| fullsyx |
| ID: | 1498536626 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 288 (282) | ||
| Sequences: | 3482 (2405.6) | ||
| Seq/Len: | 12.348 | ||
| Nf(neff/√len): | 143.3 |
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: 12.348).
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 |
| 50_N | 82_I | 2.761 | 1.00 |
| 276_G | 280_A | 2.628 | 1.00 |
| 54_V | 75_L | 2.460 | 1.00 |
| 184_D | 187_I | 2.091 | 1.00 |
| 278_I | 282_T | 2.000 | 1.00 |
| 177_F | 181_I | 1.993 | 1.00 |
| 274_I | 278_I | 1.863 | 1.00 |
| 178_A | 181_I | 1.791 | 1.00 |
| 270_I | 274_I | 1.774 | 1.00 |
| 244_V | 247_A | 1.751 | 1.00 |
| 41_R | 126_K | 1.742 | 1.00 |
| 260_K | 264_K | 1.719 | 1.00 |
| 271_C | 275_L | 1.709 | 1.00 |
| 176_I | 180_G | 1.681 | 1.00 |
| 272_C | 276_G | 1.667 | 1.00 |
| 277_I | 280_A | 1.659 | 1.00 |
| 273_V | 277_I | 1.658 | 1.00 |
| 180_G | 184_D | 1.626 | 1.00 |
| 97_E | 124_S | 1.601 | 1.00 |
| 261_A | 265_K | 1.601 | 1.00 |
| 188_S | 192_L | 1.597 | 1.00 |
| 166_E | 170_E | 1.570 | 1.00 |
| 277_I | 281_S | 1.537 | 1.00 |
| 263_R | 267_M | 1.527 | 1.00 |
| 246_R | 249_S | 1.506 | 1.00 |
| 261_A | 264_K | 1.500 | 1.00 |
| 75_L | 79_M | 1.497 | 1.00 |
| 17_D | 20_V | 1.477 | 1.00 |
| 44_I | 130_V | 1.459 | 1.00 |
| 279_I | 282_T | 1.431 | 1.00 |
| 48_A | 133_E | 1.430 | 1.00 |
| 43_F | 89_V | 1.429 | 1.00 |
| 165_L | 168_M | 1.425 | 1.00 |
| 86_A | 131_M | 1.420 | 1.00 |
| 5_T | 8_L | 1.402 | 0.99 |
| 138_Q | 208_S | 1.399 | 0.99 |
| 240_A | 243_Y | 1.391 | 0.99 |
| 163_E | 167_D | 1.383 | 0.99 |
| 246_R | 250_D | 1.382 | 0.99 |
| 214_D | 218_D | 1.379 | 0.99 |
| 15_D | 18_D | 1.357 | 0.99 |
| 36_Q | 92_K | 1.356 | 0.99 |
| 54_V | 82_I | 1.352 | 0.99 |
| 254_A | 258_Q | 1.346 | 0.99 |
| 139_S | 143_E | 1.346 | 0.99 |
| 176_I | 179_S | 1.342 | 0.99 |
| 275_L | 279_I | 1.337 | 0.99 |
| 216_F | 222_L | 1.330 | 0.99 |
| 176_I | 181_I | 1.318 | 0.99 |
| 171_S | 174_P | 1.314 | 0.99 |
| 200_S | 203_I | 1.313 | 0.99 |
| 55_K | 59_S | 1.311 | 0.99 |
| 15_D | 19_D | 1.311 | 0.99 |
| 70_K | 73_E | 1.304 | 0.99 |
| 264_K | 268_I | 1.299 | 0.99 |
| 267_M | 271_C | 1.294 | 0.99 |
| 43_F | 85_T | 1.282 | 0.99 |
| 266_I | 270_I | 1.268 | 0.99 |
| 249_S | 253_K | 1.267 | 0.99 |
| 167_D | 170_E | 1.265 | 0.99 |
| 47_I | 89_V | 1.264 | 0.99 |
| 66_N | 72_K | 1.264 | 0.99 |
| 191_A | 195_I | 1.263 | 0.99 |
| 175_A | 178_A | 1.257 | 0.99 |
| 16_D | 19_D | 1.255 | 0.99 |
| 32_E | 35_E | 1.254 | 0.99 |
| 150_Q | 154_E | 1.247 | 0.99 |
| 100_I | 116_R | 1.242 | 0.98 |
| 231_D | 235_Y | 1.239 | 0.98 |
| 168_M | 172_G | 1.238 | 0.98 |
| 279_I | 283_I | 1.218 | 0.98 |
| 131_M | 135_N | 1.218 | 0.98 |
| 178_A | 182_I | 1.215 | 0.98 |
| 7_E | 10_T | 1.213 | 0.98 |
| 268_I | 272_C | 1.209 | 0.98 |
| 154_E | 158_R | 1.205 | 0.98 |
| 6_Q | 9_R | 1.199 | 0.98 |
| 4_R | 7_E | 1.187 | 0.98 |
| 89_V | 127_F | 1.184 | 0.98 |
