| agrc 200-425 |
| ID: | 1380857740 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 226 (203) | ||
| Sequences: | 44210 (34970) | ||
| Seq/Len: | 217.783 | ||
| Nf(neff/√len): | 2454.4 |
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: 217.783).
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 |
| 170_N | 174_D | 3.503 | 1.00 |
| 202_K | 206_D | 3.046 | 1.00 |
| 125_L | 208_A | 2.700 | 1.00 |
| 156_A | 167_I | 2.692 | 1.00 |
| 113_S | 154_R | 2.658 | 1.00 |
| 145_S | 171_K | 2.654 | 1.00 |
| 53_I | 69_I | 2.463 | 1.00 |
| 179_I | 215_T | 2.457 | 1.00 |
| 113_S | 152_I | 2.412 | 1.00 |
| 216_I | 219_N | 2.388 | 1.00 |
| 152_I | 171_K | 2.339 | 1.00 |
| 115_E | 156_A | 2.306 | 1.00 |
| 154_R | 169_M | 2.267 | 1.00 |
| 133_S | 205_A | 2.202 | 1.00 |
| 50_S | 74_D | 2.198 | 1.00 |
| 201_L | 211_V | 2.182 | 1.00 |
| 205_A | 210_N | 2.103 | 1.00 |
| 158_I | 165_T | 2.077 | 1.00 |
| 183_F | 211_V | 2.066 | 1.00 |
| 50_S | 73_K | 2.057 | 1.00 |
| 156_A | 169_M | 2.045 | 1.00 |
| 111_P | 152_I | 2.024 | 1.00 |
| 178_R | 181_E | 2.017 | 1.00 |
| 181_E | 187_F | 1.995 | 1.00 |
| 175_D | 182_L | 1.989 | 1.00 |
| 179_I | 213_L | 1.926 | 1.00 |
| 115_E | 154_R | 1.883 | 1.00 |
| 125_L | 130_L | 1.851 | 1.00 |
| 181_E | 184_Q | 1.849 | 1.00 |
| 139_D | 143_E | 1.829 | 1.00 |
| 158_I | 167_I | 1.811 | 1.00 |
| 133_S | 201_L | 1.758 | 1.00 |
| 92_R | 125_L | 1.750 | 1.00 |
| 133_S | 204_I | 1.738 | 1.00 |
| 160_S | 165_T | 1.687 | 1.00 |
| 175_D | 178_R | 1.684 | 1.00 |
| 151_P | 171_K | 1.653 | 1.00 |
| 178_R | 187_F | 1.616 | 1.00 |
| 183_F | 213_L | 1.559 | 1.00 |
| 134_I | 166_F | 1.520 | 1.00 |
| 54_R | 70_V | 1.497 | 1.00 |
| 145_S | 153_I | 1.494 | 1.00 |
| 70_V | 74_D | 1.475 | 1.00 |
| 215_T | 219_N | 1.467 | 1.00 |
| 102_I | 106_Q | 1.458 | 1.00 |
| 176_I | 217_I | 1.457 | 1.00 |
| 169_M | 221_F | 1.456 | 1.00 |
| 204_I | 208_A | 1.455 | 1.00 |
| 91_V | 124_N | 1.445 | 1.00 |
| 101_K | 135_G | 1.441 | 1.00 |
| 145_S | 151_P | 1.435 | 1.00 |
| 184_Q | 187_F | 1.434 | 1.00 |
| 93_E | 96_G | 1.405 | 0.99 |
| 126_N | 129_D | 1.404 | 0.99 |
| 41_D | 132_R | 1.399 | 0.99 |
| 129_D | 132_R | 1.385 | 0.99 |
| 100_A | 131_S | 1.384 | 0.99 |
| 129_D | 207_N | 1.378 | 0.99 |
| 49_L | 73_K | 1.377 | 0.99 |
| 72_M | 75_N | 1.375 | 0.99 |
| 105_A | 142_I | 1.372 | 0.99 |
| 53_I | 70_V | 1.358 | 0.99 |
| 182_L | 213_L | 1.352 | 0.99 |
| 136_I | 201_L | 1.340 | 0.99 |
| 50_S | 77_Q | 1.324 | 0.99 |
| 58_M | 61_L | 1.309 | 0.99 |
| 32_N | 35_M | 1.279 | 0.99 |
| 205_A | 211_V | 1.264 | 0.99 |
| 48_T | 52_Y | 1.239 | 0.98 |
| 212_L | 223_Y | 1.229 | 0.98 |
| 129_D | 204_I | 1.224 | 0.98 |
| 127_M | 131_S | 1.217 | 0.98 |
| 154_R | 171_K | 1.204 | 0.98 |
| 50_S | 70_V | 1.153 | 0.97 |
| 170_N | 220_G | 1.138 | 0.97 |
| 104_R | 107_E | 1.137 | 0.97 |
| 130_L | 208_A | 1.131 | 0.97 |
| 140_N | 197_G | 1.127 | 0.97 |
| 53_I | 73_K | 1.118 | 0.96 |
| 116_I | 157_F | 1.110 | 0.96 |
| 21_Y | 24_Y | 1.101 | 0.96 |
| 203_E | 206_D | 1.094 | 0.96 |
| 167_I | 223_Y | 1.094 | 0.96 |
| 179_I | 183_F | 1.080 | 0.95 |
| 203_E | 207_N | 1.078 | 0.95 |
| 165_T | 212_L | 1.075 | 0.95 |
| 215_T | 218_E | 1.070 | 0.95 |
| 51_E | 55_E | 1.070 | 0.95 |
| 129_D | 208_A | 1.043 | 0.94 |
| 78_M | 128_I | 1.042 | 0.94 |
| 59_T | 62_R | 1.025 | 0.93 |
| 48_T | 51_E | 1.025 | 0.93 |
| 144_A | 173_A | 1.025 | 0.93 |
| 134_I | 168_V | 1.018 | 0.93 |
| 175_D | 179_I | 1.012 | 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
- 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 | |
| 3a0rA | 1 | 0.9469 | 100 | 0.364 | Contact Map |
| 4gczA | 2 | 0.9867 | 100 | 0.375 | Contact Map |
| 4i5sA | 2 | 0.9027 | 100 | 0.376 | Contact Map |
| 4ew8A | 2 | 0.9159 | 99.9 | 0.39 | Contact Map |
| 2c2aA | 1 | 0.9336 | 99.9 | 0.396 | Contact Map |
| 3d36A | 2 | 0.8805 | 99.9 | 0.412 | Contact Map |
| 1y8oA | 1 | 0.969 | 99.9 | 0.418 | Contact Map |
| 4mpcA | 1 | 0.9513 | 99.9 | 0.418 | Contact Map |
| 3jz3A | 2 | 0.615 | 99.9 | 0.427 | Contact Map |
| 2e0aA | 2 | 0.9912 | 99.9 | 0.428 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)