| carm1 |
| ID: | 1410461175 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 341 (317) | ||
| Sequences: | 831 (579) | ||
| Seq/Len: | 2.621 | ||
| Nf(neff/√len): | 32.5 |
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: 2.621).
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 |
| 80_A | 98_V | 3.517 | 1.00 |
| 70_K | 97_V | 2.924 | 1.00 |
| 157_P | 211_A | 2.894 | 1.00 |
| 54_C | 75_E | 2.788 | 1.00 |
| 73_A | 98_V | 2.760 | 1.00 |
| 88_K | 93_T | 2.662 | 1.00 |
| 140_L | 144_G | 2.465 | 1.00 |
| 309_Y | 315_A | 2.133 | 1.00 |
| 72_Y | 112_V | 2.049 | 1.00 |
| 21_Q | 25_Q | 2.047 | 1.00 |
| 311_I | 315_A | 2.001 | 0.99 |
| 123_M | 250_F | 1.990 | 0.99 |
| 250_F | 281_C | 1.975 | 0.99 |
| 156_A | 251_W | 1.905 | 0.99 |
| 236_K | 296_S | 1.826 | 0.99 |
| 309_Y | 312_S | 1.826 | 0.99 |
| 125_F | 218_V | 1.824 | 0.99 |
| 54_C | 83_A | 1.816 | 0.99 |
| 64_A | 92_L | 1.780 | 0.98 |
| 118_E | 127_E | 1.706 | 0.98 |
| 54_C | 60_S | 1.704 | 0.98 |
| 72_Y | 99_I | 1.682 | 0.98 |
| 75_E | 80_A | 1.678 | 0.98 |
| 19_Q | 126_N | 1.637 | 0.97 |
| 125_F | 153_V | 1.626 | 0.97 |
| 61_F | 182_V | 1.623 | 0.97 |
| 30_T | 62_F | 1.622 | 0.97 |
| 122_Y | 126_N | 1.622 | 0.97 |
| 44_F | 147_F | 1.612 | 0.97 |
| 10_Y | 14_Y | 1.603 | 0.97 |
| 45_K | 48_I | 1.591 | 0.96 |
| 84_E | 88_K | 1.586 | 0.96 |
| 312_S | 315_A | 1.579 | 0.96 |
| 307_Q | 311_I | 1.568 | 0.96 |
| 50_L | 108_L | 1.567 | 0.96 |
| 11_F | 14_Y | 1.538 | 0.95 |
| 89_S | 183_D | 1.530 | 0.95 |
| 307_Q | 312_S | 1.528 | 0.95 |
| 239_M | 289_A | 1.522 | 0.95 |
| 157_P | 237_F | 1.520 | 0.95 |
| 81_Q | 100_P | 1.514 | 0.95 |
| 247_G | 280_R | 1.514 | 0.95 |
| 61_F | 92_L | 1.513 | 0.95 |
| 307_Q | 315_A | 1.509 | 0.95 |
| 64_A | 95_R | 1.503 | 0.94 |
| 242_S | 291_A | 1.502 | 0.94 |
| 247_G | 251_W | 1.468 | 0.94 |
| 92_L | 96_I | 1.453 | 0.93 |
| 155_L | 248_L | 1.450 | 0.93 |
| 267_T | 274_T | 1.440 | 0.93 |
| 135_H | 138_K | 1.430 | 0.92 |
| 119_P | 133_Y | 1.413 | 0.92 |
| 223_A | 228_L | 1.399 | 0.91 |
| 87_V | 101_G | 1.395 | 0.91 |
| 242_S | 290_K | 1.394 | 0.91 |
| 308_S | 312_S | 1.392 | 0.91 |
| 44_F | 114_I | 1.386 | 0.91 |
| 74_V | 103_V | 1.385 | 0.91 |
| 117_S | 121_G | 1.384 | 0.91 |
| 60_S | 73_A | 1.373 | 0.90 |
| 49_V | 71_I | 1.371 | 0.90 |
| 102_K | 105_E | 1.366 | 0.90 |
| 308_S | 315_A | 1.355 | 0.89 |
| 104_E | 129_M | 1.346 | 0.89 |
| 224_K | 227_D | 1.336 | 0.88 |
| 103_V | 139_Y | 1.334 | 0.88 |
| 89_S | 186_A | 1.331 | 0.88 |
| 51_D | 59_L | 1.310 | 0.87 |
| 10_Y | 13_F | 1.307 | 0.87 |
| 127_E | 276_W | 1.298 | 0.87 |
| 19_Q | 122_Y | 1.279 | 0.85 |
| 179_F | 184_L | 1.270 | 0.85 |
| 52_V | 59_L | 1.248 | 0.83 |
| 219_N | 289_A | 1.229 | 0.82 |
| 266_S | 271_E | 1.221 | 0.82 |
| 149_T | 157_P | 1.219 | 0.81 |
| 16_Y | 19_Q | 1.219 | 0.81 |
| 308_S | 311_I | 1.215 | 0.81 |
| 75_E | 254_V | 1.214 | 0.81 |
| 75_E | 79_M | 1.210 | 0.81 |
| 13_F | 16_Y | 1.208 | 0.81 |
| 36_A | 147_F | 1.208 | 0.81 |
| 124_L | 151_G | 1.207 | 0.81 |
| 23_M | 29_R | 1.205 | 0.80 |
| 158_F | 247_G | 1.187 | 0.79 |
