| LckKD Jackhmmer test |
| ID: | 1396507057 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 265 (257) | ||
| Sequences: | 77515 (52554) | ||
| Seq/Len: | 301.615 | ||
| Nf(neff/√len): | 3278.2 |
Jackhmmer Results: (2014_03_19)
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: 301.615).
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 |
| 242_K | 247_D | 3.431 | 1.00 |
| 109_A | 194_L | 3.125 | 1.00 |
| 25_M | 33_K | 3.061 | 1.00 |
| 135_L | 145_A | 3.013 | 1.00 |
| 13_E | 25_M | 2.737 | 1.00 |
| 14_R | 22_E | 2.551 | 1.00 |
| 117_A | 252_D | 2.395 | 1.00 |
| 187_V | 240_C | 2.388 | 1.00 |
| 117_A | 121_E | 2.379 | 1.00 |
| 239_L | 249_P | 2.307 | 1.00 |
| 26_G | 34_V | 2.255 | 1.00 |
| 26_G | 36_V | 2.238 | 1.00 |
| 239_L | 257_V | 2.220 | 1.00 |
| 14_R | 17_A | 2.204 | 1.00 |
| 89_V | 132_A | 2.185 | 1.00 |
| 240_C | 254_L | 2.165 | 1.00 |
| 102_I | 230_P | 2.133 | 1.00 |
| 60_Q | 66_R | 2.123 | 1.00 |
| 61_H | 118_F | 2.046 | 1.00 |
| 113_A | 190_F | 2.038 | 1.00 |
| 111_Q | 142_C | 2.026 | 1.00 |
| 111_Q | 141_S | 2.002 | 1.00 |
| 116_M | 190_F | 1.983 | 1.00 |
| 130_R | 167_P | 1.969 | 1.00 |
| 112_I | 134_I | 1.953 | 1.00 |
| 10_K | 27_Y | 1.941 | 1.00 |
| 81_E | 143_K | 1.940 | 1.00 |
| 134_I | 142_C | 1.921 | 1.00 |
| 25_M | 82_Y | 1.917 | 1.00 |
| 137_S | 141_S | 1.904 | 1.00 |
| 191_G | 240_C | 1.888 | 1.00 |
| 84_E | 138_D | 1.853 | 1.00 |
| 244_R | 247_D | 1.814 | 1.00 |
| 68_Y | 81_E | 1.804 | 1.00 |
| 12_V | 27_Y | 1.799 | 1.00 |
| 101_T | 104_K | 1.763 | 1.00 |
| 172_A | 185_S | 1.747 | 1.00 |
| 27_Y | 33_K | 1.741 | 1.00 |
| 137_S | 143_K | 1.737 | 1.00 |
| 87_S | 90_D | 1.719 | 1.00 |
| 8_T | 28_Y | 1.675 | 1.00 |
| 10_K | 29_N | 1.616 | 1.00 |
| 129_L | 193_L | 1.591 | 1.00 |
| 166_F | 171_T | 1.589 | 1.00 |
| 66_R | 81_E | 1.576 | 1.00 |
| 187_V | 251_F | 1.561 | 1.00 |
| 116_M | 251_F | 1.542 | 1.00 |
| 14_R | 24_W | 1.535 | 1.00 |
| 27_Y | 31_H | 1.523 | 1.00 |
| 105_L | 198_V | 1.519 | 1.00 |
| 63_R | 115_G | 1.493 | 1.00 |
| 36_V | 79_I | 1.489 | 1.00 |
| 110_A | 259_E | 1.479 | 1.00 |
| 250_T | 253_Y | 1.478 | 1.00 |
| 114_E | 255_R | 1.457 | 1.00 |
| 109_A | 190_F | 1.456 | 1.00 |
| 113_A | 254_L | 1.450 | 1.00 |
| 89_V | 93_K | 1.447 | 1.00 |
| 170_W | 196_E | 1.441 | 1.00 |
| 109_A | 197_I | 1.440 | 1.00 |
| 115_G | 144_I | 1.436 | 1.00 |
| 121_E | 252_D | 1.434 | 1.00 |
| 116_M | 129_L | 1.416 | 1.00 |
| 107_D | 111_Q | 1.415 | 1.00 |
| 110_A | 114_E | 1.409 | 1.00 |
| 32_T | 68_Y | 1.398 | 0.99 |
| 249_P | 257_V | 1.397 | 0.99 |
| 12_V | 25_M | 1.389 | 0.99 |
| 17_A | 22_E | 1.389 | 0.99 |
| 198_V | 233_L | 1.385 | 0.99 |
| 117_A | 255_R | 1.382 | 0.99 |
| 124_Y | 150_A | 1.379 | 0.99 |
| 134_I | 193_L | 1.377 | 0.99 |
