| armTRY2 |
| ID: | 1431624536 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 81 (80) | ||
| Sequences: | 2852 (1714.2) | ||
| Seq/Len: | 35.650 | ||
| Nf(neff/√len): | 191.7 |
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: 35.650).
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 |
| 5_E | 9_Q | 3.023 | 1.00 |
| 47_K | 51_D | 2.828 | 1.00 |
| 15_R | 18_Q | 1.997 | 1.00 |
| 34_W | 75_W | 1.954 | 1.00 |
| 58_F | 76_A | 1.894 | 1.00 |
| 21_T | 60_K | 1.872 | 1.00 |
| 75_W | 78_G | 1.663 | 1.00 |
| 40_A | 49_V | 1.610 | 1.00 |
| 65_S | 69_V | 1.593 | 1.00 |
| 34_W | 37_T | 1.575 | 1.00 |
| 19_F | 28_L | 1.539 | 1.00 |
| 13_V | 48_V | 1.536 | 1.00 |
| 31_E | 34_W | 1.435 | 1.00 |
| 7_V | 12_V | 1.396 | 0.99 |
| 48_V | 52_H | 1.371 | 0.99 |
| 36_L | 76_A | 1.338 | 0.99 |
| 78_G | 81_A | 1.335 | 0.99 |
| 30_F | 66_S | 1.334 | 0.99 |
| 34_W | 38_N | 1.329 | 0.99 |
| 37_T | 75_W | 1.322 | 0.99 |
| 21_T | 57_I | 1.305 | 0.99 |
| 38_N | 79_N | 1.278 | 0.99 |
| 17_V | 54_A | 1.257 | 0.99 |
| 60_K | 63_G | 1.253 | 0.99 |
| 34_W | 78_G | 1.218 | 0.98 |
| 24_D | 28_L | 1.187 | 0.98 |
| 70_R | 74_V | 1.179 | 0.98 |
| 49_V | 54_A | 1.165 | 0.97 |
| 26_P | 29_Q | 1.164 | 0.97 |
| 16_F | 35_A | 1.148 | 0.97 |
| 61_L | 69_V | 1.139 | 0.97 |
| 13_V | 52_H | 1.097 | 0.96 |
| 57_I | 60_K | 1.077 | 0.95 |
| 72_Q | 78_G | 1.068 | 0.95 |
| 30_F | 72_Q | 1.060 | 0.95 |
| 28_L | 39_I | 1.054 | 0.95 |
| 34_W | 46_T | 1.009 | 0.93 |
| 4_I | 39_I | 1.008 | 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 | |
| 3opbA | 2 | 0.9877 | 99.5 | 0.141 | Contact Map |
| 3tt9A | 1 | 0.9877 | 99.3 | 0.217 | Contact Map |
| 2z6gA | 1 | 0.9877 | 99.3 | 0.244 | Contact Map |
| 3l6xA | 1 | 0.9877 | 99.3 | 0.245 | Contact Map |
| 4db6A | 1 | 0.9877 | 99.3 | 0.251 | Contact Map |
| 1xm9A | 1 | 0.9877 | 99.2 | 0.255 | Contact Map |
| 2z6hA | 1 | 0.9877 | 99.2 | 0.258 | Contact Map |
| 3grlA | 1 | 0.9877 | 99.2 | 0.274 | Contact Map |
| 3nmwA | 2 | 0.9877 | 99.2 | 0.278 | Contact Map |
| 1xqrA | 2 | 1 | 99.1 | 0.287 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)