| T0776 |
| ID: | 1440608617 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 256 (215) | ||
| Sequences: | 4093 (3272) | ||
| Seq/Len: | 19.037 | ||
| Nf(neff/√len): | 223.1 |
HHblits Results: (2015_06)
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: 19.037).
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 |
| 174_E | 211_F | 4.503 | 1.00 |
| 51_F | 57_T | 2.974 | 1.00 |
| 107_V | 153_D | 2.807 | 1.00 |
| 49_I | 127_S | 2.754 | 1.00 |
| 155_R | 206_E | 2.714 | 1.00 |
| 174_E | 213_P | 2.661 | 1.00 |
| 115_E | 160_Y | 2.604 | 1.00 |
| 213_P | 216_S | 2.581 | 1.00 |
| 173_C | 249_W | 2.506 | 1.00 |
| 175_P | 197_R | 2.279 | 1.00 |
| 151_E | 202_K | 2.203 | 1.00 |
| 169_Q | 210_I | 2.189 | 1.00 |
| 126_L | 161_T | 2.183 | 1.00 |
| 159_K | 207_F | 2.126 | 1.00 |
| 126_L | 168_T | 2.125 | 1.00 |
| 214_F | 245_M | 1.966 | 1.00 |
| 55_S | 236_H | 1.901 | 1.00 |
| 82_T | 250_M | 1.877 | 1.00 |
| 248_M | 251_E | 1.875 | 1.00 |
| 158_L | 172_L | 1.846 | 1.00 |
| 110_L | 130_I | 1.805 | 1.00 |
| 51_F | 127_S | 1.802 | 1.00 |
| 212_V | 252_A | 1.785 | 1.00 |
| 57_T | 101_G | 1.783 | 1.00 |
| 154_L | 200_A | 1.753 | 1.00 |
| 155_R | 207_F | 1.713 | 1.00 |
| 155_R | 159_K | 1.690 | 1.00 |
| 81_F | 243_Q | 1.674 | 1.00 |
| 107_V | 157_L | 1.664 | 1.00 |
| 240_P | 243_Q | 1.633 | 1.00 |
| 133_N | 236_H | 1.622 | 1.00 |
| 243_Q | 247_N | 1.621 | 1.00 |
| 85_Q | 250_M | 1.615 | 1.00 |
| 48_V | 96_K | 1.576 | 1.00 |
| 172_L | 200_A | 1.571 | 1.00 |
| 201_R | 211_F | 1.565 | 1.00 |
| 56_I | 132_V | 1.561 | 1.00 |
| 150_Y | 154_L | 1.543 | 1.00 |
| 82_T | 249_W | 1.531 | 1.00 |
| 155_R | 203_L | 1.530 | 1.00 |
| 134_D | 153_D | 1.519 | 1.00 |
| 51_F | 79_V | 1.513 | 1.00 |
| 111_R | 156_A | 1.492 | 1.00 |
| 212_V | 249_W | 1.480 | 1.00 |
| 151_E | 199_S | 1.472 | 1.00 |
| 158_L | 209_T | 1.449 | 1.00 |
| 113_R | 117_D | 1.435 | 1.00 |
| 125_V | 171_V | 1.431 | 1.00 |
| 198_K | 202_K | 1.417 | 1.00 |
| 201_R | 205_E | 1.396 | 0.99 |
| 48_V | 124_D | 1.391 | 0.99 |
| 55_S | 133_N | 1.384 | 0.99 |
| 107_V | 154_L | 1.379 | 0.99 |
| 159_K | 163_E | 1.377 | 0.99 |
| 85_Q | 247_N | 1.364 | 0.99 |
| 108_Y | 153_D | 1.352 | 0.99 |
| 174_E | 201_R | 1.347 | 0.99 |
| 58_D | 103_S | 1.346 | 0.99 |
| 171_V | 212_V | 1.315 | 0.99 |
