| carm1 |
| ID: | 1410461218 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 341 (316) | ||
| Sequences: | 939 (633.6) | ||
| Seq/Len: | 2.972 | ||
| Nf(neff/√len): | 35.6 |
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: 2.972).
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 |
| 157_P | 211_A | 3.876 | 1.00 |
| 80_A | 98_V | 3.289 | 1.00 |
| 70_K | 97_V | 3.124 | 1.00 |
| 88_K | 93_T | 2.611 | 1.00 |
| 140_L | 144_G | 2.505 | 1.00 |
| 54_C | 75_E | 2.449 | 1.00 |
| 73_A | 98_V | 2.358 | 1.00 |
| 309_Y | 315_A | 2.169 | 1.00 |
| 72_Y | 99_I | 2.121 | 1.00 |
| 21_Q | 25_Q | 2.060 | 1.00 |
| 54_C | 83_A | 2.001 | 1.00 |
| 64_A | 92_L | 1.978 | 1.00 |
| 156_A | 251_W | 1.972 | 1.00 |
| 72_Y | 112_V | 1.965 | 1.00 |
| 236_K | 296_S | 1.895 | 0.99 |
| 75_E | 80_A | 1.870 | 0.99 |
| 118_E | 127_E | 1.856 | 0.99 |
| 123_M | 250_F | 1.848 | 0.99 |
| 250_F | 281_C | 1.845 | 0.99 |
| 54_C | 60_S | 1.842 | 0.99 |
| 311_I | 315_A | 1.824 | 0.99 |
| 210_M | 243_G | 1.792 | 0.99 |
| 61_F | 92_L | 1.791 | 0.99 |
| 242_S | 291_A | 1.785 | 0.99 |
| 125_F | 218_V | 1.740 | 0.99 |
| 309_Y | 312_S | 1.723 | 0.98 |
| 45_K | 48_I | 1.708 | 0.98 |
| 135_H | 138_K | 1.691 | 0.98 |
| 157_P | 237_F | 1.672 | 0.98 |
| 11_F | 14_Y | 1.653 | 0.98 |
| 267_T | 274_T | 1.646 | 0.98 |
| 44_F | 147_F | 1.596 | 0.97 |
| 30_T | 62_F | 1.585 | 0.97 |
| 84_E | 88_K | 1.583 | 0.97 |
| 10_Y | 14_Y | 1.572 | 0.97 |
| 81_Q | 100_P | 1.568 | 0.97 |
| 92_L | 96_I | 1.558 | 0.97 |
| 19_Q | 126_N | 1.550 | 0.97 |
| 237_F | 247_G | 1.537 | 0.96 |
| 125_F | 153_V | 1.514 | 0.96 |
| 242_S | 290_K | 1.513 | 0.96 |
| 122_Y | 126_N | 1.508 | 0.96 |
| 119_P | 133_Y | 1.505 | 0.96 |
| 247_G | 280_R | 1.504 | 0.96 |
| 312_S | 315_A | 1.492 | 0.95 |
| 61_F | 182_V | 1.488 | 0.95 |
| 44_F | 114_I | 1.460 | 0.95 |
| 239_M | 289_A | 1.459 | 0.95 |
| 49_V | 71_I | 1.443 | 0.94 |
| 89_S | 183_D | 1.428 | 0.94 |
| 101_G | 106_V | 1.421 | 0.94 |
| 155_L | 248_L | 1.417 | 0.93 |
| 89_S | 186_A | 1.410 | 0.93 |
| 307_Q | 312_S | 1.403 | 0.93 |
| 23_M | 29_R | 1.394 | 0.93 |
| 103_V | 139_Y | 1.376 | 0.92 |
| 38_L | 65_Q | 1.373 | 0.92 |
| 104_E | 129_M | 1.370 | 0.92 |
| 64_A | 95_R | 1.363 | 0.92 |
| 123_M | 281_C | 1.361 | 0.92 |
| 46_D | 69_R | 1.359 | 0.91 |
| 74_V | 103_V | 1.358 | 0.91 |
| 223_A | 228_L | 1.345 | 0.91 |
| 121_G | 126_N | 1.341 | 0.91 |
| 307_Q | 311_I | 1.339 | 0.91 |
| 127_E | 276_W | 1.338 | 0.91 |
| 72_Y | 110_E | 1.337 | 0.91 |
| 307_Q | 315_A | 1.307 | 0.89 |
| 308_S | 312_S | 1.305 | 0.89 |
| 124_L | 151_G | 1.304 | 0.89 |
| 102_K | 105_E | 1.298 | 0.89 |
| 117_S | 121_G | 1.293 | 0.89 |
| 10_Y | 13_F | 1.283 | 0.88 |
| 68_A | 71_I | 1.280 | 0.88 |
| 239_M | 245_V | 1.272 | 0.87 |
| 247_G | 251_W | 1.241 | 0.86 |
| 19_Q | 122_Y | 1.239 | 0.86 |
| 60_S | 73_A | 1.236 | 0.85 |
| 50_L | 108_L | 1.232 | 0.85 |
| 191_A | 246_H | 1.227 | 0.85 |
| 12_Q | 15_G | 1.221 | 0.84 |
| 149_T | 157_P | 1.219 | 0.84 |
| 224_K | 227_D | 1.219 | 0.84 |
