 0.98 |
| 112_R | 184_S | 1.223 | 0.98 |
| 99_I | 108_I | 1.216 | 0.98 |
| 88_E | 113_V | 1.210 | 0.98 |
| 90_K | 158_G | 1.205 | 0.98 |
| 153_V | 159_V | 1.204 | 0.98 |
| 235_I | 239_D | 1.197 | 0.98 |
| 139_L | 177_L | 1.189 | 0.98 |
| 175_E | 179_A | 1.188 | 0.98 |
| 142_M | 149_A | 1.185 | 0.98 |
| 134_F | 139_L | 1.180 | 0.98 |
| 197_S | 205_D | 1.176 | 0.98 |
| 221_T | 234_E | 1.166 | 0.97 |
| 145_D | 149_A | 1.149 | 0.97 |
| 222_I | 235_I | 1.146 | 0.97 |
| 134_F | 158_G | 1.141 | 0.97 |
| 110_E | 181_D | 1.140 | 0.97 |
| 142_M | 153_V | 1.117 | 0.96 |
| 221_T | 232_P | 1.115 | 0.96 |
| 92_K | 111_V | 1.095 | 0.96 |
| 122_K | 127_K | 1.093 | 0.96 |
| 77_G | 174_D | 1.081 | 0.95 |
| 92_K | 113_V | 1.081 | 0.95 |
| 175_E | 178_R | 1.078 | 0.95 |
| 195_V | 209_T | 1.071 | 0.95 |
| 139_L | 172_L | 1.063 | 0.95 |
| 82_H | 136_S | 1.051 | 0.94 |
| 80_V | 163_V | 1.036 | 0.94 |
| 215_A | 237_F | 1.035 | 0.94 |
| 151_Y | 154_R | 1.033 | 0.94 |
| 96_E | 111_V | 1.017 | 0.93 |
| 227_F | 231_T | 1.012 | 0.93 |
| 177_L | 181_D | 1.011 | 0.93 |
| 211_Q | 221_T | 1.009 | 0.93 |
| 172_L | 177_L | 1.008 | 0.93 |
| 94_N | 156_T | 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 | |
| 2jvvA | 1 | 0.2346 | 100 | 0.4 | Contact Map |
| 2ougA | 4 | 0.5761 | 100 | 0.414 | Contact Map |
| 1m1hA | 1 | 0.4733 | 100 | 0.418 | Contact Map |
| 2lq8A | 1 | 0.6749 | 100 | 0.436 | Contact Map |
| 3p8bB | 2 | 0.5885 | 100 | 0.528 | Contact Map |
| 2xhcA | 1 | 0.9506 | 100 | 0.55 | Contact Map |
| 1nz8A | 1 | 0.4691 | 99.9 | 0.61 | Contact Map |
| 3lpeA | 4 | 0.3457 | 99.6 | 0.729 | Contact Map |
| 2mi6A | 1 | 0.2551 | 99 | 0.8 | Contact Map |
| 1nz9A | 1 | 0.2387 | 98.9 | 0.801 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)