| PstC |
| ID: | 1441106970 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 317 (297) | ||
| Sequences: | 4958 (2830.4) | ||
| Seq/Len: | 16.694 | ||
| Nf(neff/√len): | 164.2 |
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: 16.694).
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 |
| 207_S | 217_T | 5.595 | 1.00 |
| 91_L | 177_S | 4.693 | 1.00 |
| 109_E | 204_R | 4.385 | 1.00 |
| 46_L | 50_S | 3.864 | 1.00 |
| 121_T | 193_R | 3.308 | 1.00 |
| 97_I | 234_I | 3.103 | 1.00 |
| 61_L | 65_T | 2.744 | 1.00 |
| 213_T | 216_E | 2.729 | 1.00 |
| 95_L | 181_A | 2.464 | 1.00 |
| 215_W | 219_F | 2.281 | 1.00 |
| 196_L | 222_L | 2.191 | 1.00 |
| 89_S | 238_L | 2.169 | 1.00 |
| 174_L | 263_L | 2.135 | 1.00 |
| 104_A | 192_A | 2.050 | 1.00 |
| 35_V | 39_L | 2.049 | 1.00 |
| 88_N | 268_T | 2.031 | 1.00 |
| 144_I | 175_P | 2.027 | 1.00 |
| 199_L | 222_L | 2.002 | 1.00 |
| 272_L | 291_A | 1.974 | 1.00 |
| 105_L | 223_I | 1.967 | 1.00 |
| 269_I | 291_A | 1.955 | 1.00 |
| 207_S | 212_A | 1.931 | 1.00 |
| 195_S | 229_G | 1.911 | 1.00 |
| 62_G | 66_N | 1.865 | 1.00 |
| 201_P | 205_Q | 1.850 | 1.00 |
| 273_L | 292_G | 1.838 | 1.00 |
| 111_F | 214_R | 1.811 | 1.00 |
| 304_I | 308_L | 1.808 | 1.00 |
| 93_L | 238_L | 1.777 | 1.00 |
| 18_L | 22_L | 1.774 | 1.00 |
| 207_S | 221_V | 1.774 | 1.00 |
| 96_A | 184_I | 1.718 | 1.00 |
| 91_L | 95_L | 1.690 | 1.00 |
| 63_F | 78_I | 1.684 | 1.00 |
| 172_G | 175_P | 1.645 | 1.00 |
| 115_K | 118_T | 1.640 | 1.00 |
| 106_F | 112_I | 1.632 | 1.00 |
| 27_K | 31_L | 1.625 | 1.00 |
| 101_I | 230_I | 1.619 | 1.00 |
| 31_L | 35_V | 1.613 | 1.00 |
| 177_S | 181_A | 1.600 | 1.00 |
| 96_A | 188_I | 1.591 | 1.00 |
| 176_A | 248_V | 1.581 | 1.00 |
| 125_E | 190_A | 1.580 | 1.00 |
| 212_A | 216_E | 1.569 | 1.00 |
| 78_I | 82_M | 1.563 | 1.00 |
| 100_G | 185_L | 1.558 | 1.00 |
| 101_I | 192_A | 1.557 | 1.00 |
| 90_G | 94_L | 1.554 | 1.00 |
| 276_Q | 284_Q | 1.554 | 1.00 |
| 191_I | 233_G | 1.548 | 1.00 |
| 111_F | 218_I | 1.547 | 1.00 |
| 130_I | 135_Y | 1.543 | 1.00 |
| 108_S | 197_A | 1.541 | 1.00 |
| 204_R | 222_L | 1.537 | 1.00 |
| 192_A | 196_L | 1.520 | 1.00 |
| 193_R | 197_A | 1.504 | 1.00 |
| 78_I | 294_V | 1.493 | 1.00 |
| 100_G | 192_A | 1.476 | 1.00 |
| 79_L | 258_L | 1.458 | 1.00 |
| 28_Y | 31_L | 1.451 | 1.00 |
| 192_A | 230_I | 1.436 | 1.00 |
| 42_L | 46_L | 1.428 | 1.00 |
| 100_G | 237_A | 1.428 | 1.00 |
| 49_L | 293_F | 1.417 | 1.00 |
| 103_T | 189_T | 1.411 | 1.00 |
| 208_L | 214_R | 1.402 | 0.99 |
| 29_L | 33_F | 1.400 | 0.99 |
| 117_R | 197_A | 1.393 | 0.99 |
| 105_L | 218_I | 1.385 | 0.99 |
| 223_I | 230_I | 1.383 | 0.99 |
| 206_A | 209_G | 1.383 | 0.99 |
| 188_I | 237_A | 1.365 | 0.99 |
| 216_E | 220_R | 1.360 | 0.99 |
| 305_L | 308_L | 1.357 | 0.99 |
| 78_I | 291_A | 1.355 | 0.99 |
| 171_P | 175_P | 1.354 | 0.99 |
