| THIO_ALIAC |
| ID: | 1430407820 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 103 (100) | ||
| Sequences: | 14772 (10981) | ||
| Seq/Len: | 147.720 | ||
| Nf(neff/√len): | 1098.1 |
HHblits Results: (2013_03)
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: 147.720).
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 |
| 83_P | 86_Q | 2.403 | 1.00 |
| 41_E | 93_K | 2.239 | 1.00 |
| 45_A | 97_E | 2.231 | 1.00 |
| 97_E | 101_A | 2.123 | 1.00 |
| 19_P | 79_K | 2.119 | 1.00 |
| 76_I | 86_Q | 2.086 | 1.00 |
| 85_K | 99_Q | 2.043 | 1.00 |
| 20_V | 51_T | 2.033 | 1.00 |
| 18_K | 51_T | 1.845 | 1.00 |
| 29_C | 32_C | 1.817 | 1.00 |
| 92_P | 95_Q | 1.783 | 1.00 |
| 5_L | 53_A | 1.768 | 1.00 |
| 57_V | 64_T | 1.737 | 1.00 |
| 11_Q | 66_Q | 1.736 | 1.00 |
| 36_A | 54_K | 1.708 | 1.00 |
| 57_V | 72_I | 1.705 | 1.00 |
| 76_I | 83_P | 1.693 | 1.00 |
| 7_D | 62_E | 1.664 | 1.00 |
| 67_F | 78_F | 1.622 | 1.00 |
| 35_M | 75_L | 1.575 | 1.00 |
| 25_W | 54_K | 1.559 | 1.00 |
| 38_V | 93_K | 1.505 | 1.00 |
| 9_N | 13_A | 1.479 | 1.00 |
| 34_M | 90_Y | 1.429 | 1.00 |
| 46_H | 101_A | 1.425 | 1.00 |
| 93_K | 97_E | 1.402 | 0.99 |
| 7_D | 63_T | 1.400 | 0.99 |
| 46_H | 97_E | 1.389 | 0.99 |
| 6_T | 9_N | 1.389 | 0.99 |
| 78_F | 83_P | 1.378 | 0.99 |
| 20_V | 53_A | 1.299 | 0.99 |
| 45_A | 93_K | 1.297 | 0.99 |
| 19_P | 77_L | 1.283 | 0.99 |
| 87_L | 91_Q | 1.279 | 0.99 |
| 27_A | 56_N | 1.267 | 0.99 |
| 21_L | 75_L | 1.261 | 0.99 |
| 38_V | 41_E | 1.259 | 0.99 |
| 23_D | 75_L | 1.253 | 0.99 |
| 7_D | 60_N | 1.242 | 0.98 |
| 23_D | 36_A | 1.228 | 0.98 |
| 91_Q | 95_Q | 1.227 | 0.98 |
| 24_F | 67_F | 1.219 | 0.98 |
| 5_L | 13_A | 1.218 | 0.98 |
| 87_L | 99_Q | 1.215 | 0.98 |
| 21_L | 39_L | 1.209 | 0.98 |
| 23_D | 54_K | 1.196 | 0.98 |
| 56_N | 59_E | 1.165 | 0.97 |
| 95_Q | 98_A | 1.159 | 0.97 |
| 21_L | 77_L | 1.121 | 0.97 |
| 69_I | 74_T | 1.072 | 0.95 |
| 23_D | 35_M | 1.071 | 0.95 |
| 5_L | 9_N | 1.067 | 0.95 |
| 13_A | 51_T | 1.039 | 0.94 |
| 22_V | 78_F | 1.036 | 0.94 |
| 77_L | 99_Q | 1.033 | 0.94 |
| 13_A | 53_A | 1.009 | 0.93 |
| 6_T | 60_N | 1.002 | 0.92 |
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 | |
| 2vocA | 2 | 0.9903 | 99.8 | 0.03 | Contact Map |
| 2yzuA | 1 | 1 | 99.8 | 0.031 | Contact Map |
| 2yj7A | 2 | 1 | 99.8 | 0.032 | Contact Map |
| 2r2jA | 1 | 0.9806 | 99.8 | 0.041 | Contact Map |
| 3f8uA | 2 | 1 | 99.8 | 0.061 | Contact Map |
| 3wgxA | 2 | 0.9903 | 99.8 | 0.078 | Contact Map |
| 4ekzA | 1 | 1 | 99.8 | 0.078 | Contact Map |
| 2b5eA | 1 | 1 | 99.8 | 0.08 | Contact Map |
| 3apsA | 2 | 1 | 99.8 | 0.097 | Contact Map |
| 4kcaA | 2 | 0.9903 | 99.8 | 0.1 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)