| 1okc |
| ID: | 1408344776 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 292 (288) | ||
| Sequences: | 7503 (5172.2) | ||
| Seq/Len: | 26.052 | ||
| Nf(neff/√len): | 304.8 |
HHblits Results: (2013_03)
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: 26.052).
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 |
| 260_A | 268_F | 4.020 | 1.00 |
| 163_F | 171_L | 3.727 | 1.00 |
| 60_P | 68_F | 3.203 | 1.00 |
| 254_D | 258_K | 3.141 | 1.00 |
| 57_V | 61_K | 2.937 | 1.00 |
| 160_T | 164_K | 2.904 | 1.00 |
| 157_N | 161_K | 2.870 | 1.00 |
| 54_D | 58_R | 2.807 | 1.00 |
| 257_R | 261_K | 2.779 | 1.00 |
| 162_I | 170_G | 2.771 | 1.00 |
| 259_I | 267_A | 2.610 | 1.00 |
| 235_R | 263_E | 2.597 | 1.00 |
| 256_W | 268_F | 2.583 | 1.00 |
| 153_T | 157_N | 2.388 | 1.00 |
| 232_V | 256_W | 2.368 | 1.00 |
| 263_E | 267_A | 2.267 | 1.00 |
| 33_L | 63_Q | 2.243 | 1.00 |
| 138_R | 166_D | 2.230 | 1.00 |
| 249_Y | 255_C | 2.224 | 1.00 |
| 258_K | 262_D | 2.207 | 1.00 |
| 93_Y | 124_T | 2.189 | 1.00 |
| 161_K | 165_S | 2.120 | 1.00 |
| 159_I | 171_L | 2.082 | 1.00 |
| 59_I | 67_S | 2.047 | 1.00 |
| 249_Y | 254_D | 1.999 | 1.00 |
| 251_G | 254_D | 1.971 | 1.00 |
| 119_G | 183_I | 1.959 | 1.00 |
| 56_V | 68_F | 1.947 | 1.00 |
| 28_E | 31_K | 1.914 | 1.00 |
| 166_D | 170_G | 1.904 | 1.00 |
| 49_Y | 55_C | 1.903 | 1.00 |
| 152_F | 158_C | 1.898 | 1.00 |
| 31_K | 35_Q | 1.842 | 1.00 |
| 260_A | 265_P | 1.822 | 1.00 |
| 93_Y | 120_A | 1.806 | 1.00 |
| 152_F | 157_N | 1.769 | 1.00 |
| 154_G | 157_N | 1.745 | 1.00 |
| 25_A | 29_R | 1.721 | 1.00 |
| 13_G | 17_A | 1.671 | 1.00 |
| 215_A | 223_G | 1.659 | 1.00 |
| 212_W | 215_A | 1.629 | 1.00 |
| 89_F | 93_Y | 1.626 | 1.00 |
| 250_T | 254_D | 1.620 | 1.00 |
| 58_R | 62_E | 1.618 | 1.00 |
| 30_V | 56_V | 1.613 | 1.00 |
| 224_L | 272_A | 1.582 | 1.00 |
| 115_L | 187_A | 1.575 | 1.00 |
| 50_K | 54_D | 1.565 | 1.00 |
| 219_T | 230_D | 1.555 | 1.00 |
| 263_E | 270_K | 1.543 | 1.00 |
| 220_A | 223_G | 1.541 | 1.00 |
| 227_Y | 275_N | 1.512 | 1.00 |
| 192_V | 221_V | 1.485 | 1.00 |
| 206_V | 210_V | 1.469 | 1.00 |
| 163_F | 168_L | 1.456 | 1.00 |
| 134_F | 138_R | 1.454 | 1.00 |
| 89_F | 124_T | 1.449 | 1.00 |
| 29_R | 33_L | 1.448 | 1.00 |
| 253_V | 257_R | 1.441 | 1.00 |
| 167_G | 170_G | 1.415 | 1.00 |
| 272_A | 276_V | 1.414 | 1.00 |
| 81_P | 84_A | 1.414 | 1.00 |
| 166_D | 173_Q | 1.410 | 1.00 |
| 284_F | 288_L | 1.402 | 0.99 |
| 135_A | 159_I | 1.380 | 0.99 |
| 72_N | 76_V | 1.380 | 0.99 |
| 90_K | 194_D | 1.368 | 0.99 |
| 25_A | 69_W | 1.343 | 0.99 |