| 308_S | 311_I | 1.216 | 0.84 |
| 105_E | 108_L | 1.213 | 0.84 |
| 72_Y | 106_V | 1.213 | 0.84 |
| 73_A | 269_P | 1.209 | 0.84 |
| 75_E | 254_V | 1.209 | 0.84 |
| 158_F | 247_G | 1.204 | 0.83 |
| 23_M | 51_D | 1.199 | 0.83 |
| 51_D | 59_L | 1.187 | 0.82 |
| 308_S | 315_A | 1.184 | 0.82 |
| 48_I | 70_K | 1.182 | 0.82 |
| 150_I | 217_T | 1.180 | 0.82 |
| 36_A | 147_F | 1.179 | 0.81 |
| 23_M | 118_E | 1.178 | 0.81 |
| 29_R | 51_D | 1.177 | 0.81 |
| 129_M | 275_H | 1.175 | 0.81 |
| 101_G | 109_P | 1.174 | 0.81 |
| 136_A | 139_Y | 1.173 | 0.81 |
| 103_V | 132_S | 1.163 | 0.80 |
| 5_S | 8_V | 1.163 | 0.80 |
| 52_V | 59_L | 1.154 | 0.79 |
| 275_H | 278_Q | 1.151 | 0.79 |
| 125_F | 131_E | 1.148 | 0.79 |
| 238_H | 294_T | 1.143 | 0.79 |
| 36_A | 265_L | 1.141 | 0.78 |
| 204_F | 247_G | 1.141 | 0.78 |
| 267_T | 278_Q | 1.132 | 0.78 |
| 236_K | 294_T | 1.132 | 0.78 |
| 5_S | 9_Q | 1.128 | 0.77 |
| 65_Q | 182_V | 1.124 | 0.77 |
| 113_D | 141_K | 1.120 | 0.77 |
| 14_Y | 23_M | 1.119 | 0.77 |
| 30_T | 126_N | 1.117 | 0.76 |
| 31_G | 34_Q | 1.111 | 0.76 |
| 87_V | 96_I | 1.111 | 0.76 |
| 54_C | 73_A | 1.110 | 0.76 |
| 103_V | 136_A | 1.109 | 0.76 |
| 156_A | 209_L | 1.108 | 0.76 |
| 75_E | 79_M | 1.099 | 0.75 |
| 13_F | 16_Y | 1.095 | 0.74 |
| 51_D | 58_I | 1.093 | 0.74 |
| 48_I | 72_Y | 1.090 | 0.74 |
| 131_E | 303_A | 1.087 | 0.74 |
| 274_T | 278_Q | 1.081 | 0.73 |
| 53_G | 118_E | 1.070 | 0.72 |
| 223_A | 227_D | 1.067 | 0.72 |
| 49_V | 68_A | 1.065 | 0.71 |
| 50_L | 112_V | 1.065 | 0.71 |
| 9_Q | 12_Q | 1.063 | 0.71 |
| 85_V | 89_S | 1.061 | 0.71 |
| 58_I | 62_F | 1.056 | 0.70 |
| 51_D | 56_S | 1.055 | 0.70 |
| 123_M | 126_N | 1.054 | 0.70 |
| 104_E | 132_S | 1.052 | 0.70 |
| 16_Y | 19_Q | 1.052 | 0.70 |
| 266_S | 271_E | 1.052 | 0.70 |
| 23_M | 127_E | 1.049 | 0.70 |
| 204_F | 280_R | 1.047 | 0.70 |
| 87_V | 98_V | 1.046 | 0.69 |
| 245_V | 295_L | 1.041 | 0.69 |
| 66_A | 116_I | 1.039 | 0.69 |
| 254_V | 265_L | 1.037 | 0.68 |
| 179_F | 184_L | 1.036 | 0.68 |
| 19_Q | 22_N | 1.036 | 0.68 |
| 204_F | 249_A | 1.036 | 0.68 |
| 61_F | 65_Q | 1.035 | 0.68 |
| 26_D | 29_R | 1.033 | 0.68 |
| 113_D | 117_S | 1.028 | 0.67 |
| 151_G | 220_F | 1.024 | 0.67 |
| 23_M | 30_T | 1.022 | 0.67 |
| 37_I | 44_F | 1.021 | 0.67 |
| 210_M | 245_V | 1.021 | 0.67 |
| 87_V | 101_G | 1.015 | 0.66 |
| 85_V | 88_K | 1.011 | 0.66 |
| 119_P | 129_M | 1.003 | 0.65 |
| 111_Q | 142_P | 1.003 | 0.65 |
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 | |
| 4ikpA | 4 | 0.9824 | 100 | 0.332 | Contact Map |
| 3b3jA | 1 | 0.9736 | 100 | 0.379 | Contact Map |
| 1g6q1 | 6 | 0.9208 | 100 | 0.39 | Contact Map |
| 3q7eA | 1 | 0.8974 | 100 | 0.395 | Contact Map |
| 2fytA | 1 | 0.9003 | 100 | 0.401 | Contact Map |
| 4lwoB | 4 | 0.8622 | 100 | 0.417 | Contact Map |
| 4qqkA | 1 | 0.9179 | 100 | 0.417 | Contact Map |
| 3r0qC | 4 | 0.9443 | 100 | 0.421 | Contact Map |
| 3ua3A | 2 | 0.912 | 100 | 0.438 | Contact Map |
| 4c4aA | 1 | 0.8856 | 100 | 0.471 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)