| MutL-NTD |
| ID: | 1484577768 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 332 (328) | ||
| Sequences: | 8250 (4106.7) | ||
| Seq/Len: | 25.152 | ||
| Nf(neff/√len): | 226.8 |
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: 25.152).
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 |
| 40_T | 59_N | 6.960 | 1.00 |
| 113_R | 141_V | 3.570 | 1.00 |
| 38_G | 61_C | 3.561 | 1.00 |
| 30_L | 99_L | 3.544 | 1.00 |
| 109_T | 122_Q | 3.491 | 1.00 |
| 35_L | 185_V | 3.464 | 1.00 |
| 43_D | 188_N | 3.291 | 1.00 |
| 44_I | 175_I | 3.012 | 1.00 |
| 111_T | 122_Q | 2.979 | 1.00 |
| 109_T | 124_Y | 2.824 | 1.00 |
| 41_R | 186_T | 2.804 | 1.00 |
| 45_D | 55_R | 2.766 | 1.00 |
| 27_V | 54_I | 2.733 | 1.00 |
| 107_R | 148_L | 2.689 | 1.00 |
| 55_R | 144_T | 2.649 | 1.00 |
| 107_R | 149_D | 2.648 | 1.00 |
| 55_R | 146_E | 2.643 | 1.00 |
| 57_R | 144_T | 2.587 | 1.00 |
| 235_T | 293_E | 2.509 | 1.00 |
| 41_R | 59_N | 2.461 | 1.00 |
| 47_E | 55_R | 2.398 | 1.00 |
| 111_T | 146_E | 2.374 | 1.00 |
| 43_D | 57_R | 2.367 | 1.00 |
| 111_T | 144_T | 2.332 | 1.00 |
| 45_D | 57_R | 2.310 | 1.00 |
| 190_S | 194_K | 2.265 | 1.00 |
| 72_L | 108_L | 2.237 | 1.00 |
| 47_E | 53_L | 2.169 | 1.00 |
| 43_D | 190_S | 2.150 | 1.00 |
| 110_L | 145_L | 2.138 | 1.00 |
| 109_T | 146_E | 2.138 | 1.00 |
| 113_R | 140_P | 2.113 | 1.00 |
| 275_A | 323_Y | 2.110 | 1.00 |
| 53_L | 148_L | 2.089 | 1.00 |
| 237_R | 293_E | 1.990 | 1.00 |
| 81_A | 87_E | 1.973 | 1.00 |
| 53_L | 146_E | 1.967 | 1.00 |
| 115_A | 141_V | 1.956 | 1.00 |
| 4_Q | 81_A | 1.954 | 1.00 |
| 111_T | 120_A | 1.947 | 1.00 |
| 68_L | 112_S | 1.945 | 1.00 |
| 168_F | 189_L | 1.903 | 1.00 |
| 64_K | 67_E | 1.879 | 1.00 |
| 7_P | 10_L | 1.865 | 1.00 |
| 65_K | 121_W | 1.839 | 1.00 |
| 45_D | 190_S | 1.835 | 1.00 |
| 71_A | 99_L | 1.807 | 1.00 |
| 31_V | 175_I | 1.804 | 1.00 |
| 71_A | 145_L | 1.797 | 1.00 |
| 41_R | 188_N | 1.787 | 1.00 |
| 254_Q | 288_F | 1.760 | 1.00 |
| 109_T | 148_L | 1.753 | 1.00 |
| 238_G | 290_L | 1.745 | 1.00 |
| 39_A | 59_N | 1.716 | 1.00 |
| 270_H | 319_H | 1.677 | 1.00 |
| 186_T | 196_V | 1.676 | 1.00 |
| 183_F | 228_E | 1.658 | 1.00 |
| 272_I | 288_F | 1.636 | 1.00 |
| 47_E | 192_N | 1.626 | 1.00 |
| 46_I | 171_I | 1.615 | 1.00 |
| 168_F | 191_H | 1.595 | 1.00 |
| 212_L | 239_W | 1.594 | 1.00 |
| 179_A | 199_Y | 1.580 | 1.00 |
| 26_V | 150_L | 1.541 | 1.00 |
| 68_L | 121_W | 1.524 | 1.00 |
| 325_G | 328_S | 1.501 | 1.00 |
| 186_T | 198_Q | 1.500 | 1.00 |
| 31_V | 44_I | 1.498 | 1.00 |
| 5_V | 73_A | 1.485 | 1.00 |
| 314_Q | 317_L | 1.477 | 1.00 |
| 209_E | 213_G | 1.476 | 1.00 |
| 172_D | 189_L | 1.475 | 1.00 |
| 63_I | 71_A | 1.469 | 1.00 |
| 264_R | 308_H | 1.464 | 1.00 |
| 299_V | 310_V | 1.447 | 1.00 |
| 207_Q | 210_R | 1.415 | 1.00 |
| 70_L | 76_A | 1.407 | 0.99 |
| 216_C | 241_A | 1.401 | 0.99 |
| 127_G | 152_Y | 1.399 | 0.99 |
| 258_V | 310_V | 1.398 | 0.99 |
| 28_K | 171_I | 1.395 | 0.99 |
| 99_L | 108_L | 1.361 | 0.99 |
