| Cr_arsM for coevolution analysis |
| ID: | 1485933008 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 379 (358) | ||
| Sequences: | 381 (244.2) | ||
| Seq/Len: | 1.064 | ||
| Nf(neff/√len): | 12.9 |
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: 1.064).
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 |
| 118_P | 147_Q | 4.611 | 1.00 |
| 296_T | 336_H | 3.222 | 1.00 |
| 184_E | 187_R | 2.730 | 1.00 |
| 210_V | 222_A | 2.612 | 1.00 |
| 206_L | 264_A | 2.566 | 1.00 |
| 160_D | 187_R | 2.562 | 1.00 |
| 44_S | 251_Q | 2.266 | 0.98 |
| 160_D | 184_E | 2.258 | 0.98 |
| 312_F | 318_M | 2.239 | 0.98 |
| 184_E | 188_V | 2.236 | 0.98 |
| 284_C | 321_C | 2.163 | 0.98 |
| 86_R | 112_T | 2.158 | 0.98 |
| 85_L | 165_L | 2.068 | 0.97 |
| 310_H | 321_C | 2.039 | 0.97 |
| 112_T | 163_F | 2.007 | 0.96 |
| 166_V | 185_C | 1.900 | 0.94 |
| 213_H | 260_Q | 1.887 | 0.94 |
| 179_A | 236_K | 1.878 | 0.94 |
| 98_C | 128_A | 1.865 | 0.93 |
| 244_Q | 269_I | 1.861 | 0.93 |
| 64_P | 132_C | 1.849 | 0.93 |
| 254_D | 258_R | 1.845 | 0.93 |
| 62_D | 103_K | 1.809 | 0.92 |
| 63_V | 100_V | 1.802 | 0.92 |
| 110_S | 144_T | 1.782 | 0.91 |
| 33_E | 119_A | 1.776 | 0.91 |
| 200_V | 220_C | 1.767 | 0.91 |
| 44_S | 254_D | 1.765 | 0.91 |
| 24_R | 27_V | 1.730 | 0.90 |
| 152_Y | 155_R | 1.702 | 0.89 |
| 172_I | 181_V | 1.700 | 0.89 |
| 125_I | 128_A | 1.677 | 0.88 |
| 86_R | 163_F | 1.621 | 0.85 |
| 133_R | 141_S | 1.620 | 0.85 |
| 101_A | 167_I | 1.583 | 0.83 |
| 25_A | 28_K | 1.578 | 0.83 |
| 220_C | 266_F | 1.568 | 0.82 |
| 232_R | 282_D | 1.557 | 0.82 |
| 201_Y | 242_P | 1.548 | 0.81 |
| 67_V | 99_Y | 1.517 | 0.79 |
| 206_L | 213_H | 1.456 | 0.75 |
| 292_V | 340_I | 1.455 | 0.75 |
| 72_Y | 220_C | 1.444 | 0.75 |
| 92_C | 98_C | 1.435 | 0.74 |
| 71_F | 77_P | 1.434 | 0.74 |
| 86_R | 110_S | 1.412 | 0.72 |
| 62_D | 135_K | 1.410 | 0.72 |
| 59_A | 63_V | 1.403 | 0.72 |
| 291_A | 339_I | 1.400 | 0.71 |
| 294_K | 338_T | 1.396 | 0.71 |
| 42_R | 254_D | 1.362 | 0.68 |
| 320_V | 324_T | 1.362 | 0.68 |
| 29_E | 33_E | 1.361 | 0.68 |
| 234_C | 273_L | 1.359 | 0.68 |
| 325_A | 339_I | 1.299 | 0.63 |
| 62_D | 102_A | 1.298 | 0.63 |
| 173_N | 220_C | 1.283 | 0.61 |
| 211_R | 222_A | 1.278 | 0.61 |
| 200_V | 266_F | 1.278 | 0.61 |
| 128_A | 133_R | 1.271 | 0.60 |
| 206_L | 222_A | 1.269 | 0.60 |
| 289_Q | 321_C | 1.269 | 0.60 |
| 291_A | 317_P | 1.264 | 0.60 |
| 208_Q | 212_S | 1.260 | 0.59 |
| 376_G | 379_C | 1.260 | 0.59 |
| 284_C | 310_H | 1.254 | 0.59 |
| 64_P | 130_A | 1.242 | 0.58 |
| 149_E | 175_S | 1.240 | 0.58 |
| 186_Y | 275_K | 1.239 | 0.57 |
| 52_P | 56_V | 1.232 | 0.57 |
| 227_N | 269_I | 1.230 | 0.57 |
| 284_C | 324_T | 1.230 | 0.57 |
| 296_T | 301_S | 1.223 | 0.56 |
| 325_A | 343_R | 1.222 | 0.56 |
| 88_L | 163_F | 1.210 | 0.55 |
| 242_P | 273_L | 1.199 | 0.54 |
| 160_D | 188_V | 1.199 | 0.54 |
| 146_I | 177_D | 1.199 | 0.54 |
| 251_Q | 258_R | 1.197 | 0.54 |
| 53_P | 221_L | 1.195 | 0.53 |
| 285_E | 323_N | 1.191 | 0.53 |
| 281_E | 346_H | 1.191 | 0.53 |
| 59_A | 103_K | 1.184 | 0.52 |
