| job 5 out of 6 4CH9_A |
| ID: | 1482422079 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 292 (283) | ||
| Sequences: | 12196 (8531.5) | ||
| Seq/Len: | 43.095 | ||
| Nf(neff/√len): | 507.1 |
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: 43.095).
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 |
| 100_L | 118_A | 4.044 | 1.00 |
| 147_K | 167_Q | 4.033 | 1.00 |
| 53_H | 71_V | 3.639 | 1.00 |
| 196_Q | 214_V | 3.512 | 1.00 |
| 215_Y | 220_N | 3.382 | 1.00 |
| 119_Y | 124_N | 3.380 | 1.00 |
| 168_Y | 173_N | 3.187 | 1.00 |
| 72_Y | 77_D | 2.783 | 1.00 |
| 262_Y | 267_D | 2.427 | 1.00 |
| 243_L | 261_Y | 2.422 | 1.00 |
| 93_G | 141_V | 2.394 | 1.00 |
| 140_G | 190_V | 2.345 | 1.00 |
| 46_G | 94_A | 2.226 | 1.00 |
| 147_K | 169_N | 2.197 | 1.00 |
| 100_L | 120_S | 2.096 | 1.00 |
| 189_G | 237_V | 2.087 | 1.00 |
| 53_H | 73_D | 2.027 | 1.00 |
| 167_Q | 178_V | 2.011 | 1.00 |
| 25_Y | 30_D | 2.003 | 1.00 |
| 196_Q | 216_D | 1.998 | 1.00 |
| 118_A | 127_F | 1.990 | 1.00 |
| 118_A | 129_V | 1.939 | 1.00 |
| 71_V | 82_I | 1.924 | 1.00 |
| 167_Q | 176_I | 1.897 | 1.00 |
| 94_A | 103_A | 1.863 | 1.00 |
| 139_V | 150_A | 1.855 | 1.00 |
| 86_Q | 117_E | 1.852 | 1.00 |
| 136_R | 166_E | 1.837 | 1.00 |
| 214_V | 225_V | 1.823 | 1.00 |
| 190_V | 199_A | 1.819 | 1.00 |
| 243_L | 263_N | 1.786 | 1.00 |
| 198_Y | 214_V | 1.774 | 1.00 |
| 95_A | 148_L | 1.763 | 1.00 |
| 48_V | 101_L | 1.712 | 1.00 |
| 89_R | 117_E | 1.695 | 1.00 |
| 104_V | 148_L | 1.659 | 1.00 |
| 146_G | 171_A | 1.658 | 1.00 |
| 97_L | 143_V | 1.653 | 1.00 |
| 7_V | 24_C | 1.643 | 1.00 |
| 142_G | 197_L | 1.638 | 1.00 |
| 182_S | 213_E | 1.636 | 1.00 |
| 99_D | 122_K | 1.621 | 1.00 |
| 120_S | 123_T | 1.617 | 1.00 |
| 95_A | 141_V | 1.587 | 1.00 |
| 102_Y | 118_A | 1.579 | 1.00 |
| 141_V | 150_A | 1.576 | 1.00 |
| 149_Y | 167_Q | 1.571 | 1.00 |
| 39_P | 70_D | 1.569 | 1.00 |
| 185_R | 211_S | 1.565 | 1.00 |
| 214_V | 223_K | 1.564 | 1.00 |
| 229_N | 260_E | 1.518 | 1.00 |
| 237_V | 246_V | 1.516 | 1.00 |
| 92_L | 103_A | 1.515 | 1.00 |
| 185_R | 213_E | 1.512 | 1.00 |
| 179_A | 220_N | 1.494 | 1.00 |
| 195_G | 218_G | 1.491 | 1.00 |
| 50_M | 96_V | 1.466 | 1.00 |
| 71_V | 80_T | 1.464 | 1.00 |
| 93_G | 139_V | 1.463 | 1.00 |
| 73_D | 76_K | 1.453 | 1.00 |
| 102_Y | 116_V | 1.452 | 1.00 |
| 130_A | 173_N | 1.440 | 1.00 |
| 119_Y | 126_W | 1.438 | 1.00 |
| 49_F | 74_G | 1.432 | 1.00 |
| 47_V | 56_A | 1.431 | 1.00 |
| 55_Y | 71_V | 1.429 | 1.00 |
| 191_G | 244_L | 1.418 | 1.00 |
| 140_G | 188_A | 1.418 | 1.00 |
| 188_A | 199_A | 1.412 | 1.00 |
| 136_R | 164_T | 1.410 | 1.00 |
| 116_V | 129_V | 1.389 | 0.99 |
| 52_G | 75_V | 1.386 | 0.99 |
| 133_N | 166_E | 1.368 | 0.99 |
| 104_V | 116_V | 1.356 | 0.99 |
| 61_N | 66_V | 1.354 | 0.99 |
| 149_Y | 165_V | 1.347 | 0.99 |
| 190_V | 197_L | 1.340 | 0.99 |
| 83_A | 124_N | 1.332 | 0.99 |
| 169_N | 172_T | 1.330 | 0.99 |
| 55_Y | 101_L | 1.328 | 0.99 |
| 108_D | 113_L | 1.326 | 0.99 |
| 245_Y | 261_Y | 1.326 | 0.99 |
| 46_G | 92_L | 1.325 | 0.99 |
| 148_L | 170_P | 1.305 | 0.99 |
| 144_V | 192_V | 1.297 | 0.99 |
| 151_V | 197_L | 1.293 | 0.99 |
| 48_V | 94_A | 1.289 | 0.99 |