| 286_L | 290_D | 1.334 | 0.99 |
| 188_A | 225_V | 1.322 | 0.99 |
| 233_R | 237_M | 1.310 | 0.99 |
| 281_G | 284_F | 1.295 | 0.99 |
| 193_Y | 290_D | 1.281 | 0.99 |
| 63_Q | 67_S | 1.274 | 0.99 |
| 93_Y | 117_S | 1.268 | 0.99 |
| 36_V | 141_A | 1.265 | 0.99 |
| 63_Q | 70_R | 1.262 | 0.99 |
| 59_I | 63_Q | 1.259 | 0.99 |
| 281_G | 285_V | 1.250 | 0.99 |
| 49_Y | 54_D | 1.249 | 0.99 |
| 227_Y | 231_T | 1.244 | 0.98 |
| 249_Y | 258_K | 1.241 | 0.98 |
| 175_F | 179_V | 1.241 | 0.98 |
| 230_D | 233_R | 1.232 | 0.98 |
| 36_V | 234_R | 1.226 | 0.98 |
| 82_T | 86_N | 1.223 | 0.98 |
| 168_L | 172_Y | 1.222 | 0.98 |
| 28_E | 136_R | 1.214 | 0.98 |
| 255_C | 258_K | 1.209 | 0.98 |
| 119_G | 187_A | 1.209 | 0.98 |
| 97_F | 117_S | 1.187 | 0.98 |
| 162_I | 166_D | 1.185 | 0.98 |
| 157_N | 160_T | 1.184 | 0.98 |
| 118_G | 187_A | 1.174 | 0.98 |
| 158_C | 162_I | 1.169 | 0.97 |
| 87_F | 190_F | 1.164 | 0.97 |
| 123_A | 179_V | 1.160 | 0.97 |
| 255_C | 259_I | 1.160 | 0.97 |
| 136_R | 140_A | 1.154 | 0.97 |
| 15_V | 19_I | 1.152 | 0.97 |
| 177_V | 252_T | 1.134 | 0.97 |
| 116_A | 120_A | 1.117 | 0.96 |
| 60_P | 65_F | 1.115 | 0.96 |
| 85_L | 89_F | 1.104 | 0.96 |
| 11_L | 14_G | 1.100 | 0.96 |
| 78_R | 82_T | 1.092 | 0.96 |
| 130_Y | 134_F | 1.089 | 0.96 |
| 135_A | 155_L | 1.083 | 0.96 |
| 216_Q | 280_M | 1.080 | 0.95 |
| 14_G | 80_F | 1.080 | 0.95 |
| 224_L | 276_V | 1.076 | 0.95 |
| 254_D | 257_R | 1.074 | 0.95 |
| 182_I | 185_Y | 1.063 | 0.95 |
| 133_D | 233_R | 1.058 | 0.95 |
| 91_D | 94_K | 1.057 | 0.95 |
| 54_D | 57_V | 1.052 | 0.95 |
| 26_P | 31_K | 1.051 | 0.94 |
| 265_P | 269_F | 1.048 | 0.94 |
| 9_D | 91_D | 1.047 | 0.94 |
| 188_A | 192_V | 1.046 | 0.94 |
| 182_I | 189_Y | 1.041 | 0.94 |
| 25_A | 72_N | 1.032 | 0.94 |
| 207_H | 211_S | 1.028 | 0.94 |
| 12_A | 16_A | 1.023 | 0.93 |
| 253_V | 256_W | 1.019 | 0.93 |
| 85_L | 128_F | 1.013 | 0.93 |
| 55_C | 59_I | 1.010 | 0.93 |
| 161_K | 164_K | 1.009 | 0.93 |
| 232_V | 255_C | 1.007 | 0.93 |
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 | |
| 1okcA | 1 | 1 | 100 | 0.112 | Contact Map |
| 4c9gA | 1 | 0.9007 | 100 | 0.153 | Contact Map |
| 2lckA | 1 | 0.9452 | 100 | 0.179 | Contact Map |
| 4jjfA | 2 | 0.3082 | 10 | 0.96 | Contact Map |
| 3fblA | 1 | 0.2808 | 6.4 | 0.964 | Contact Map |
| 2b2hA | 1 | 0.4315 | 3.8 | 0.967 | Contact Map |
| 2l5rA | 1 | 0.0788 | 3.4 | 0.968 | Contact Map |
| 4b19A | 1 | 0.1027 | 2.5 | 0.97 | Contact Map |
| 1wdpA | 1 | 0.2466 | 2.1 | 0.971 | Contact Map |
| 3vjjA | 2 | 0.3459 | 2 | 0.972 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)