| T0768 |
| ID: | 1401217827 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 170 (167) | ||
| Sequences: | 1985 (1652.3) | ||
| Seq/Len: | 11.886 | ||
| Nf(neff/√len): | 127.9 |
Jackhmmer Results: (2014_04_16)
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: 11.886).
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 |
| 137_K | 159_D | 3.187 | 1.00 |
| 84_A | 87_E | 2.938 | 1.00 |
| 114_S | 137_K | 2.344 | 1.00 |
| 56_A | 61_A | 2.170 | 1.00 |
| 141_I | 163_M | 2.110 | 1.00 |
| 58_S | 61_A | 2.098 | 1.00 |
| 91_T | 114_S | 2.051 | 1.00 |
| 56_A | 59_T | 2.014 | 1.00 |
| 144_S | 166_M | 2.003 | 1.00 |
| 118_L | 122_L | 1.891 | 1.00 |
| 112_S | 135_A | 1.843 | 1.00 |
| 33_V | 36_Y | 1.800 | 1.00 |
| 67_V | 75_Y | 1.796 | 1.00 |
| 72_G | 77_V | 1.789 | 1.00 |
| 117_K | 140_T | 1.636 | 1.00 |
| 133_C | 155_S | 1.633 | 1.00 |
| 72_G | 75_Y | 1.616 | 1.00 |
| 141_I | 145_V | 1.583 | 1.00 |
| 35_P | 38_F | 1.572 | 1.00 |
| 48_L | 51_Y | 1.568 | 1.00 |
| 124_Y | 127_E | 1.568 | 1.00 |
| 85_F | 107_F | 1.566 | 1.00 |
| 99_V | 122_L | 1.559 | 1.00 |
| 39_E | 42_F | 1.544 | 1.00 |
| 130_F | 152_F | 1.540 | 1.00 |
| 141_I | 144_S | 1.499 | 1.00 |
| 110_C | 133_C | 1.499 | 1.00 |
| 102_I | 106_A | 1.486 | 1.00 |
| 33_V | 38_F | 1.481 | 1.00 |
| 148_M | 151_P | 1.476 | 1.00 |
| 121_N | 144_S | 1.470 | 1.00 |
| 59_T | 62_D | 1.464 | 1.00 |
| 51_Y | 56_A | 1.461 | 1.00 |
| 56_A | 60_Y | 1.454 | 1.00 |
| 34_G | 40_I | 1.421 | 1.00 |
| 92_G | 115_D | 1.415 | 1.00 |
| 93_V | 116_V | 1.407 | 0.99 |
| 118_L | 141_I | 1.388 | 0.99 |
| 89_N | 112_S | 1.383 | 0.99 |
| 95_V | 99_V | 1.379 | 0.99 |
| 107_F | 130_F | 1.370 | 0.99 |
| 31_V | 35_P | 1.359 | 0.99 |
| 29_S | 33_V | 1.345 | 0.99 |
| 57_G | 60_Y | 1.344 | 0.99 |
| 123_I | 146_E | 1.342 | 0.99 |
| 115_D | 138_E | 1.336 | 0.99 |
| 125_I | 129_A | 1.328 | 0.99 |
| 32_Q | 38_F | 1.309 | 0.99 |
| 155_S | 161_V | 1.291 | 0.99 |
| 119_S | 140_T | 1.282 | 0.99 |
| 142_P | 164_E | 1.277 | 0.99 |
| 142_P | 162_Y | 1.265 | 0.99 |
| 81_G | 85_F | 1.261 | 0.99 |
| 101_S | 124_Y | 1.259 | 0.99 |
| 64_P | 67_V | 1.235 | 0.98 |
| 103_G | 106_A | 1.235 | 0.98 |
| 91_T | 112_S | 1.213 | 0.98 |
| 81_G | 84_A | 1.207 | 0.98 |
| 33_V | 37_T | 1.197 | 0.98 |
| 95_V | 118_L | 1.191 | 0.98 |
| 145_V | 168_A | 1.186 | 0.98 |
| 21_A | 24_A | 1.182 | 0.98 |
| 131_A | 153_R | 1.180 | 0.98 |
| 104_R | 127_E | 1.162 | 0.97 |
| 143_A | 165_G | 1.138 | 0.97 |
| 135_A | 157_A | 1.119 | 0.96 |
| 77_V | 81_G | 1.115 | 0.96 |
| 36_Y | 40_I | 1.093 | 0.96 |
| 123_I | 126_N | 1.092 | 0.96 |
| 107_F | 110_C | 1.083 | 0.96 |
| 80_I | 84_A | 1.071 | 0.95 |
| 34_G | 37_T | 1.064 | 0.95 |
| 32_Q | 36_Y | 1.063 | 0.95 |
| 122_L | 145_V | 1.056 | 0.95 |
| 32_Q | 37_T | 1.056 | 0.95 |
| 35_P | 39_E | 1.055 | 0.95 |
| 116_V | 133_C | 1.052 | 0.95 |
| 36_Y | 39_E | 1.050 | 0.94 |
| 57_G | 61_A | 1.049 | 0.94 |
| 56_A | 62_D | 1.045 | 0.94 |
| 66_S | 89_N | 1.042 | 0.94 |
| 126_N | 129_A | 1.041 | 0.94 |
| 102_I | 107_F | 1.040 | 0.94 |
| 107_F | 152_F | 1.027 | 0.94 |
| 102_I | 125_I | 1.024 | 0.93 |
| 100_I | 123_I | 1.015 | 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 | |
| 3zyiA | 1 | 0.8059 | 99.6 | 0.453 | Contact Map |
| 3t6qA | 2 | 0.7824 | 99.6 | 0.454 | Contact Map |
| 4hq1A | 1 | 0.8529 | 99.6 | 0.473 | Contact Map |
| 3zyjA | 2 | 0.8059 | 99.6 | 0.479 | Contact Map |
| 2id5A | 4 | 0.8059 | 99.6 | 0.484 | Contact Map |
| 4gt6A | 1 | 0.8353 | 99.6 | 0.484 | Contact Map |
| 1ziwA | 1 | 0.7471 | 99.6 | 0.486 | Contact Map |
| 4kt1A | 1 | 0.8059 | 99.6 | 0.486 | Contact Map |
| 2z63A | 1 | 0.7824 | 99.6 | 0.487 | Contact Map |
| 4cnmA | 1 | 0.8235 | 99.5 | 0.49 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)