| 178_V | 220_N | 1.274 | 0.99 |
| 50_M | 121_Y | 1.266 | 0.99 |
| 57_V | 101_L | 1.262 | 0.99 |
| 235_A | 246_V | 1.260 | 0.99 |
| 42_R | 45_A | 1.257 | 0.99 |
| 89_R | 92_L | 1.256 | 0.99 |
| 101_L | 121_Y | 1.255 | 0.99 |
| 24_C | 35_I | 1.245 | 0.98 |
| 232_R | 260_E | 1.239 | 0.98 |
| 200_T | 212_V | 1.238 | 0.98 |
| 48_V | 96_V | 1.232 | 0.98 |
| 155_D | 162_L | 1.228 | 0.98 |
| 89_R | 115_S | 1.227 | 0.98 |
| 57_V | 94_A | 1.214 | 0.98 |
| 151_V | 165_V | 1.214 | 0.98 |
| 191_G | 239_A | 1.205 | 0.98 |
| 142_G | 192_V | 1.201 | 0.98 |
| 189_G | 235_A | 1.191 | 0.98 |
| 116_V | 168_Y | 1.189 | 0.98 |
| 70_D | 81_S | 1.185 | 0.98 |
| 117_E | 128_F | 1.182 | 0.98 |
| 56_A | 79_W | 1.180 | 0.98 |
| 143_V | 170_P | 1.176 | 0.98 |
| 149_Y | 197_L | 1.173 | 0.98 |
| 129_V | 173_N | 1.172 | 0.98 |
| 237_V | 244_L | 1.167 | 0.97 |
| 200_T | 237_V | 1.160 | 0.97 |
| 144_V | 217_P | 1.159 | 0.97 |
| 161_C | 186_S | 1.159 | 0.97 |
| 42_R | 70_D | 1.151 | 0.97 |
| 166_E | 177_Y | 1.151 | 0.97 |
| 191_G | 237_V | 1.150 | 0.97 |
| 97_L | 170_P | 1.148 | 0.97 |
| 263_N | 266_T | 1.144 | 0.97 |
| 55_Y | 69_V | 1.142 | 0.97 |
| 141_V | 148_L | 1.140 | 0.97 |
| 215_Y | 222_W | 1.137 | 0.97 |
| 142_G | 190_V | 1.135 | 0.97 |
| 103_A | 126_W | 1.134 | 0.97 |
| 57_V | 69_V | 1.134 | 0.97 |
| 212_V | 225_V | 1.131 | 0.97 |
| 261_Y | 272_L | 1.130 | 0.97 |
| 36_A | 77_D | 1.122 | 0.97 |
| 96_V | 121_Y | 1.121 | 0.97 |
| 195_G | 217_P | 1.120 | 0.96 |
| 95_A | 143_V | 1.118 | 0.96 |
| 94_A | 101_L | 1.115 | 0.96 |
| 9_I | 24_C | 1.111 | 0.96 |
| 47_V | 54_V | 1.107 | 0.96 |
| 26_D | 29_E | 1.107 | 0.96 |
| 42_R | 68_T | 1.103 | 0.96 |
| 232_R | 249_G | 1.101 | 0.96 |
| 183_T | 213_E | 1.099 | 0.96 |
| 193_L | 239_A | 1.087 | 0.96 |
| 261_Y | 270_T | 1.083 | 0.96 |
| 82_I | 124_N | 1.081 | 0.95 |
| 216_D | 219_T | 1.077 | 0.95 |
| 107_F | 137_S | 1.075 | 0.95 |
| 165_V | 178_V | 1.074 | 0.95 |
| 102_Y | 148_L | 1.073 | 0.95 |
| 226_A | 267_D | 1.070 | 0.95 |
| 72_Y | 79_W | 1.066 | 0.95 |
| 232_R | 258_S | 1.064 | 0.95 |
| 200_T | 244_L | 1.060 | 0.95 |
| 213_E | 224_Q | 1.057 | 0.95 |
| 69_V | 82_I | 1.056 | 0.95 |
| 204_D | 209_R | 1.050 | 0.94 |
| 104_V | 141_V | 1.046 | 0.94 |
| 112_G | 137_S | 1.043 | 0.94 |
| 198_Y | 244_L | 1.039 | 0.94 |
| 185_R | 188_A | 1.036 | 0.94 |
| 60_F | 90_S | 1.034 | 0.94 |
| 99_D | 121_Y | 1.024 | 0.93 |
| 7_V | 26_D | 1.021 | 0.93 |
| 151_V | 190_V | 1.020 | 0.93 |
| 91_T | 138_S | 1.015 | 0.93 |
| 133_N | 175_W | 1.007 | 0.93 |
| 54_V | 74_G | 1.006 | 0.93 |
| 102_Y | 168_Y | 1.004 | 0.93 |
| 128_F | 131_P | 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 | |
| 4chbA | 2 | 0.9795 | 100 | 0.074 | Contact Map |
| 1zgkA | 1 | 0.9726 | 100 | 0.096 | Contact Map |
| 2vpjA | 1 | 0.9726 | 100 | 0.097 | Contact Map |
| 3ii7A | 1 | 0.976 | 100 | 0.112 | Contact Map |
| 4yy8A | 2 | 0.976 | 100 | 0.132 | Contact Map |
| 2wozA | 1 | 0.9623 | 100 | 0.16 | Contact Map |
| 4ascA | 1 | 0.9521 | 100 | 0.16 | Contact Map |
| 2uvkA | 2 | 0.9144 | 100 | 0.212 | Contact Map |
| 1k3iA | 1 | 0.9795 | 100 | 0.252 | Contact Map |
| 2zwaA | 2 | 0.8973 | 100 | 0.274 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)