| CC ParA |
| ID: | 1491029027 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 267 (257) | ||
| Sequences: | 15859 (8862.4) | ||
| Seq/Len: | 61.708 | ||
| Nf(neff/√len): | 552.8 |
HHblits Results: (2016_02)
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: 61.708).
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 |
| 24_A | 129_L | 4.568 | 1.00 |
| 87_D | 125_Y | 4.423 | 1.00 |
| 220_P | 247_A | 3.822 | 1.00 |
| 31_L | 127_Y | 3.247 | 1.00 |
| 10_A | 147_A | 3.228 | 1.00 |
| 36_E | 127_Y | 3.194 | 1.00 |
| 191_M | 221_R | 3.156 | 1.00 |
| 7_R | 149_A | 2.924 | 1.00 |
| 34_C | 253_R | 2.899 | 1.00 |
| 23_T | 248_Y | 2.895 | 1.00 |
| 39_L | 125_Y | 2.846 | 1.00 |
| 11_I | 27_L | 2.606 | 1.00 |
| 40_L | 49_C | 2.542 | 1.00 |
| 234_P | 237_L | 2.509 | 1.00 |
| 37_R | 126_T | 2.332 | 1.00 |
| 25_I | 49_C | 2.322 | 1.00 |
| 31_L | 129_L | 2.238 | 1.00 |
| 24_A | 40_L | 2.196 | 1.00 |
| 33_A | 249_L | 2.159 | 1.00 |
| 155_Q | 191_M | 2.067 | 1.00 |
| 28_G | 40_L | 2.046 | 1.00 |
| 8_V | 130_I | 2.001 | 1.00 |
| 23_T | 188_V | 2.000 | 1.00 |
| 188_V | 251_L | 1.952 | 1.00 |
| 204_K | 208_A | 1.947 | 1.00 |
| 28_G | 129_L | 1.911 | 1.00 |
| 30_A | 252_A | 1.907 | 1.00 |
| 11_I | 151_F | 1.857 | 1.00 |
| 25_I | 53_L | 1.831 | 1.00 |
| 52_G | 159_F | 1.829 | 1.00 |
| 189_L | 203_A | 1.713 | 1.00 |
| 43_A | 143_A | 1.708 | 1.00 |
| 30_A | 236_L | 1.697 | 1.00 |
| 219_I | 244_G | 1.681 | 1.00 |
| 217_A | 251_L | 1.680 | 1.00 |
| 224_R | 227_E | 1.676 | 1.00 |
| 25_I | 52_G | 1.661 | 1.00 |
| 21_T | 52_G | 1.637 | 1.00 |
| 149_A | 186_G | 1.612 | 1.00 |
| 75_V | 124_P | 1.610 | 1.00 |
| 36_E | 126_T | 1.600 | 1.00 |
| 28_G | 49_C | 1.599 | 1.00 |
| 43_A | 130_I | 1.583 | 1.00 |
| 217_A | 254_E | 1.561 | 1.00 |
| 39_L | 128_V | 1.549 | 1.00 |
| 10_A | 132_C | 1.504 | 1.00 |
| 36_E | 256_I | 1.501 | 1.00 |
| 32_A | 86_L | 1.491 | 1.00 |
| 27_L | 255_V | 1.474 | 1.00 |
| 51_T | 162_E | 1.470 | 1.00 |
| 27_L | 252_A | 1.459 | 1.00 |
| 192_Y | 218_V | 1.448 | 1.00 |
| 34_C | 249_L | 1.447 | 1.00 |
| 7_R | 148_D | 1.444 | 1.00 |
| 193_D | 221_R | 1.443 | 1.00 |
| 11_I | 24_A | 1.431 | 1.00 |
| 55_I | 88_V | 1.428 | 1.00 |
| 246_Q | 249_L | 1.404 | 0.99 |
| 149_A | 185_Q | 1.385 | 0.99 |
| 153_P | 190_T | 1.376 | 0.99 |
| 19_G | 190_T | 1.360 | 0.99 |
| 23_T | 190_T | 1.356 | 0.99 |
| 203_A | 207_R | 1.345 | 0.99 |
| 227_E | 231_F | 1.331 | 0.99 |
| 6_L | 128_V | 1.312 | 0.99 |
| 9_L | 127_Y | 1.310 | 0.99 |
| 32_A | 85_G | 1.300 | 0.99 |
| 150_V | 171_I | 1.281 | 0.99 |
| 205_D | 208_A | 1.279 | 0.99 |
| 11_I | 129_L | 1.271 | 0.99 |
| 110_Y | 113_R | 1.264 | 0.99 |
| 74_V | 89_I | 1.263 | 0.99 |
| 222_N | 244_G | 1.258 | 0.99 |
