| 1CZFA |
| ID: | 1411606772 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 335 (325) | ||
| Sequences: | 1371 (1014.7) | ||
| Seq/Len: | 4.218 | ||
| Nf(neff/√len): | 56.3 |
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: 4.218).
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 |
| 212_K | 241_S | 3.416 | 1.00 |
| 184_N | 213_N | 3.413 | 1.00 |
| 247_N | 286_S | 3.235 | 1.00 |
| 217_E | 246_S | 3.035 | 1.00 |
| 109_S | 131_D | 3.034 | 1.00 |
| 135_T | 167_K | 2.957 | 1.00 |
| 167_K | 189_G | 2.944 | 1.00 |
| 166_I | 188_T | 2.836 | 1.00 |
| 246_S | 285_E | 2.688 | 1.00 |
| 240_V | 243_I | 2.652 | 1.00 |
| 176_C | 192_C | 2.610 | 1.00 |
| 162_G | 184_N | 2.558 | 1.00 |
| 131_D | 162_G | 2.490 | 1.00 |
| 188_T | 217_E | 2.454 | 1.00 |
| 218_H | 247_N | 2.432 | 1.00 |
| 213_N | 242_E | 2.357 | 1.00 |
| 107_L | 110_S | 2.332 | 1.00 |
| 302_C | 307_C | 2.312 | 1.00 |
| 156_D | 180_N | 2.200 | 1.00 |
| 189_G | 218_H | 2.172 | 1.00 |
| 134_F | 137_V | 2.046 | 1.00 |
| 219_S | 248_I | 2.031 | 1.00 |
| 34_L | 38_G | 1.982 | 1.00 |
| 241_S | 280_Q | 1.941 | 1.00 |
| 196_H | 264_Y | 1.930 | 1.00 |
| 104_A | 107_L | 1.913 | 1.00 |
| 130_N | 161_V | 1.889 | 1.00 |
| 223_N | 252_G | 1.878 | 1.00 |
| 12_K | 16_A | 1.874 | 1.00 |
| 286_S | 314_D | 1.871 | 1.00 |
| 129_A | 132_I | 1.870 | 1.00 |
| 227_A | 250_M | 1.841 | 1.00 |
| 242_E | 281_D | 1.838 | 1.00 |
| 196_H | 229_R | 1.811 | 1.00 |
| 120_T | 124_A | 1.796 | 1.00 |
| 249_V | 288_T | 1.781 | 1.00 |
| 177_L | 187_F | 1.760 | 0.99 |
| 151_N | 264_Y | 1.760 | 0.99 |
| 183_E | 212_K | 1.756 | 0.99 |
| 279_I | 282_V | 1.717 | 0.99 |
| 285_E | 313_D | 1.695 | 0.99 |
| 156_D | 178_A | 1.693 | 0.99 |
| 136_D | 167_K | 1.684 | 0.99 |
| 101_F | 117_I | 1.648 | 0.99 |
| 157_V | 165_I | 1.623 | 0.99 |
| 190_G | 219_S | 1.609 | 0.99 |
| 68_E | 108_D | 1.593 | 0.99 |
| 123_M | 180_N | 1.580 | 0.99 |
| 10_A | 14_G | 1.569 | 0.98 |
| 112_I | 115_L | 1.552 | 0.98 |
| 127_V | 134_F | 1.542 | 0.98 |
| 110_S | 132_I | 1.542 | 0.98 |
| 196_H | 199_S | 1.539 | 0.98 |
| 281_D | 309_D | 1.534 | 0.98 |
| 11_A | 14_G | 1.531 | 0.98 |
| 191_T | 222_S | 1.512 | 0.98 |
| 160_S | 163_V | 1.510 | 0.98 |
| 69_H | 109_S | 1.508 | 0.98 |
| 115_L | 137_V | 1.506 | 0.98 |
| 284_L | 287_V | 1.495 | 0.98 |
| 229_R | 264_Y | 1.474 | 0.97 |
| 79_L | 118_K | 1.439 | 0.97 |
| 221_V | 224_S | 1.437 | 0.97 |
| 280_Q | 309_D | 1.431 | 0.97 |
| 135_T | 166_I | 1.417 | 0.97 |
| 222_S | 251_S | 1.411 | 0.97 |
| 168_P | 190_G | 1.406 | 0.96 |
| 108_D | 130_N | 1.405 | 0.96 |
| 228_V | 284_L | 1.384 | 0.96 |
| 130_N | 162_G | 1.381 | 0.96 |
| 216_I | 219_S | 1.379 | 0.96 |
| 126_S | 158_G | 1.375 | 0.96 |
| 228_V | 248_I | 1.359 | 0.95 |
| 303_G | 306_S | 1.356 | 0.95 |
| 81_N | 119_N | 1.332 | 0.95 |
| 230_I | 260_I | 1.327 | 0.95 |