| 56_V | 59_A | 1.184 | 0.52 |
| 224_A | 266_F | 1.166 | 0.51 |
| 231_I | 282_D | 1.166 | 0.51 |
| 247_C | 357_T | 1.163 | 0.50 |
| 251_Q | 254_D | 1.161 | 0.50 |
| 222_A | 264_A | 1.157 | 0.50 |
| 32_G | 41_L | 1.156 | 0.50 |
| 132_C | 136_L | 1.156 | 0.50 |
| 207_P | 264_A | 1.153 | 0.49 |
| 73_G | 115_D | 1.143 | 0.48 |
| 179_A | 233_L | 1.140 | 0.48 |
| 29_E | 34_T | 1.139 | 0.48 |
| 244_Q | 358_T | 1.135 | 0.48 |
| 228_N | 232_R | 1.133 | 0.48 |
| 290_V | 317_P | 1.133 | 0.48 |
| 64_P | 136_L | 1.130 | 0.47 |
| 65_T | 114_V | 1.121 | 0.46 |
| 200_V | 250_I | 1.120 | 0.46 |
| 151_E | 175_S | 1.118 | 0.46 |
| 351_D | 377_A | 1.110 | 0.45 |
| 205_R | 226_Y | 1.109 | 0.45 |
| 89_D | 174_L | 1.107 | 0.45 |
| 129_D | 133_R | 1.105 | 0.45 |
| 67_V | 132_C | 1.102 | 0.45 |
| 360_G | 363_A | 1.099 | 0.44 |
| 191_P | 302_H | 1.099 | 0.44 |
| 35_L | 41_L | 1.095 | 0.44 |
| 49_C | 185_C | 1.094 | 0.44 |
| 202_V | 206_L | 1.094 | 0.44 |
| 55_A | 299_G | 1.093 | 0.44 |
| 247_C | 308_D | 1.090 | 0.44 |
| 83_E | 108_K | 1.079 | 0.42 |
| 132_C | 143_M | 1.077 | 0.42 |
| 149_E | 176_P | 1.077 | 0.42 |
| 168_S | 171_V | 1.076 | 0.42 |
| 77_P | 244_Q | 1.076 | 0.42 |
| 361_G | 364_S | 1.074 | 0.42 |
| 304_Y | 332_W | 1.073 | 0.42 |
| 64_P | 332_W | 1.071 | 0.42 |
| 182_L | 271_Y | 1.069 | 0.42 |
| 57_R | 314_T | 1.063 | 0.41 |
| 130_A | 135_K | 1.062 | 0.41 |
| 57_R | 217_L | 1.057 | 0.40 |
| 214_P | 264_A | 1.052 | 0.40 |
| 77_P | 101_A | 1.052 | 0.40 |
| 208_Q | 222_A | 1.051 | 0.40 |
| 168_S | 174_L | 1.051 | 0.40 |
| 28_K | 149_E | 1.048 | 0.40 |
| 120_Q | 173_N | 1.045 | 0.39 |
| 167_I | 213_H | 1.040 | 0.39 |
| 68_K | 195_M | 1.040 | 0.39 |
| 206_L | 210_V | 1.036 | 0.39 |
| 32_G | 35_L | 1.027 | 0.38 |
| 112_T | 162_S | 1.027 | 0.38 |
| 35_L | 38_S | 1.025 | 0.38 |
| 67_V | 117_T | 1.024 | 0.38 |
| 205_R | 348_G | 1.023 | 0.37 |
| 228_N | 231_I | 1.022 | 0.37 |
| 185_C | 210_V | 1.022 | 0.37 |
| 357_T | 360_G | 1.019 | 0.37 |
| 182_L | 273_L | 1.019 | 0.37 |
| 56_V | 187_R | 1.018 | 0.37 |
| 210_V | 213_H | 1.014 | 0.37 |
| 260_Q | 377_A | 1.012 | 0.36 |
| 144_T | 330_E | 1.010 | 0.36 |
| 89_D | 168_S | 1.009 | 0.36 |
| 80_A | 333_L | 1.008 | 0.36 |
| 27_V | 116_M | 1.008 | 0.36 |
| 163_F | 359_T | 1.007 | 0.36 |
| 281_E | 323_N | 1.007 | 0.36 |
| 239_F | 242_P | 1.007 | 0.36 |
| 47_T | 220_C | 1.004 | 0.36 |
| 281_E | 321_C | 1.003 | 0.36 |
| 261_V | 264_A | 1.002 | 0.36 |
| 132_C | 245_L | 1.001 | 0.35 |
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 | |
| 4fsdA | 1 | 0.8206 | 100 | 0.627 | Contact Map |
| 4obxA | 4 | 0.5515 | 99.9 | 0.844 | Contact Map |
| 2o57A | 4 | 0.6966 | 99.9 | 0.849 | Contact Map |
| 4pneA | 2 | 0.6755 | 99.9 | 0.849 | Contact Map |
| 4krgA | 2 | 0.591 | 99.9 | 0.849 | Contact Map |
| 3ujcA | 1 | 0.6596 | 99.9 | 0.85 | Contact Map |
| 3busA | 2 | 0.6148 | 99.9 | 0.854 | Contact Map |
| 1xtpA | 1 | 0.5831 | 99.9 | 0.854 | Contact Map |
| 3kkzA | 2 | 0.6201 | 99.9 | 0.854 | Contact Map |
| 4p7cA | 2 | 0.7361 | 99.9 | 0.855 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)