| 105_L | 197_I | 1.349 | 0.99 |
| 108_M | 142_C | 1.346 | 0.99 |
| 83_M | 137_S | 1.329 | 0.99 |
| 123_N | 183_I | 1.319 | 0.99 |
| 63_R | 114_E | 1.310 | 0.99 |
| 234_Y | 238_R | 1.303 | 0.99 |
| 86_G | 94_T | 1.288 | 0.99 |
| 131_A | 193_L | 1.280 | 0.99 |
| 38_S | 77_Y | 1.274 | 0.99 |
| 83_M | 143_K | 1.267 | 0.99 |
| 38_S | 75_P | 1.263 | 0.99 |
| 120_E | 251_F | 1.258 | 0.99 |
| 249_P | 254_L | 1.256 | 0.99 |
| 194_L | 236_L | 1.254 | 0.99 |
| 34_V | 79_I | 1.254 | 0.99 |
| 131_A | 170_W | 1.246 | 0.98 |
| 23_V | 35_A | 1.240 | 0.98 |
| 89_V | 196_E | 1.228 | 0.98 |
| 118_F | 122_R | 1.221 | 0.98 |
| 237_M | 241_W | 1.213 | 0.98 |
| 113_A | 255_R | 1.207 | 0.98 |
| 236_L | 249_P | 1.201 | 0.98 |
| 131_A | 196_E | 1.172 | 0.98 |
| 113_A | 251_F | 1.169 | 0.97 |
| 251_F | 254_L | 1.163 | 0.97 |
| 58_Q | 152_L | 1.156 | 0.97 |
| 33_K | 82_Y | 1.139 | 0.97 |
| 236_L | 257_V | 1.136 | 0.97 |
| 114_E | 259_E | 1.130 | 0.97 |
| 36_V | 77_Y | 1.121 | 0.97 |
| 110_A | 255_R | 1.118 | 0.96 |
| 196_E | 203_I | 1.117 | 0.96 |
| 128_D | 133_N | 1.117 | 0.96 |
| 92_L | 196_E | 1.116 | 0.96 |
| 55_L | 150_A | 1.116 | 0.96 |
| 236_L | 254_L | 1.097 | 0.96 |
| 184_K | 250_T | 1.096 | 0.96 |
| 136_V | 142_C | 1.096 | 0.96 |
| 223_M | 226_P | 1.094 | 0.96 |
| 215_Q | 219_R | 1.093 | 0.96 |
| 112_I | 142_C | 1.092 | 0.96 |
| 24_W | 38_S | 1.091 | 0.96 |
| 172_A | 175_A | 1.090 | 0.96 |
| 11_L | 24_W | 1.085 | 0.96 |
| 239_L | 242_K | 1.074 | 0.95 |
| 216_N | 220_G | 1.070 | 0.95 |
| 192_I | 241_W | 1.064 | 0.95 |
| 58_Q | 122_R | 1.060 | 0.95 |
| 28_Y | 32_T | 1.053 | 0.95 |
| 35_A | 82_Y | 1.052 | 0.95 |
| 67_L | 70_V | 1.049 | 0.94 |
| 34_V | 68_Y | 1.047 | 0.94 |
| 12_V | 33_K | 1.040 | 0.94 |
| 235_Q | 239_L | 1.032 | 0.94 |
| 71_V | 77_Y | 1.029 | 0.94 |
| 65_V | 80_T | 1.028 | 0.94 |
| 236_L | 240_C | 1.026 | 0.94 |
| 91_F | 100_L | 1.023 | 0.93 |
| 127_R | 181_F | 1.021 | 0.93 |
| 175_A | 185_S | 1.019 | 0.93 |
| 190_F | 240_C | 1.018 | 0.93 |
| 83_M | 135_L | 1.017 | 0.93 |
| 126_H | 129_L | 1.016 | 0.93 |
| 242_K | 249_P | 1.008 | 0.93 |
| 65_V | 83_M | 1.006 | 0.93 |
| 91_F | 136_V | 1.003 | 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 | |
| 2h8hA | 1 | 1 | 100 | 0.012 | Contact Map |
| 1fmkA | 1 | 0.9472 | 100 | 0.012 | Contact Map |
| 1qcfA | 1 | 1 | 100 | 0.015 | Contact Map |
| 1opkA | 1 | 1 | 100 | 0.023 | Contact Map |
| 2psqA | 2 | 1 | 100 | 0.049 | Contact Map |
| 2ozoA | 1 | 0.9509 | 100 | 0.049 | Contact Map |
| 1k9aA | 6 | 0.966 | 100 | 0.051 | Contact Map |
| 4fl3A | 1 | 0.9509 | 100 | 0.052 | Contact Map |
| 2j0jA | 1 | 0.9585 | 100 | 0.053 | Contact Map |
| 3cblA | 1 | 0.9962 | 100 | 0.054 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)