| 216_D | 254_E | 1.256 | 0.99 |
| 29_T | 33_A | 1.255 | 0.99 |
| 53_L | 86_L | 1.255 | 0.99 |
| 222_N | 242_C | 1.253 | 0.99 |
| 26_N | 29_T | 1.249 | 0.99 |
| 53_L | 88_V | 1.238 | 0.98 |
| 48_N | 159_F | 1.230 | 0.98 |
| 233_K | 238_Y | 1.226 | 0.98 |
| 242_C | 245_S | 1.215 | 0.98 |
| 253_R | 257_S | 1.208 | 0.98 |
| 34_C | 256_I | 1.206 | 0.98 |
| 31_L | 38_V | 1.195 | 0.98 |
| 156_C | 189_L | 1.182 | 0.98 |
| 30_A | 249_L | 1.170 | 0.97 |
| 22_T | 229_P | 1.157 | 0.97 |
| 250_K | 253_R | 1.154 | 0.97 |
| 165_T | 209_H | 1.154 | 0.97 |
| 63_T | 66_D | 1.153 | 0.97 |
| 233_K | 237_L | 1.148 | 0.97 |
| 67_V | 77_A | 1.147 | 0.97 |
| 23_T | 27_L | 1.146 | 0.97 |
| 80_K | 87_D | 1.146 | 0.97 |
| 249_L | 253_R | 1.145 | 0.97 |
| 151_F | 188_V | 1.144 | 0.97 |
| 73_P | 76_D | 1.142 | 0.97 |
| 169_R | 172_E | 1.141 | 0.97 |
| 30_A | 34_C | 1.138 | 0.97 |
| 77_A | 89_I | 1.138 | 0.97 |
| 33_A | 236_L | 1.138 | 0.97 |
| 204_K | 218_V | 1.130 | 0.97 |
| 247_A | 250_K | 1.110 | 0.96 |
| 156_C | 192_Y | 1.110 | 0.96 |
| 21_T | 49_C | 1.104 | 0.96 |
| 28_G | 86_L | 1.099 | 0.96 |
| 205_D | 209_H | 1.098 | 0.96 |
| 26_N | 236_L | 1.087 | 0.96 |
| 11_I | 23_T | 1.084 | 0.96 |
| 48_N | 163_G | 1.083 | 0.96 |
| 125_Y | 128_V | 1.081 | 0.95 |
| 39_L | 78_A | 1.079 | 0.95 |
| 225_V | 244_G | 1.078 | 0.95 |
| 127_Y | 256_I | 1.076 | 0.95 |
| 41_I | 128_V | 1.076 | 0.95 |
| 157_E | 160_A | 1.066 | 0.95 |
| 65_Y | 69_M | 1.057 | 0.95 |
| 30_A | 248_Y | 1.053 | 0.95 |
| 9_L | 149_A | 1.046 | 0.94 |
| 88_V | 93_A | 1.042 | 0.94 |
| 43_A | 64_L | 1.040 | 0.94 |
| 251_L | 255_V | 1.039 | 0.94 |
| 41_I | 130_I | 1.039 | 0.94 |
| 72_A | 76_D | 1.037 | 0.94 |
| 87_D | 123_G | 1.035 | 0.94 |
| 23_T | 153_P | 1.034 | 0.94 |
| 203_A | 218_V | 1.032 | 0.94 |
| 243_A | 246_Q | 1.030 | 0.94 |
| 206_V | 210_F | 1.028 | 0.94 |
| 15_K | 20_K | 1.024 | 0.93 |
| 31_L | 252_A | 1.021 | 0.93 |
| 108_R | 139_L | 1.018 | 0.93 |
| 22_T | 225_V | 1.007 | 0.93 |
| 81_T | 87_D | 1.006 | 0.93 |
| 223_V | 227_E | 1.003 | 0.93 |
| 129_L | 255_V | 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 | |
| 4pfsA | 2 | 0.9101 | 100 | 0.167 | Contact Map |
| 1wcv1 | 1 | 0.9101 | 100 | 0.198 | Contact Map |
| 4rz3A | 2 | 0.8876 | 100 | 0.221 | Contact Map |
| 1g3qA | 1 | 0.8839 | 100 | 0.221 | Contact Map |
| 3ea0A | 2 | 0.8839 | 100 | 0.229 | Contact Map |
| 1hyqA | 1 | 0.8652 | 100 | 0.23 | Contact Map |
| 3pg5A | 4 | 0.8577 | 100 | 0.239 | Contact Map |
| 3ez9A | 2 | 0.8315 | 100 | 0.241 | Contact Map |
| 3q9lA | 2 | 0.9363 | 100 | 0.245 | Contact Map |
| 2ynmA | 2 | 0.9101 | 100 | 0.247 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)