| 105_N | 113_R | 1.305 | 0.99 |
| 150_Y | 200_A | 1.301 | 0.99 |
| 81_F | 246_A | 1.300 | 0.99 |
| 160_Y | 164_K | 1.285 | 0.99 |
| 237_P | 242_R | 1.255 | 0.99 |
| 150_Y | 196_F | 1.243 | 0.98 |
| 177_T | 190_Y | 1.241 | 0.98 |
| 230_W | 241_G | 1.240 | 0.98 |
| 111_R | 153_D | 1.236 | 0.98 |
| 47_C | 124_D | 1.221 | 0.98 |
| 81_F | 85_Q | 1.214 | 0.98 |
| 203_L | 207_F | 1.203 | 0.98 |
| 204_S | 211_F | 1.190 | 0.98 |
| 76_S | 239_L | 1.189 | 0.98 |
| 246_A | 250_M | 1.184 | 0.98 |
| 82_T | 246_A | 1.181 | 0.98 |
| 160_Y | 163_E | 1.170 | 0.97 |
| 194_D | 215_Q | 1.166 | 0.97 |
| 136_W | 235_V | 1.163 | 0.97 |
| 162_K | 207_F | 1.147 | 0.97 |
| 135_Y | 196_F | 1.142 | 0.97 |
| 127_S | 171_V | 1.134 | 0.97 |
| 172_L | 204_S | 1.132 | 0.97 |
| 57_T | 78_Y | 1.128 | 0.97 |
| 49_I | 97_I | 1.117 | 0.96 |
| 81_F | 239_L | 1.102 | 0.96 |
| 154_L | 158_L | 1.102 | 0.96 |
| 52_Q | 100_R | 1.093 | 0.96 |
| 78_Y | 249_W | 1.090 | 0.96 |
| 83_A | 97_I | 1.078 | 0.95 |
| 50_L | 124_D | 1.076 | 0.95 |
| 111_R | 157_L | 1.075 | 0.95 |
| 180_D | 222_V | 1.072 | 0.95 |
| 120_A | 123_P | 1.070 | 0.95 |
| 107_V | 150_Y | 1.068 | 0.95 |
| 48_V | 98_Y | 1.055 | 0.95 |
| 161_T | 168_T | 1.053 | 0.95 |
| 57_T | 129_L | 1.048 | 0.94 |
| 248_M | 252_A | 1.046 | 0.94 |
| 177_T | 219_D | 1.045 | 0.94 |
| 105_N | 109_Q | 1.044 | 0.94 |
| 105_N | 130_I | 1.042 | 0.94 |
| 157_L | 160_Y | 1.042 | 0.94 |
| 151_E | 155_R | 1.042 | 0.94 |
| 199_S | 202_K | 1.038 | 0.94 |
| 162_K | 170_I | 1.035 | 0.94 |
| 78_Y | 242_R | 1.028 | 0.94 |
| 129_L | 132_V | 1.021 | 0.93 |
| 175_P | 193_F | 1.018 | 0.93 |
| 76_S | 84_T | 1.014 | 0.93 |
| 215_Q | 219_D | 1.011 | 0.93 |
| 127_S | 173_C | 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 | |
| 4q9aA | 2 | 0.8516 | 100 | 0.328 | Contact Map |
| 4jhlA | 2 | 0.8203 | 100 | 0.387 | Contact Map |
| 3rjtA | 2 | 0.8164 | 100 | 0.392 | Contact Map |
| 3bzwA | 6 | 0.7891 | 100 | 0.407 | Contact Map |
| 1escA | 1 | 0.8203 | 100 | 0.407 | Contact Map |
| 4tx1A | 3 | 0.7383 | 100 | 0.411 | Contact Map |
| 2q0qA | 8 | 0.7539 | 100 | 0.423 | Contact Map |
| 4hyqA | 1 | 0.7891 | 100 | 0.423 | Contact Map |
| 3dc7A | 3 | 0.7617 | 100 | 0.425 | Contact Map |
| 1vjgA | 1 | 0.7578 | 100 | 0.426 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)