| 237_F | 247_G | 1.187 | 0.79 |
| 114_I | 145_N | 1.187 | 0.79 |
| 23_M | 51_D | 1.186 | 0.79 |
| 5_S | 9_Q | 1.183 | 0.79 |
| 38_L | 65_Q | 1.182 | 0.79 |
| 30_T | 126_N | 1.173 | 0.78 |
| 23_M | 127_E | 1.168 | 0.77 |
| 129_M | 275_H | 1.167 | 0.77 |
| 247_G | 283_F | 1.167 | 0.77 |
| 253_D | 266_S | 1.165 | 0.77 |
| 121_G | 126_N | 1.165 | 0.77 |
| 12_Q | 15_G | 1.162 | 0.77 |
| 31_G | 34_Q | 1.155 | 0.76 |
| 9_Q | 12_Q | 1.149 | 0.76 |
| 128_R | 133_Y | 1.144 | 0.75 |
| 36_A | 265_L | 1.142 | 0.75 |
| 274_T | 278_Q | 1.140 | 0.75 |
| 46_D | 69_R | 1.136 | 0.75 |
| 72_Y | 110_E | 1.130 | 0.74 |
| 26_D | 33_Y | 1.129 | 0.74 |
| 103_V | 136_A | 1.128 | 0.74 |
| 105_E | 108_L | 1.125 | 0.74 |
| 87_V | 96_I | 1.124 | 0.74 |
| 29_R | 51_D | 1.118 | 0.73 |
| 5_S | 8_V | 1.115 | 0.73 |
| 51_D | 58_I | 1.108 | 0.72 |
| 164_Y | 199_P | 1.107 | 0.72 |
| 65_Q | 182_V | 1.106 | 0.72 |
| 37_I | 44_F | 1.105 | 0.72 |
| 103_V | 112_V | 1.104 | 0.72 |
| 157_P | 292_G | 1.104 | 0.72 |
| 123_M | 281_C | 1.100 | 0.71 |
| 101_G | 106_V | 1.099 | 0.71 |
| 245_V | 295_L | 1.091 | 0.70 |
| 223_A | 227_D | 1.084 | 0.70 |
| 23_M | 118_E | 1.083 | 0.70 |
| 101_G | 109_P | 1.082 | 0.69 |
| 64_A | 98_V | 1.076 | 0.69 |
| 61_F | 65_Q | 1.066 | 0.68 |
| 275_H | 278_Q | 1.066 | 0.68 |
| 103_V | 132_S | 1.065 | 0.68 |
| 210_M | 243_G | 1.062 | 0.67 |
| 30_T | 180_H | 1.059 | 0.67 |
| 54_C | 73_A | 1.057 | 0.67 |
| 267_T | 278_Q | 1.057 | 0.67 |
| 118_E | 276_W | 1.057 | 0.67 |
| 28_V | 265_L | 1.056 | 0.67 |
| 19_Q | 22_N | 1.055 | 0.67 |
| 125_F | 131_E | 1.054 | 0.67 |
| 239_M | 245_V | 1.054 | 0.67 |
| 204_F | 280_R | 1.050 | 0.66 |
| 150_I | 217_T | 1.047 | 0.66 |
| 152_D | 266_S | 1.046 | 0.66 |
| 68_A | 71_I | 1.045 | 0.66 |
| 123_M | 301_L | 1.043 | 0.65 |
| 14_Y | 19_Q | 1.042 | 0.65 |
| 310_D | 313_I | 1.038 | 0.65 |
| 104_E | 132_S | 1.038 | 0.65 |
| 119_P | 129_M | 1.034 | 0.64 |
| 209_L | 243_G | 1.033 | 0.64 |
| 75_E | 83_A | 1.022 | 0.63 |
| 151_G | 220_F | 1.022 | 0.63 |
| 23_M | 30_T | 1.022 | 0.63 |
| 79_M | 83_A | 1.019 | 0.63 |
| 53_G | 118_E | 1.019 | 0.63 |
| 289_A | 295_L | 1.014 | 0.62 |
| 85_V | 245_V | 1.013 | 0.62 |
| 34_Q | 38_L | 1.009 | 0.62 |
| 123_M | 126_N | 1.008 | 0.61 |
| 129_M | 132_S | 1.007 | 0.61 |
| 123_M | 279_V | 1.007 | 0.61 |
| 51_D | 56_S | 1.007 | 0.61 |
| 236_K | 294_T | 1.006 | 0.61 |
| 131_E | 303_A | 1.004 | 0.61 |
| 113_D | 141_K | 1.003 | 0.61 |
| 87_V | 98_V | 1.003 | 0.61 |
| 53_G | 127_E | 1.001 | 0.61 |
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 | 0.32 | Contact Map |
| 3b3jA | 1 | 0.9736 | 100 | 0.366 | Contact Map |
| 1g6q1 | 6 | 0.9326 | 100 | 0.393 | Contact Map |
| 3q7eA | 1 | 0.8974 | 100 | 0.402 | Contact Map |
| 2fytA | 1 | 0.9003 | 100 | 0.409 | Contact Map |
| 4lwoB | 4 | 0.8622 | 100 | 0.424 | Contact Map |
| 4qqkA | 1 | 0.9179 | 100 | 0.426 | Contact Map |
| 3r0qC | 4 | 0.9619 | 100 | 0.428 | Contact Map |
| 3ua3A | 2 | 0.912 | 100 | 0.444 | Contact Map |
| 4c4aA | 1 | 0.8856 | 100 | 0.478 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)