| THIO_4ekz_only_seq |
| ID: | 1444814709 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 110 (108) | ||
| Sequences: | 24683 (16572.5) | ||
| Seq/Len: | 228.546 | ||
| Nf(neff/√len): | 1594.7 |
HHblits Results: (2015_06)
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: 228.546).
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 |
| 60_A | 67_A | 2.247 | 1.00 |
| 41_K | 98_A | 2.156 | 1.00 |
| 86_T | 91_E | 2.087 | 1.00 |
| 45_K | 102_V | 2.076 | 1.00 |
| 79_K | 91_E | 2.065 | 1.00 |
| 102_V | 106_K | 2.014 | 1.00 |
| 20_L | 54_R | 1.969 | 1.00 |
| 29_C | 32_C | 1.966 | 1.00 |
| 18_K | 54_R | 1.836 | 1.00 |
| 11_A | 69_Q | 1.811 | 1.00 |
| 25_Y | 57_K | 1.809 | 1.00 |
| 35_L | 78_I | 1.748 | 1.00 |
| 60_A | 75_Y | 1.745 | 1.00 |
| 79_K | 86_T | 1.729 | 1.00 |
| 36_A | 57_K | 1.727 | 1.00 |
| 70_Y | 81_F | 1.708 | 1.00 |
| 97_E | 100_D | 1.672 | 1.00 |
| 20_L | 56_A | 1.625 | 1.00 |
| 21_L | 78_I | 1.602 | 1.00 |
| 46_L | 102_V | 1.602 | 1.00 |
| 90_K | 104_W | 1.584 | 1.00 |
| 7_K | 65_D | 1.582 | 1.00 |
| 19_Y | 82_R | 1.510 | 1.00 |
| 46_L | 106_K | 1.482 | 1.00 |
| 6_R | 9_N | 1.476 | 1.00 |
| 38_E | 98_A | 1.467 | 1.00 |
| 23_E | 57_K | 1.461 | 1.00 |
| 7_K | 66_L | 1.432 | 1.00 |
| 19_Y | 80_F | 1.408 | 1.00 |
| 104_W | 108_R | 1.404 | 0.99 |
| 81_F | 86_T | 1.396 | 0.99 |
| 23_E | 78_I | 1.392 | 0.99 |
| 80_F | 108_R | 1.381 | 0.99 |
| 98_A | 102_V | 1.365 | 0.99 |
| 92_Y | 96_R | 1.365 | 0.99 |
| 7_K | 63_E | 1.360 | 0.99 |
| 38_E | 41_K | 1.346 | 0.99 |
| 45_K | 98_A | 1.323 | 0.99 |
| 92_Y | 104_W | 1.308 | 0.99 |
| 9_N | 13_A | 1.307 | 0.99 |
| 27_P | 59_D | 1.300 | 0.99 |
| 5_L | 56_A | 1.299 | 0.99 |
| 34_A | 95_G | 1.281 | 0.99 |
| 24_F | 70_Y | 1.263 | 0.99 |
| 22_V | 81_F | 1.251 | 0.99 |
| 82_R | 87_A | 1.229 | 0.98 |
| 23_E | 36_A | 1.184 | 0.98 |
| 72_V | 77_T | 1.160 | 0.97 |
| 104_W | 107_K | 1.148 | 0.97 |
| 23_E | 35_L | 1.118 | 0.96 |
| 100_D | 103_N | 1.118 | 0.96 |
| 24_F | 60_A | 1.116 | 0.96 |
| 13_A | 56_A | 1.091 | 0.96 |
| 31_H | 34_A | 1.080 | 0.95 |
| 35_L | 96_R | 1.056 | 0.95 |
| 24_F | 72_V | 1.051 | 0.94 |
| 82_R | 85_D | 1.049 | 0.94 |
| 80_F | 104_W | 1.043 | 0.94 |
| 42_A | 102_V | 1.040 | 0.94 |
| 21_L | 39_Y | 1.025 | 0.93 |
| 26_A | 75_Y | 1.023 | 0.93 |
| 59_D | 62_E | 1.011 | 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 | |
| 3f8uA | 2 | 0.9545 | 99.8 | -0.035 | Contact Map |
| 2b5eA | 1 | 0.9818 | 99.7 | -0.028 | Contact Map |
| 2r2jA | 1 | 0.9727 | 99.7 | -0.027 | Contact Map |
| 4ekzA | 1 | 1 | 99.7 | -0.025 | Contact Map |
| 3apoA | 1 | 0.8818 | 99.7 | -0.02 | Contact Map |
| 3idvA | 1 | 0.9727 | 99.7 | 0.024 | Contact Map |
| 3apqA | 2 | 0.9545 | 99.7 | 0.037 | Contact Map |
| 3ed3A | 2 | 0.9636 | 99.7 | 0.038 | Contact Map |
| 1sjiA | 2 | 0.9545 | 99.7 | 0.039 | Contact Map |
| 4kcaA | 2 | 0.9455 | 99.7 | 0.041 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)