| gal4dbd 1-70 |
| ID: | 1384290151 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (67) | ||
| Sequences: | 1139 (844.1) | ||
| Seq/Len: | 17.000 | ||
| Nf(neff/√len): | 103.1 |
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: 17.000).
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 |
| 60_R | 65_E | 4.383 | 1.00 |
| 11_C | 14_C | 2.420 | 1.00 |
| 14_C | 18_K | 2.114 | 1.00 |
| 53_H | 58_E | 2.102 | 1.00 |
| 10_A | 23_K | 2.089 | 1.00 |
| 31_C | 38_C | 1.954 | 1.00 |
| 28_C | 31_C | 1.840 | 1.00 |
| 12_D | 41_S | 1.834 | 1.00 |
| 48_P | 52_A | 1.760 | 1.00 |
| 22_S | 29_A | 1.704 | 1.00 |
| 11_C | 18_K | 1.689 | 1.00 |
| 21_C | 31_C | 1.542 | 1.00 |
| 14_C | 17_K | 1.513 | 1.00 |
| 28_C | 38_C | 1.392 | 0.99 |
| 7_I | 23_K | 1.352 | 0.99 |
| 21_C | 28_C | 1.309 | 0.99 |
| 57_V | 61_L | 1.307 | 0.99 |
| 61_L | 64_L | 1.282 | 0.99 |
| 10_A | 14_C | 1.267 | 0.99 |
| 11_C | 17_K | 1.263 | 0.99 |
| 27_K | 32_L | 1.244 | 0.98 |
| 21_C | 38_C | 1.241 | 0.98 |
| 26_P | 31_C | 1.222 | 0.98 |
| 21_C | 26_P | 1.220 | 0.98 |
| 58_E | 61_L | 1.215 | 0.98 |
| 13_I | 16_L | 1.204 | 0.98 |
| 54_L | 57_V | 1.126 | 0.97 |
| 24_E | 29_A | 1.112 | 0.96 |
| 36_W | 39_R | 1.078 | 0.95 |
| 64_L | 68_F | 1.070 | 0.95 |
| 11_C | 15_R | 1.058 | 0.95 |
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 | |
| 1hwtC | 4 | 0.9571 | 99.2 | 0.226 | Contact Map |
| 1pyiA | 2 | 0.9143 | 99.2 | 0.235 | Contact Map |
| 1d66A | 2 | 0.8143 | 99.2 | 0.244 | Contact Map |
| 3coqA | 2 | 0.9 | 99.2 | 0.253 | Contact Map |
| 1zmeC | 2 | 0.8857 | 99.1 | 0.271 | Contact Map |
| 2er8A | 4 | 0.9143 | 99 | 0.298 | Contact Map |
| 1cldA | 1 | 0.4714 | 98.8 | 0.35 | Contact Map |
| 1f4sP | 1 | 0.7429 | 98.2 | 0.459 | Contact Map |
| 1hbwA | 2 | 0.3 | 43.1 | 0.796 | Contact Map |
| 2kz5A | 1 | 0.3429 | 16.7 | 0.834 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)