| txnl4b |
| ID: | 1517314905 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 149 (98) | ||
| Sequences: | 58794 (42240.1) | ||
| Seq/Len: | 599.939 | ||
| Nf(neff/√len): | 4266.9 |
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: 599.939).
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 |
| 47_K | 99_H | 2.244 | 1.00 |
| 26_L | 57_A | 2.112 | 1.00 |
| 51_D | 103_V | 2.047 | 1.00 |
| 103_V | 107_K | 2.037 | 1.00 |
| 35_D | 38_C | 1.988 | 1.00 |
| 63_V | 70_T | 1.969 | 1.00 |
| 91_K | 105_S | 1.903 | 1.00 |
| 25_V | 85_F | 1.848 | 1.00 |
| 99_H | 103_V | 1.793 | 1.00 |
| 24_K | 57_A | 1.769 | 1.00 |
| 26_L | 59_Y | 1.746 | 1.00 |
| 89_H | 92_V | 1.731 | 1.00 |
| 52_L | 103_V | 1.650 | 1.00 |
| 31_G | 60_L | 1.645 | 1.00 |
| 98_D | 101_K | 1.633 | 1.00 |
| 82_V | 92_V | 1.616 | 1.00 |
| 42_D | 60_L | 1.573 | 1.00 |
| 13_E | 17_A | 1.552 | 1.00 |
| 44_I | 99_H | 1.522 | 1.00 |
| 93_D | 97_P | 1.509 | 1.00 |
| 52_L | 107_K | 1.500 | 1.00 |
| 11_K | 68_V | 1.446 | 1.00 |
| 51_D | 99_H | 1.435 | 1.00 |
| 63_V | 78_I | 1.427 | 1.00 |
| 81_T | 84_F | 1.410 | 1.00 |
| 37_V | 40_Q | 1.410 | 1.00 |
| 15_D | 72_Y | 1.407 | 0.99 |
| 84_F | 88_Q | 1.370 | 0.99 |
| 41_L | 81_T | 1.369 | 0.99 |
| 29_R | 41_L | 1.311 | 0.99 |
| 49_S | 53_S | 1.303 | 0.99 |
| 44_I | 47_K | 1.290 | 0.99 |
| 101_K | 104_G | 1.289 | 0.99 |
| 73_F | 84_F | 1.287 | 0.99 |
| 105_S | 108_T | 1.256 | 0.99 |
| 40_Q | 96_S | 1.244 | 0.98 |
| 42_D | 46_S | 1.243 | 0.98 |
| 82_V | 89_H | 1.222 | 0.98 |
| 48_T | 52_L | 1.207 | 0.98 |
| 29_R | 42_D | 1.173 | 0.98 |
| 32_R | 78_I | 1.171 | 0.98 |
| 11_K | 69_Y | 1.160 | 0.97 |
| 46_S | 50_S | 1.131 | 0.97 |
| 29_R | 60_L | 1.130 | 0.97 |
| 68_V | 72_Y | 1.128 | 0.97 |
| 15_D | 19_K | 1.126 | 0.97 |
| 33_D | 62_D | 1.120 | 0.96 |
| 97_P | 101_K | 1.118 | 0.96 |
| 11_K | 66_T | 1.112 | 0.96 |
| 69_Y | 73_F | 1.070 | 0.95 |
| 25_V | 83_F | 1.051 | 0.94 |
| 84_F | 89_H | 1.026 | 0.94 |
| 17_A | 59_Y | 1.019 | 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 | |
| 1qgvA | 1 | 0.8322 | 99.8 | 0.344 | Contact Map |
| 3gixA | 2 | 0.8792 | 99.8 | 0.35 | Contact Map |
| 2av4A | 1 | 0.8255 | 99.8 | 0.355 | Contact Map |
| 4oo4A | 2 | 0.7047 | 99.8 | 0.395 | Contact Map |
| 2r2jA | 1 | 0.8456 | 99.8 | 0.397 | Contact Map |
| 3f8uA | 2 | 0.9664 | 99.8 | 0.398 | Contact Map |
| 3apoA | 1 | 0.906 | 99.8 | 0.399 | Contact Map |
| 4i6xA | 1 | 0.7383 | 99.8 | 0.401 | Contact Map |
| 2yoiA | 2 | 0.7114 | 99.8 | 0.407 | Contact Map |
| 1xwbA | 4 | 0.7114 | 99.8 | 0.409 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)