| 301_I | 305_L | 1.338 | 0.99 |
| 108_S | 196_L | 1.336 | 0.99 |
| 56_I | 290_Y | 1.328 | 0.99 |
| 28_Y | 32_A | 1.308 | 0.99 |
| 100_G | 188_I | 1.298 | 0.99 |
| 226_A | 229_G | 1.297 | 0.99 |
| 260_W | 264_N | 1.293 | 0.99 |
| 158_F | 161_I | 1.292 | 0.99 |
| 188_I | 192_A | 1.292 | 0.99 |
| 176_A | 252_I | 1.277 | 0.99 |
| 83_V | 87_V | 1.272 | 0.99 |
| 196_L | 226_A | 1.268 | 0.99 |
| 133_V | 250_M | 1.253 | 0.99 |
| 116_I | 120_L | 1.252 | 0.99 |
| 108_S | 193_R | 1.243 | 0.98 |
| 23_E | 26_F | 1.241 | 0.98 |
| 207_S | 220_R | 1.219 | 0.98 |
| 85_T | 270_A | 1.213 | 0.98 |
| 94_L | 98_P | 1.210 | 0.98 |
| 252_I | 266_A | 1.206 | 0.98 |
| 98_P | 102_G | 1.195 | 0.98 |
| 93_L | 97_I | 1.195 | 0.98 |
| 104_A | 108_S | 1.183 | 0.98 |
| 139_G | 179_V | 1.171 | 0.98 |
| 114_S | 117_R | 1.168 | 0.97 |
| 20_K | 24_K | 1.164 | 0.97 |
| 140_I | 171_P | 1.163 | 0.97 |
| 127_L | 135_Y | 1.160 | 0.97 |
| 272_L | 276_Q | 1.160 | 0.97 |
| 100_G | 189_T | 1.159 | 0.97 |
| 23_E | 27_K | 1.157 | 0.97 |
| 201_P | 204_R | 1.153 | 0.97 |
| 192_A | 233_G | 1.147 | 0.97 |
| 55_A | 290_Y | 1.146 | 0.97 |
| 239_G | 302_V | 1.146 | 0.97 |
| 67_N | 79_L | 1.144 | 0.97 |
| 212_A | 217_T | 1.140 | 0.97 |
| 192_A | 226_A | 1.135 | 0.97 |
| 87_V | 173_M | 1.135 | 0.97 |
| 95_L | 99_L | 1.132 | 0.97 |
| 154_L | 157_Y | 1.121 | 0.97 |
| 113_P | 116_I | 1.111 | 0.96 |
| 249_T | 271_S | 1.104 | 0.96 |
| 57_K | 61_L | 1.103 | 0.96 |
| 93_L | 234_I | 1.098 | 0.96 |
| 61_L | 64_I | 1.091 | 0.96 |
| 185_L | 189_T | 1.085 | 0.96 |
| 140_I | 145_P | 1.081 | 0.95 |
| 21_N | 24_K | 1.077 | 0.95 |
| 96_A | 181_A | 1.076 | 0.95 |
| 159_G | 162_P | 1.073 | 0.95 |
| 268_T | 271_S | 1.072 | 0.95 |
| 24_K | 27_K | 1.064 | 0.95 |
| 24_K | 28_Y | 1.061 | 0.95 |
| 86_L | 90_G | 1.061 | 0.95 |
| 308_L | 312_K | 1.053 | 0.95 |
| 95_L | 177_S | 1.048 | 0.94 |
| 300_F | 303_N | 1.039 | 0.94 |
| 267_N | 272_L | 1.038 | 0.94 |
| 26_F | 29_L | 1.029 | 0.94 |
| 199_L | 225_A | 1.029 | 0.94 |
| 32_A | 39_L | 1.024 | 0.93 |
| 312_K | 315_A | 1.020 | 0.93 |
| 156_E | 161_I | 1.016 | 0.93 |
| 271_S | 288_L | 1.010 | 0.93 |
| 124_V | 189_T | 1.008 | 0.93 |
| 92_A | 177_S | 1.006 | 0.93 |
| 22_L | 25_G | 1.003 | 0.93 |
| 101_I | 188_I | 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 | |
| 2onkC | 4 | 0.795 | 100 | 0.456 | Contact Map |
| 4tquM | 1 | 0 | 100 | 0.467 | Contact Map |
| 3d31C | 2 | 0.7823 | 100 | 0.469 | Contact Map |
| 3rlfF | 1 | 0.9306 | 100 | 0.512 | Contact Map |
| 3rlfG | 1 | 0.836 | 100 | 0.537 | Contact Map |
| 4tquN | 1 | 0 | 100 | 0.54 | Contact Map |
| 4ymuD | 2 | 0 | 100 | 0.596 | Contact Map |
| 3tuiA | 4 | 0.6625 | 99.9 | 0.609 | Contact Map |
| 2mfrA | 1 | 0.1514 | 7.3 | 0.963 | Contact Map |
| 2k1eA | 4 | 0.2713 | 4.9 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)