| 1SVN |
| ID: | 1446560040 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 269 (267) | ||
| Sequences: | 13646 (9507.1) | ||
| Seq/Len: | 51.109 | ||
| Nf(neff/√len): | 581.8 |
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: 51.109).
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 |
| 22_T | 85_S | 3.014 | 1.00 |
| 224_A | 264_A | 2.848 | 1.00 |
| 94_L | 100_G | 2.821 | 1.00 |
| 172_G | 193_V | 2.761 | 1.00 |
| 203_Y | 209_A | 2.668 | 1.00 |
| 28_V | 70_I | 2.555 | 1.00 |
| 173_A | 181_A | 2.430 | 1.00 |
| 224_A | 262_V | 2.381 | 1.00 |
| 121_N | 218_T | 2.346 | 1.00 |
| 249_T | 263_N | 2.344 | 1.00 |
| 65_H | 216_M | 2.264 | 1.00 |
| 24_S | 85_S | 2.245 | 1.00 |
| 181_A | 197_V | 2.214 | 1.00 |
| 27_K | 87_E | 2.195 | 1.00 |
| 173_A | 183_F | 2.192 | 1.00 |
| 65_H | 201_S | 2.152 | 1.00 |
| 91_V | 111_W | 2.107 | 1.00 |
| 183_F | 197_V | 2.075 | 1.00 |
| 27_K | 89_Y | 1.969 | 1.00 |
| 173_A | 196_G | 1.946 | 1.00 |
| 68_G | 201_S | 1.943 | 1.00 |
| 146_L | 225_A | 1.921 | 1.00 |
| 138_N | 167_N | 1.884 | 1.00 |
| 68_G | 202_T | 1.882 | 1.00 |
| 236_S | 239_Q | 1.879 | 1.00 |
| 69_T | 220_H | 1.868 | 1.00 |
| 203_Y | 211_L | 1.823 | 1.00 |
| 163_A | 170_A | 1.822 | 1.00 |
| 59_G | 96_A | 1.816 | 1.00 |
| 91_V | 108_G | 1.810 | 1.00 |
| 110_E | 139_S | 1.795 | 1.00 |
| 66_V | 121_N | 1.792 | 1.00 |
| 30_V | 70_I | 1.764 | 1.00 |
| 66_V | 219_P | 1.762 | 1.00 |
| 225_A | 240_I | 1.697 | 1.00 |
| 7_G | 220_H | 1.690 | 1.00 |
| 148_V | 225_A | 1.688 | 1.00 |
| 82_V | 223_G | 1.681 | 1.00 |
| 247_T | 267_A | 1.649 | 1.00 |
| 10_R | 178_N | 1.645 | 1.00 |
| 58_D | 61_G | 1.640 | 1.00 |
| 218_T | 222_A | 1.631 | 1.00 |
| 229_K | 240_I | 1.630 | 1.00 |
| 89_Y | 117_M | 1.630 | 1.00 |
| 28_V | 226_A | 1.612 | 1.00 |
| 146_L | 169_M | 1.609 | 1.00 |
| 29_A | 112_A | 1.607 | 1.00 |
| 118_H | 229_K | 1.599 | 1.00 |
| 211_L | 216_M | 1.589 | 1.00 |
| 71_A | 88_L | 1.587 | 1.00 |
| 172_G | 184_S | 1.587 | 1.00 |
| 242_N | 246_N | 1.585 | 1.00 |
| 121_N | 222_A | 1.569 | 1.00 |
| 29_A | 117_M | 1.555 | 1.00 |
| 21_L | 230_Q | 1.538 | 1.00 |
| 228_V | 267_A | 1.530 | 1.00 |
| 72_A | 202_T | 1.529 | 1.00 |
| 101_S | 104_S | 1.514 | 1.00 |
| 111_W | 115_N | 1.512 | 1.00 |
| 35_I | 90_A | 1.510 | 1.00 |
| 148_V | 218_T | 1.460 | 1.00 |
| 31_L | 93_V | 1.446 | 1.00 |
| 65_H | 211_L | 1.439 | 1.00 |
| 232_N | 235_W | 1.431 | 1.00 |
| 241_R | 245_K | 1.417 | 1.00 |
| 148_V | 221_V | 1.416 | 1.00 |
| 113_G | 140_A | 1.414 | 1.00 |
| 180_R | 193_V | 1.413 | 1.00 |
| 263_N | 266_A | 1.398 | 0.99 |
| 67_A | 88_L | 1.395 | 0.99 |
| 110_E | 114_N | 1.382 | 0.99 |
| 26_V | 229_K | 1.379 | 0.99 |
| 113_G | 145_V | 1.374 | 0.99 |
| 119_V | 222_A | 1.373 | 0.99 |
| 235_W | 243_H | 1.367 | 0.99 |
| 178_N | 261_L | 1.367 | 0.99 |
| 232_N | 243_H | 1.366 | 0.99 |
| 180_R | 184_S | 1.366 | 0.99 |
