| AP test 1ALK |
| ID: | 1494442508 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 55 (50) | ||
| Sequences: | 650 (412) | ||
| Seq/Len: | 13.000 | ||
| Nf(neff/√len): | 58.3 |
HHblits Results: (2016_02)
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: 13.000).
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_Q | 22_Y | 3.962 | 1.00 |
| 46_E | 50_N | 3.549 | 1.00 |
| 14_A | 44_I | 2.935 | 1.00 |
| 8_T | 11_A | 2.287 | 1.00 |
| 9_P | 19_R | 2.241 | 1.00 |
| 42_G | 46_E | 1.897 | 1.00 |
| 17_T | 21_C | 1.714 | 1.00 |
| 7_A | 19_R | 1.694 | 1.00 |
| 23_G | 26_A | 1.605 | 1.00 |
| 5_Q | 45_T | 1.526 | 1.00 |
| 6_D | 9_P | 1.488 | 1.00 |
| 3_E | 6_D | 1.446 | 1.00 |
| 31_C | 41_K | 1.428 | 1.00 |
| 6_D | 19_R | 1.314 | 0.99 |
| 2_A | 6_D | 1.288 | 0.99 |
| 13_V | 48_L | 1.264 | 0.99 |
| 6_D | 22_Y | 1.252 | 0.99 |
| 3_E | 22_Y | 1.187 | 0.98 |
| 4_L | 15_H | 1.170 | 0.97 |
| 28_S | 31_C | 1.147 | 0.97 |
| 2_A | 9_P | 1.140 | 0.97 |
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 | |
| 1k7hA | 2 | 0.9273 | 99.5 | 0.207 | Contact Map |
| 1zedA | 1 | 0.9091 | 99.3 | 0.28 | Contact Map |
| 3e2dA | 2 | 0.6545 | 99.2 | 0.314 | Contact Map |
| 3tg0A | 4 | 1 | 98.9 | 0.412 | Contact Map |
| 2x98A | 2 | 0.6545 | 98.6 | 0.474 | Contact Map |
| 3a52A | 2 | 0.6545 | 97.9 | 0.559 | Contact Map |
| 3wbhA | 2 | 0.6545 | 97.9 | 0.56 | Contact Map |
| 2w5vA | 2 | 1 | 81.3 | 0.767 | Contact Map |
| 3htxA | 2 | 0.4727 | 3.6 | 0.892 | Contact Map |
| 4kngE | 2 | 0.1818 | 3.5 | 0.893 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)