| cbd |
| ID: | 1516628646 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 216 (211) | ||
| Sequences: | 3047 (2730.7) | ||
| Seq/Len: | 14.441 | ||
| Nf(neff/√len): | 188.0 |
Jackhmmer Results: (2016_04)
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: 14.441).
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 |
| 31_R | 43_E | 5.068 | 1.00 |
| 42_E | 49_V | 4.539 | 1.00 |
| 104_E | 152_T | 3.830 | 1.00 |
| 32_A | 46_P | 3.497 | 1.00 |
| 34_L | 49_V | 3.383 | 1.00 |
| 102_F | 152_T | 3.015 | 1.00 |
| 102_F | 154_K | 3.005 | 1.00 |
| 84_R | 104_E | 2.976 | 1.00 |
| 8_H | 13_G | 2.917 | 1.00 |
| 33_I | 43_E | 2.832 | 1.00 |
| 36_H | 41_I | 2.797 | 1.00 |
| 124_D | 128_Q | 2.758 | 1.00 |
| 87_S | 91_Y | 2.742 | 1.00 |
| 42_E | 52_A | 2.635 | 1.00 |
| 79_V | 110_K | 2.601 | 1.00 |
| 100_T | 154_K | 2.552 | 1.00 |
| 72_G | 182_H | 2.484 | 1.00 |
| 100_T | 156_P | 2.459 | 1.00 |
| 45_S | 48_T | 2.447 | 1.00 |
| 81_K | 108_E | 2.387 | 1.00 |
| 34_L | 56_L | 2.383 | 1.00 |
| 163_K | 191_E | 2.339 | 1.00 |
| 107_V | 149_Y | 2.264 | 1.00 |
| 82_E | 106_D | 2.253 | 1.00 |
| 112_D | 145_K | 2.168 | 1.00 |
| 86_K | 104_E | 2.155 | 1.00 |
| 21_D | 24_A | 2.148 | 1.00 |
| 112_D | 146_K | 2.116 | 1.00 |
| 4_K | 7_E | 2.004 | 1.00 |
| 32_A | 49_V | 1.957 | 1.00 |
| 33_I | 40_I | 1.947 | 1.00 |
| 104_E | 150_L | 1.890 | 1.00 |
| 106_D | 150_L | 1.877 | 1.00 |
| 6_K | 9_K | 1.876 | 1.00 |
| 9_K | 30_D | 1.862 | 1.00 |
| 34_L | 41_I | 1.850 | 1.00 |
| 78_A | 170_L | 1.818 | 1.00 |
| 36_H | 56_L | 1.814 | 1.00 |
| 95_F | 101_L | 1.782 | 1.00 |
| 79_V | 108_E | 1.675 | 1.00 |
| 22_M | 50_T | 1.644 | 1.00 |
| 83_V | 168_V | 1.575 | 1.00 |
| 122_I | 190_F | 1.571 | 1.00 |
| 77_K | 111_E | 1.549 | 1.00 |
| 7_E | 11_K | 1.518 | 1.00 |
| 6_K | 27_I | 1.507 | 1.00 |
| 26_K | 47_E | 1.501 | 1.00 |
| 108_E | 149_Y | 1.494 | 1.00 |
| 9_K | 15_I | 1.493 | 1.00 |
| 184_I | 187_V | 1.476 | 1.00 |
| 34_L | 52_A | 1.476 | 1.00 |
| 4_K | 13_G | 1.470 | 1.00 |
| 96_P | 99_D | 1.430 | 1.00 |
| 19_S | 25_V | 1.426 | 1.00 |
| 26_K | 50_T | 1.424 | 1.00 |
| 2_F | 8_H | 1.421 | 1.00 |
| 44_G | 48_T | 1.403 | 0.99 |
| 3_R | 7_E | 1.396 | 0.99 |
| 5_L | 28_L | 1.379 | 0.99 |
| 7_E | 10_Q | 1.360 | 0.99 |
| 88_E | 99_D | 1.325 | 0.99 |
| 119_G | 132_G | 1.324 | 0.99 |
| 5_L | 8_H | 1.313 | 0.99 |
| 84_R | 106_D | 1.310 | 0.99 |
| 76_F | 79_V | 1.295 | 0.99 |
| 19_S | 28_L | 1.287 | 0.99 |
| 123_R | 129_D | 1.281 | 0.99 |
| 26_K | 51_Q | 1.280 | 0.99 |
| 6_K | 10_Q | 1.278 | 0.99 |
| 108_E | 148_K | 1.276 | 0.99 |
| 40_I | 43_E | 1.275 | 0.99 |
| 34_L | 42_E | 1.273 | 0.99 |
| 101_L | 157_L | 1.264 | 0.99 |
| 17_F | 25_V | 1.252 | 0.99 |
| 106_D | 148_K | 1.202 | 0.98 |
| 25_V | 32_A | 1.202 | 0.98 |
| 119_G | 134_N | 1.200 | 0.98 |
| 4_K | 8_H | 1.192 | 0.98 |
| 122_I | 159_L | 1.173 | 0.98 |
| 95_F | 99_D | 1.171 | 0.98 |
| 84_R | 92_T | 1.136 | 0.97 |
| 42_E | 48_T | 1.134 | 0.97 |
| 2_F | 6_K | 1.118 | 0.96 |
| 105_L | 118_A | 1.103 | 0.96 |
| 109_A | 144_L | 1.080 | 0.95 |
| 17_F | 24_A | 1.050 | 0.94 |
| 2_F | 13_G | 1.027 | 0.94 |
| 87_S | 90_G | 1.022 | 0.93 |
| 23_N | 27_I | 1.018 | 0.93 |
| 49_V | 52_A | 1.017 | 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 | |
| 2r5oA | 2 | 0.7454 | 99.8 | 0.58 | Contact Map |
| 1vplA | 1 | 0.3102 | 99 | 0.755 | Contact Map |
| 2oljA | 2 | 0.3056 | 98.9 | 0.757 | Contact Map |
| 1b0uA | 1 | 0.3102 | 98.9 | 0.76 | Contact Map |
| 4u00A | 1 | 0 | 98.9 | 0.76 | Contact Map |
| 4ymuJ | 2 | 0 | 98.9 | 0.762 | Contact Map |
| 4wbsA | 2 | 0.3009 | 98.9 | 0.763 | Contact Map |
| 1g6hA | 1 | 0.3056 | 98.8 | 0.765 | Contact Map |
| 4rvcA | 1 | 0.3194 | 98.8 | 0.766 | Contact Map |
| 3tuiC | 4 | 0.7037 | 98.8 | 0.766 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)