| 187_F | 216_I | 1.323 | 0.94 |
| 113_T | 135_T | 1.321 | 0.94 |
| 50_T | 81_N | 1.319 | 0.94 |
| 198_L | 216_I | 1.308 | 0.94 |
| 185_I | 214_V | 1.306 | 0.94 |
| 186_W | 215_T | 1.302 | 0.94 |
| 153_D | 174_D | 1.300 | 0.94 |
| 80_I | 101_F | 1.298 | 0.94 |
| 241_S | 281_D | 1.293 | 0.94 |
| 36_L | 39_L | 1.287 | 0.93 |
| 250_M | 253_I | 1.277 | 0.93 |
| 161_V | 184_N | 1.276 | 0.93 |
| 43_T | 47_F | 1.273 | 0.93 |
| 312_W | 315_V | 1.273 | 0.93 |
| 200_I | 211_V | 1.269 | 0.93 |
| 44_K | 73_T | 1.267 | 0.93 |
| 137_V | 168_P | 1.255 | 0.92 |
| 114_G | 136_D | 1.249 | 0.92 |
| 40_T | 43_T | 1.240 | 0.92 |
| 202_S | 231_K | 1.239 | 0.92 |
| 199_S | 264_Y | 1.232 | 0.91 |
| 120_T | 141_N | 1.224 | 0.91 |
| 179_V | 211_V | 1.224 | 0.91 |
| 217_E | 247_N | 1.223 | 0.91 |
| 227_A | 253_I | 1.215 | 0.90 |
| 220_T | 249_V | 1.211 | 0.90 |
| 217_E | 285_E | 1.188 | 0.89 |
| 34_L | 39_L | 1.188 | 0.89 |
| 230_I | 240_V | 1.183 | 0.89 |
| 226_N | 256_Y | 1.178 | 0.89 |
| 74_G | 78_H | 1.175 | 0.88 |
| 245_Y | 284_L | 1.172 | 0.88 |
| 35_D | 38_G | 1.171 | 0.88 |
| 9_A | 13_A | 1.149 | 0.87 |
| 70_I | 107_L | 1.143 | 0.87 |
| 225_E | 254_S | 1.136 | 0.86 |
| 129_A | 286_S | 1.135 | 0.86 |
| 98_K | 123_M | 1.126 | 0.85 |
| 165_I | 168_P | 1.110 | 0.84 |
| 87_W | 99_P | 1.107 | 0.84 |
| 64_S | 67_G | 1.105 | 0.84 |
| 304_S | 328_N | 1.103 | 0.84 |
| 195_G | 224_S | 1.101 | 0.84 |
| 45_V | 72_V | 1.100 | 0.84 |
| 179_V | 185_I | 1.098 | 0.83 |
| 186_W | 217_E | 1.097 | 0.83 |
| 227_A | 257_G | 1.089 | 0.83 |
| 220_T | 247_N | 1.079 | 0.82 |
| 288_T | 316_K | 1.079 | 0.82 |
| 244_T | 283_K | 1.075 | 0.82 |
| 13_A | 17_K | 1.072 | 0.81 |
| 191_T | 220_T | 1.067 | 0.81 |
| 260_I | 300_L | 1.066 | 0.81 |
| 284_L | 300_L | 1.061 | 0.80 |
| 88_W | 229_R | 1.059 | 0.80 |
| 199_S | 229_R | 1.056 | 0.80 |
| 71_T | 113_T | 1.044 | 0.79 |
| 101_F | 104_A | 1.044 | 0.79 |
| 161_V | 183_E | 1.042 | 0.79 |
| 265_E | 270_T | 1.040 | 0.79 |
| 157_V | 160_S | 1.035 | 0.78 |
| 46_I | 51_T | 1.033 | 0.78 |
| 177_L | 216_I | 1.031 | 0.78 |
| 221_V | 248_I | 1.031 | 0.78 |
| 287_V | 315_V | 1.028 | 0.77 |
| 41_S | 77_G | 1.027 | 0.77 |
| 10_A | 13_A | 1.011 | 0.76 |
| 177_L | 198_L | 1.010 | 0.76 |
| 112_I | 134_F | 1.000 | 0.75 |
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 | |
| 1czfA | 2 | 1 | 100 | 0.15 | Contact Map |
| 1nhcA | 6 | 1 | 100 | 0.156 | Contact Map |
| 2iq7A | 7 | 1 | 100 | 0.167 | Contact Map |
| 1ia5A | 1 | 0.994 | 100 | 0.176 | Contact Map |
| 1hg8A | 1 | 1 | 100 | 0.181 | Contact Map |
| 1k5cA | 1 | 0.9582 | 100 | 0.208 | Contact Map |
| 4c2lA | 1 | 0.9791 | 100 | 0.271 | Contact Map |
| 1bheA | 1 | 0.9284 | 100 | 0.329 | Contact Map |
| 1rmgA | 1 | 0.9343 | 100 | 0.334 | Contact Map |
| 3jurA | 4 | 0.9373 | 100 | 0.347 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)