| 226_A | 237_R | 1.361 | 0.99 |
| 122_Q | 136_P | 1.360 | 0.99 |
| 113_R | 120_A | 1.356 | 0.99 |
| 107_R | 126_E | 1.354 | 0.99 |
| 48_R | 192_N | 1.353 | 0.99 |
| 323_Y | 327_L | 1.352 | 0.99 |
| 123_A | 130_M | 1.345 | 0.99 |
| 216_C | 255_Y | 1.336 | 0.99 |
| 47_E | 146_E | 1.335 | 0.99 |
| 120_A | 139_H | 1.319 | 0.99 |
| 278_D | 282_A | 1.308 | 0.99 |
| 2_P | 64_K | 1.297 | 0.99 |
| 49_G | 53_L | 1.293 | 0.99 |
| 27_V | 31_V | 1.291 | 0.99 |
| 168_F | 172_D | 1.287 | 0.99 |
| 113_R | 144_T | 1.284 | 0.99 |
| 274_Q | 323_Y | 1.281 | 0.99 |
| 247_T | 284_Q | 1.270 | 0.99 |
| 28_K | 32_E | 1.266 | 0.99 |
| 256_C | 263_M | 1.266 | 0.99 |
| 266_R | 270_H | 1.264 | 0.99 |
| 72_L | 125_A | 1.262 | 0.99 |
| 319_H | 323_Y | 1.255 | 0.99 |
| 126_E | 132_V | 1.252 | 0.99 |
| 258_V | 263_M | 1.244 | 0.98 |
| 168_F | 195_I | 1.241 | 0.98 |
| 227_I | 238_G | 1.240 | 0.98 |
| 276_C | 330_L | 1.235 | 0.98 |
| 322_I | 326_V | 1.231 | 0.98 |
| 63_I | 68_L | 1.228 | 0.98 |
| 58_D | 62_G | 1.208 | 0.98 |
| 2_P | 67_E | 1.197 | 0.98 |
| 27_V | 171_I | 1.194 | 0.98 |
| 216_C | 287_A | 1.191 | 0.98 |
| 258_V | 294_I | 1.190 | 0.98 |
| 46_I | 54_I | 1.187 | 0.98 |
| 327_L | 331_Q | 1.187 | 0.98 |
| 26_V | 102_I | 1.187 | 0.98 |
| 173_E | 177_R | 1.187 | 0.98 |
| 237_R | 291_Y | 1.185 | 0.98 |
| 68_L | 110_L | 1.183 | 0.98 |
| 122_Q | 135_K | 1.182 | 0.98 |
| 326_V | 330_L | 1.175 | 0.98 |
| 174_I | 178_I | 1.152 | 0.97 |
| 70_L | 73_A | 1.152 | 0.97 |
| 168_F | 196_V | 1.129 | 0.97 |
| 324_Q | 328_S | 1.128 | 0.97 |
| 202_V | 210_R | 1.118 | 0.96 |
| 166_T | 170_H | 1.118 | 0.96 |
| 8_P | 12_N | 1.118 | 0.96 |
| 195_I | 198_Q | 1.117 | 0.96 |
| 321_F | 325_G | 1.114 | 0.96 |
| 175_I | 189_L | 1.114 | 0.96 |
| 265_D | 308_H | 1.106 | 0.96 |
| 257_Y | 291_Y | 1.103 | 0.96 |
| 33_N | 36_D | 1.094 | 0.96 |
| 66_D | 114_T | 1.087 | 0.96 |
| 209_E | 226_A | 1.086 | 0.96 |
| 88_A | 297_H | 1.083 | 0.96 |
| 2_P | 61_C | 1.070 | 0.95 |
| 31_V | 187_I | 1.067 | 0.95 |
| 241_A | 247_T | 1.041 | 0.94 |
| 46_I | 168_F | 1.039 | 0.94 |
| 26_V | 147_V | 1.036 | 0.94 |
| 111_T | 139_H | 1.032 | 0.94 |
| 63_I | 69_A | 1.027 | 0.94 |
| 102_I | 147_V | 1.027 | 0.94 |
| 172_D | 176_R | 1.019 | 0.93 |
| 236_L | 292_L | 1.015 | 0.93 |
| 71_A | 110_L | 1.007 | 0.93 |
| 127_G | 149_D | 1.005 | 0.93 |
| 255_Y | 262_M | 1.003 | 0.93 |
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 | |
| 1b63A | 1 | 0.994 | 100 | 0.143 | Contact Map |
| 3h4lA | 2 | 0.9699 | 100 | 0.148 | Contact Map |
| 1h7sA | 2 | 0.8886 | 100 | 0.171 | Contact Map |
| 4p7aA | 1 | 0.8916 | 100 | 0.188 | Contact Map |
| 4wubA | 1 | 0.9247 | 100 | 0.406 | Contact Map |
| 3cwvA | 2 | 0.8886 | 100 | 0.406 | Contact Map |
| 4i3hA | 2 | 0.8494 | 100 | 0.414 | Contact Map |
| 1s16A | 2 | 0.9247 | 100 | 0.414 | Contact Map |
| 4urlA | 2 | 0.8584 | 100 | 0.415 | Contact Map |
| 1kijA | 2 | 0.9187 | 100 | 0.422 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)