| 50_N | 85_T | 1.183 | 0.98 |
| 250_D | 257_Y | 1.177 | 0.98 |
| 165_L | 169_L | 1.171 | 0.98 |
| 16_D | 20_V | 1.171 | 0.98 |
| 37_V | 123_L | 1.159 | 0.97 |
| 161_T | 164_E | 1.145 | 0.97 |
| 33_F | 212_L | 1.144 | 0.97 |
| 132_S | 136_A | 1.135 | 0.97 |
| 6_Q | 10_T | 1.135 | 0.97 |
| 193_S | 197_T | 1.132 | 0.97 |
| 198_R | 216_F | 1.123 | 0.97 |
| 204_K | 208_S | 1.121 | 0.97 |
| 133_E | 136_A | 1.121 | 0.97 |
| 220_A | 224_E | 1.120 | 0.96 |
| 154_E | 157_G | 1.120 | 0.96 |
| 52_E | 133_E | 1.113 | 0.96 |
| 181_I | 185_S | 1.108 | 0.96 |
| 11_A | 14_S | 1.106 | 0.96 |
| 195_I | 202_I | 1.102 | 0.96 |
| 45_D | 48_A | 1.102 | 0.96 |
| 6_Q | 12_K | 1.101 | 0.96 |
| 229_M | 232_R | 1.098 | 0.96 |
| 227_G | 230_I | 1.095 | 0.96 |
| 39_E | 42_G | 1.095 | 0.96 |
| 119_Q | 123_L | 1.087 | 0.96 |
| 253_K | 257_Y | 1.087 | 0.96 |
| 218_D | 222_L | 1.080 | 0.95 |
| 175_A | 180_G | 1.077 | 0.95 |
| 269_I | 273_V | 1.077 | 0.95 |
| 255_V | 258_Q | 1.075 | 0.95 |
| 152_Q | 155_I | 1.075 | 0.95 |
| 144_R | 147_G | 1.074 | 0.95 |
| 130_V | 133_E | 1.072 | 0.95 |
| 124_S | 128_V | 1.068 | 0.95 |
| 21_T | 26_R | 1.066 | 0.95 |
| 218_D | 240_A | 1.062 | 0.95 |
| 9_R | 13_D | 1.062 | 0.95 |
| 90_R | 94_K | 1.060 | 0.95 |
| 163_E | 166_E | 1.055 | 0.95 |
| 22_V | 25_D | 1.055 | 0.95 |
| 183_M | 186_S | 1.054 | 0.95 |
| 21_T | 24_V | 1.054 | 0.95 |
| 19_D | 24_V | 1.053 | 0.95 |
| 257_Y | 260_K | 1.053 | 0.95 |
| 218_D | 221_M | 1.049 | 0.94 |
| 95_S | 98_Q | 1.044 | 0.94 |
| 48_A | 130_V | 1.043 | 0.94 |
| 232_R | 235_Y | 1.037 | 0.94 |
| 7_E | 11_A | 1.036 | 0.94 |
| 93_L | 124_S | 1.032 | 0.94 |
| 122_T | 126_K | 1.031 | 0.94 |
| 185_S | 189_K | 1.030 | 0.94 |
| 193_S | 196_E | 1.030 | 0.94 |
| 47_I | 50_N | 1.028 | 0.94 |
| 6_Q | 15_D | 1.027 | 0.94 |
| 58_H | 141_Y | 1.027 | 0.94 |
| 177_F | 180_G | 1.024 | 0.93 |
| 253_K | 256_K | 1.024 | 0.93 |
| 50_N | 78_L | 1.021 | 0.93 |
| 221_M | 224_E | 1.018 | 0.93 |
| 6_Q | 14_S | 1.017 | 0.93 |
| 237_V | 240_A | 1.015 | 0.93 |
| 227_G | 231_D | 1.012 | 0.93 |
| 86_A | 93_L | 1.011 | 0.93 |
| 8_L | 12_K | 1.008 | 0.93 |
| 249_S | 252_K | 1.006 | 0.93 |
| 169_L | 172_G | 1.005 | 0.93 |
| 213_H | 217_M | 1.005 | 0.93 |
| 15_D | 23_T | 1.003 | 0.93 |
| 131_M | 195_I | 1.002 | 0.92 |
| 178_A | 185_S | 1.000 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3c98B | 1 | 0.7986 | 100 | 0.25 | Contact Map |
| 4jehB | 1 | 0.7674 | 100 | 0.316 | Contact Map |
| 2xheB | 1 | 0.7396 | 100 | 0.341 | Contact Map |
| 1fioA | 1 | 0.6493 | 99.9 | 0.538 | Contact Map |
| 2m8rA | 1 | 0.3785 | 99.9 | 0.546 | Contact Map |
| 1s94A | 2 | 0.4167 | 99.8 | 0.63 | Contact Map |
| 1jthB | 2 | 0.2326 | 99.8 | 0.636 | Contact Map |
| 1sfcB | 3 | 0.2639 | 99.7 | 0.663 | Contact Map |
| 2npsB | 1 | 0.2361 | 99.6 | 0.67 | Contact Map |
| 3b5nB | 3 | 0.2396 | 99.6 | 0.683 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)