| agrc 200-425 |
| ID: | 1380837166 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 226 (206) | ||
| Sequences: | 40138 (31893.3) | ||
| Seq/Len: | 194.845 | ||
| Nf(neff/√len): | 2222.1 |
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: 194.845).
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 | 3.469 | 1.00 |
| 202_K | 206_D | 2.970 | 1.00 |
| 212_L | 223_Y | 2.799 | 1.00 |
| 125_L | 208_A | 2.658 | 1.00 |
| 145_S | 171_K | 2.578 | 1.00 |
| 156_A | 167_I | 2.554 | 1.00 |
| 53_I | 68_N | 2.527 | 1.00 |
| 113_S | 154_R | 2.450 | 1.00 |
| 216_I | 219_N | 2.354 | 1.00 |
| 179_I | 215_T | 2.329 | 1.00 |
| 113_S | 152_I | 2.282 | 1.00 |
| 169_M | 221_F | 2.278 | 1.00 |
| 115_E | 156_A | 2.244 | 1.00 |
| 201_L | 211_V | 2.146 | 1.00 |
| 81_L | 84_N | 2.126 | 1.00 |
| 154_R | 169_M | 2.107 | 1.00 |
| 152_I | 171_K | 2.083 | 1.00 |
| 205_A | 210_N | 2.078 | 1.00 |
| 183_F | 211_V | 2.073 | 1.00 |
| 133_S | 205_A | 2.031 | 1.00 |
| 156_A | 169_M | 2.030 | 1.00 |
| 158_I | 165_T | 2.016 | 1.00 |
| 179_I | 213_L | 2.015 | 1.00 |
| 178_R | 181_E | 1.904 | 1.00 |
| 111_P | 152_I | 1.901 | 1.00 |
| 181_E | 187_F | 1.896 | 1.00 |
| 50_S | 73_K | 1.895 | 1.00 |
| 175_D | 182_L | 1.884 | 1.00 |
| 167_I | 223_Y | 1.847 | 1.00 |
| 165_T | 223_Y | 1.837 | 1.00 |
| 125_L | 130_L | 1.823 | 1.00 |
| 133_S | 204_I | 1.775 | 1.00 |
| 158_I | 167_I | 1.765 | 1.00 |
| 139_D | 143_E | 1.765 | 1.00 |
| 115_E | 154_R | 1.764 | 1.00 |
| 133_S | 201_L | 1.722 | 1.00 |
| 181_E | 184_Q | 1.680 | 1.00 |
| 167_I | 221_F | 1.679 | 1.00 |
| 175_D | 178_R | 1.639 | 1.00 |
| 178_R | 187_F | 1.594 | 1.00 |
| 160_S | 165_T | 1.534 | 1.00 |
| 204_I | 208_A | 1.530 | 1.00 |
| 151_P | 171_K | 1.514 | 1.00 |
| 176_I | 217_I | 1.506 | 1.00 |
| 126_N | 129_D | 1.497 | 1.00 |
| 165_T | 225_K | 1.468 | 1.00 |
| 101_K | 135_G | 1.462 | 1.00 |
| 145_S | 151_P | 1.454 | 1.00 |
| 129_D | 132_R | 1.431 | 1.00 |
| 81_L | 85_G | 1.431 | 1.00 |
| 215_T | 219_N | 1.429 | 1.00 |
| 102_I | 106_Q | 1.382 | 0.99 |
| 183_F | 213_L | 1.381 | 0.99 |
| 205_A | 224_S | 1.375 | 0.99 |
| 213_L | 222_F | 1.363 | 0.99 |
| 134_I | 166_F | 1.362 | 0.99 |
| 129_D | 207_N | 1.361 | 0.99 |
| 163_S | 225_K | 1.350 | 0.99 |
| 214_D | 223_Y | 1.349 | 0.99 |
| 145_S | 153_I | 1.334 | 0.99 |
| 58_M | 61_L | 1.329 | 0.99 |
| 184_Q | 187_F | 1.311 | 0.99 |
| 214_D | 221_F | 1.299 | 0.99 |
| 41_D | 132_R | 1.279 | 0.99 |
| 166_F | 224_S | 1.271 | 0.99 |
| 100_A | 131_S | 1.262 | 0.99 |
| 105_A | 142_I | 1.258 | 0.99 |
| 170_N | 220_G | 1.241 | 0.98 |
| 52_Y | 64_Y | 1.240 | 0.98 |
| 178_R | 189_T | 1.238 | 0.98 |
| 84_N | 87_E | 1.224 | 0.98 |
| 182_L | 213_L | 1.224 | 0.98 |
| 205_A | 211_V | 1.213 | 0.98 |
| 48_T | 52_Y | 1.206 | 0.98 |
| 136_I | 201_L | 1.184 | 0.98 |
| 50_S | 72_M | 1.168 | 0.97 |
| 54_R | 69_I | 1.166 | 0.97 |
| 154_R | 171_K | 1.146 | 0.97 |
| 129_D | 204_I | 1.129 | 0.97 |
| 144_A | 188_S | 1.114 | 0.96 |
| 127_M | 131_S | 1.113 | 0.96 |
| 41_D | 45_I | 1.101 | 0.96 |
| 215_T | 218_E | 1.089 | 0.96 |
| 67_K | 71_P | 1.085 | 0.96 |
| 116_I | 157_F | 1.079 | 0.95 |
| 93_E | 97_L | 1.074 | 0.95 |
| 48_T | 51_E | 1.072 | 0.95 |
| 69_I | 73_K | 1.056 | 0.95 |
| 57_D | 66_N | 1.054 | 0.95 |
| 104_R | 107_E | 1.036 | 0.94 |
| 29_E | 32_N | 1.030 | 0.94 |
| 41_D | 136_I | 1.030 | 0.94 |
| 203_E | 206_D | 1.028 | 0.94 |
| 179_I | 183_F | 1.026 | 0.94 |
| 130_L | 208_A | 1.023 | 0.93 |
| 203_E | 207_N | 1.018 | 0.93 |
| 188_S | 191_G | 1.018 | 0.93 |
| 72_M | 75_N | 1.015 | 0.93 |
| 53_I | 69_I | 1.004 | 0.93 |
| 175_D | 179_I | 1.003 | 0.93 |
| 129_D | 208_A | 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 | |
| 4gczA | 2 | 0.9867 | 100 | 0.337 | Contact Map |
| 3a0rA | 1 | 0.9469 | 100 | 0.338 | Contact Map |
| 4i5sA | 2 | 0.9071 | 100 | 0.359 | Contact Map |
| 2c2aA | 1 | 0.9336 | 100 | 0.374 | Contact Map |
| 4ew8A | 2 | 0.9159 | 100 | 0.38 | Contact Map |
| 3d36A | 2 | 0.8805 | 100 | 0.384 | Contact Map |
| 1y8oA | 1 | 0.969 | 99.9 | 0.406 | Contact Map |
| 4mpcA | 1 | 0.9558 | 99.9 | 0.406 | Contact Map |
| 3jz3A | 2 | 0.615 | 99.9 | 0.409 | Contact Map |
| 2e0aA | 2 | 0.9779 | 99.9 | 0.411 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)