| mix1 -force run |
| ID: | 1501096432 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 264 (199) | ||
| Sequences: | 54751 (39843.8) | ||
| Seq/Len: | 275.131 | ||
| Nf(neff/√len): | 2824.5 |
Jackhmmer Results: (2016_04)
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: 275.131).
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 |
| 106_F | 122_A | 4.332 | 1.00 |
| 182_V | 234_C | 3.952 | 1.00 |
| 115_V | 157_T | 3.762 | 1.00 |
| 109_L | 238_V | 3.517 | 1.00 |
| 123_S | 154_T | 2.840 | 1.00 |
| 213_T | 218_M | 2.707 | 1.00 |
| 112_H | 115_V | 2.652 | 1.00 |
| 121_H | 228_C | 2.635 | 1.00 |
| 234_C | 237_K | 2.609 | 1.00 |
| 115_V | 155_I | 2.452 | 1.00 |
| 223_T | 242_H | 2.204 | 1.00 |
| 96_I | 185_V | 2.092 | 1.00 |
| 177_E | 180_D | 2.053 | 1.00 |
| 108_M | 116_A | 2.035 | 1.00 |
| 114_N | 157_T | 1.905 | 1.00 |
| 234_C | 239_I | 1.899 | 1.00 |
| 97_V | 108_M | 1.882 | 1.00 |
| 120_T | 145_D | 1.878 | 1.00 |
| 93_K | 185_V | 1.839 | 1.00 |
| 185_V | 233_T | 1.783 | 1.00 |
| 184_I | 223_T | 1.753 | 1.00 |
| 90_A | 177_E | 1.710 | 1.00 |
| 182_V | 232_I | 1.702 | 1.00 |
| 121_H | 152_E | 1.681 | 1.00 |
| 97_V | 116_A | 1.674 | 1.00 |
| 131_D | 134_E | 1.664 | 1.00 |
| 109_L | 241_M | 1.656 | 1.00 |
| 100_T | 131_D | 1.628 | 1.00 |
| 109_L | 117_V | 1.565 | 1.00 |
| 109_L | 231_I | 1.530 | 1.00 |
| 117_V | 238_V | 1.507 | 1.00 |
| 114_N | 161_S | 1.504 | 1.00 |
| 136_E | 157_T | 1.478 | 1.00 |
| 188_S | 227_Q | 1.427 | 1.00 |
| 96_I | 107_T | 1.404 | 0.99 |
| 82_G | 85_F | 1.394 | 0.99 |
| 164_F | 170_H | 1.382 | 0.99 |
| 170_H | 173_T | 1.381 | 0.99 |
| 141_K | 159_K | 1.364 | 0.99 |
| 158_L | 162_E | 1.354 | 0.99 |
| 119_P | 122_A | 1.343 | 0.99 |
| 181_G | 197_V | 1.338 | 0.99 |
| 213_T | 216_T | 1.324 | 0.99 |
| 169_P | 237_K | 1.321 | 0.99 |
| 41_G | 44_G | 1.274 | 0.99 |
| 95_N | 233_T | 1.264 | 0.99 |
| 205_Y | 208_L | 1.260 | 0.99 |
| 214_A | 218_M | 1.255 | 0.99 |
| 213_T | 217_L | 1.252 | 0.99 |
| 118_L | 123_S | 1.252 | 0.99 |
| 111_V | 117_V | 1.243 | 0.98 |
| 113_D | 161_S | 1.241 | 0.98 |
| 192_N | 195_V | 1.240 | 0.98 |
| 153_I | 241_M | 1.222 | 0.98 |
| 110_G | 164_F | 1.220 | 0.98 |
| 182_V | 199_A | 1.218 | 0.98 |
| 242_H | 245_G | 1.215 | 0.98 |
| 123_S | 140_A | 1.208 | 0.98 |
| 173_T | 176_T | 1.208 | 0.98 |
| 143_L | 151_L | 1.202 | 0.98 |
| 42_T | 45_C | 1.195 | 0.98 |
| 140_A | 143_L | 1.191 | 0.98 |
| 116_A | 158_L | 1.190 | 0.98 |
| 219_Y | 242_H | 1.166 | 0.97 |
| 96_I | 231_I | 1.166 | 0.97 |
| 110_G | 162_E | 1.163 | 0.97 |
| 189_K | 225_A | 1.162 | 0.97 |
| 248_S | 251_F | 1.155 | 0.97 |
| 182_V | 239_I | 1.152 | 0.97 |
| 132_G | 162_E | 1.149 | 0.97 |
| 231_I | 238_V | 1.143 | 0.97 |
| 44_G | 47_G | 1.135 | 0.97 |
| 186_N | 227_Q | 1.122 | 0.97 |
| 184_I | 242_H | 1.115 | 0.96 |
| 181_G | 198_G | 1.084 | 0.96 |
| 97_V | 132_G | 1.084 | 0.96 |
| 140_A | 156_V | 1.083 | 0.96 |
| 230_G | 242_H | 1.082 | 0.96 |
| 172_P | 237_K | 1.074 | 0.95 |
| 119_P | 241_M | 1.066 | 0.95 |
| 172_P | 175_I | 1.059 | 0.95 |
| 181_G | 235_T | 1.058 | 0.95 |
| 201_T | 204_G | 1.056 | 0.95 |
| 135_V | 141_K | 1.054 | 0.95 |
| 107_T | 230_G | 1.052 | 0.95 |
| 202_E | 206_L | 1.051 | 0.94 |
| 89_V | 92_A | 1.051 | 0.94 |
| 119_P | 243_V | 1.049 | 0.94 |
| 123_S | 156_V | 1.045 | 0.94 |
| 128_I | 131_D | 1.043 | 0.94 |
| 118_L | 154_T | 1.042 | 0.94 |
| 180_D | 234_C | 1.034 | 0.94 |
| 137_V | 157_T | 1.026 | 0.94 |
| 110_G | 116_A | 1.023 | 0.93 |
| 216_T | 219_Y | 1.018 | 0.93 |
| 204_G | 207_N | 1.017 | 0.93 |
| 93_K | 194_Y | 1.013 | 0.93 |
| 140_A | 144_E | 1.006 | 0.93 |
| 98_T | 105_E | 1.003 | 0.93 |
| 139_D | 157_T | 1.001 | 0.92 |
| 141_K | 157_T | 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 | |
| 3stiA | 3 | 0.6705 | 100 | 0.464 | Contact Map |
| 1ky9A | 2 | 0.6667 | 100 | 0.467 | Contact Map |
| 3stjA | 12 | 0.6856 | 100 | 0.47 | Contact Map |
| 1lcyA | 1 | 0.6894 | 100 | 0.475 | Contact Map |
| 1l1jA | 2 | 0.6932 | 100 | 0.482 | Contact Map |
| 4ri0A | 3 | 0.6894 | 100 | 0.483 | Contact Map |
| 3tjoA | 3 | 0.678 | 100 | 0.485 | Contact Map |
| 4ic6A | 3 | 0.7273 | 100 | 0.485 | Contact Map |
| 3numA | 1 | 0.6515 | 100 | 0.485 | Contact Map |
| 3lgiA | 3 | 0.7386 | 100 | 0.485 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)