| 30_V | 66_V | 1.363 | 0.99 |
| 175_D | 197_V | 1.350 | 0.99 |
| 138_N | 142_S | 1.349 | 0.99 |
| 225_A | 244_L | 1.336 | 0.99 |
| 22_T | 230_Q | 1.335 | 0.99 |
| 83_A | 226_A | 1.334 | 0.99 |
| 150_A | 218_T | 1.330 | 0.99 |
| 28_V | 86_A | 1.312 | 0.99 |
| 192_I | 244_L | 1.303 | 0.99 |
| 158_S | 189_G | 1.301 | 0.99 |
| 131_A | 135_Q | 1.299 | 0.99 |
| 175_D | 179_N | 1.290 | 0.99 |
| 69_T | 216_M | 1.287 | 0.99 |
| 173_A | 197_V | 1.266 | 0.99 |
| 151_S | 170_A | 1.262 | 0.99 |
| 26_V | 226_A | 1.247 | 0.99 |
| 250_S | 254_T | 1.245 | 0.98 |
| 109_L | 140_A | 1.243 | 0.98 |
| 221_V | 262_V | 1.242 | 0.98 |
| 134_E | 164_R | 1.230 | 0.98 |
| 134_E | 138_N | 1.224 | 0.98 |
| 44_R | 87_E | 1.223 | 0.98 |
| 169_M | 241_R | 1.218 | 0.98 |
| 174_T | 193_V | 1.213 | 0.98 |
| 134_E | 165_Y | 1.206 | 0.98 |
| 105_I | 124_L | 1.205 | 0.98 |
| 194_A | 221_V | 1.201 | 0.98 |
| 200_Q | 210_S | 1.199 | 0.98 |
| 120_A | 145_V | 1.198 | 0.98 |
| 140_A | 147_V | 1.197 | 0.98 |
| 197_V | 212_N | 1.191 | 0.98 |
| 172_G | 190_L | 1.185 | 0.98 |
| 67_A | 90_A | 1.182 | 0.98 |
| 154_S | 185_Q | 1.181 | 0.98 |
| 174_T | 261_L | 1.177 | 0.98 |
| 36_S | 204_P | 1.170 | 0.97 |
| 71_A | 86_A | 1.168 | 0.97 |
| 155_G | 180_R | 1.167 | 0.97 |
| 38_H | 208_Y | 1.162 | 0.97 |
| 141_T | 167_N | 1.148 | 0.97 |
| 66_V | 216_M | 1.142 | 0.97 |
| 65_H | 69_T | 1.142 | 0.97 |
| 139_S | 142_S | 1.135 | 0.97 |
| 122_L | 149_A | 1.130 | 0.97 |
| 122_L | 147_V | 1.104 | 0.96 |
| 265_E | 269_R | 1.103 | 0.96 |
| 254_T | 257_Y | 1.089 | 0.96 |
| 91_V | 115_N | 1.077 | 0.95 |
| 171_V | 192_I | 1.076 | 0.95 |
| 62_H | 215_S | 1.073 | 0.95 |
| 243_H | 247_T | 1.071 | 0.95 |
| 83_A | 86_A | 1.068 | 0.95 |
| 12_Q | 15_A | 1.065 | 0.95 |
| 106_A | 136_A | 1.065 | 0.95 |
| 93_V | 108_G | 1.047 | 0.94 |
| 12_Q | 263_N | 1.041 | 0.94 |
| 146_L | 240_I | 1.032 | 0.94 |
| 216_M | 219_P | 1.028 | 0.94 |
| 228_V | 235_W | 1.025 | 0.93 |
| 149_A | 168_A | 1.024 | 0.93 |
| 192_I | 262_V | 1.023 | 0.93 |
| 171_V | 221_V | 1.023 | 0.93 |
| 31_L | 108_G | 1.016 | 0.93 |
| 30_V | 67_A | 1.009 | 0.93 |
| 109_L | 122_L | 1.008 | 0.93 |
| 186_Y | 256_L | 1.004 | 0.93 |
| 138_N | 165_Y | 1.003 | 0.93 |
| 120_A | 147_V | 1.003 | 0.93 |
| 44_R | 89_Y | 1.001 | 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 | |
| 1gciA | 1 | 1 | 100 | 0.015 | Contact Map |
| 3whiA | 2 | 1 | 100 | 0.031 | Contact Map |
| 1r0rE | 1 | 1 | 100 | 0.039 | Contact Map |
| 1to2E | 1 | 1 | 100 | 0.043 | Contact Map |
| 4j94A | 1 | 0.9963 | 100 | 0.076 | Contact Map |
| 1r6vA | 1 | 0.9963 | 100 | 0.081 | Contact Map |
| 4kg7A | 1 | 0.9926 | 100 | 0.084 | Contact Map |
| 1dbiA | 1 | 0.9591 | 100 | 0.087 | Contact Map |
| 4tr2A | 2 | 1 | 100 | 0.088 | Contact Map |
| 2x8jA | 5 | 0.9888 | 100 | 0.092 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)