| 1A1IA |
| ID: | 1411065995 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 85 (82) | ||
| Sequences: | 26981 (20934.8) | ||
| Seq/Len: | 329.037 | ||
| Nf(neff/√len): | 2311.9 |
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: 329.037).
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 |
| 36_R | 64_D | 2.223 | 1.00 |
| 36_R | 52_I | 1.880 | 1.00 |
| 6_P | 36_R | 1.876 | 1.00 |
| 64_D | 80_T | 1.842 | 1.00 |
| 62_A | 69_K | 1.838 | 1.00 |
| 37_I | 65_I | 1.815 | 1.00 |
| 34_Q | 41_N | 1.789 | 1.00 |
| 6_P | 64_D | 1.746 | 1.00 |
| 21_T | 77_K | 1.703 | 1.00 |
| 21_T | 49_T | 1.701 | 1.00 |
| 49_T | 77_K | 1.649 | 1.00 |
| 34_Q | 62_A | 1.567 | 1.00 |
| 34_Q | 39_M | 1.449 | 1.00 |
| 4_A | 11_D | 1.447 | 1.00 |
| 63_C | 66_C | 1.446 | 1.00 |
| 47_H | 50_T | 1.445 | 1.00 |
| 19_D | 22_R | 1.436 | 1.00 |
| 16_R | 19_D | 1.425 | 1.00 |
| 37_I | 52_I | 1.421 | 1.00 |
| 6_P | 24_I | 1.406 | 0.99 |
| 4_A | 62_A | 1.395 | 0.99 |
| 52_I | 80_T | 1.392 | 0.99 |
| 4_A | 13_R | 1.380 | 0.99 |
| 45_S | 49_T | 1.369 | 0.99 |
| 44_R | 47_H | 1.358 | 0.99 |
| 17_S | 21_T | 1.357 | 0.99 |
| 72_R | 75_E | 1.355 | 0.99 |
| 24_I | 52_I | 1.347 | 0.99 |
| 73_S | 77_K | 1.341 | 0.99 |
| 24_I | 80_T | 1.339 | 0.99 |
| 4_A | 34_Q | 1.331 | 0.99 |
| 62_A | 67_G | 1.313 | 0.99 |
| 65_I | 80_T | 1.299 | 0.99 |
| 9_S | 37_I | 1.252 | 0.99 |
| 22_R | 78_R | 1.245 | 0.98 |
| 9_S | 65_I | 1.234 | 0.98 |
| 41_N | 69_K | 1.224 | 0.98 |
| 13_R | 69_K | 1.195 | 0.98 |
| 22_R | 50_T | 1.188 | 0.98 |
| 23_H | 27_H | 1.167 | 0.97 |
| 9_S | 24_I | 1.156 | 0.97 |
| 13_R | 41_N | 1.145 | 0.97 |
| 40_R | 68_R | 1.119 | 0.96 |
| 50_T | 78_R | 1.098 | 0.96 |
| 5_C | 10_C | 1.087 | 0.96 |
| 6_P | 9_S | 1.060 | 0.95 |
| 75_E | 78_R | 1.041 | 0.94 |
| 49_T | 52_I | 1.030 | 0.94 |
| 66_C | 79_H | 1.029 | 0.94 |
| 17_S | 45_S | 1.020 | 0.93 |
| 12_R | 68_R | 1.014 | 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 | |
| 1a1hA | 1 | 1 | 99.5 | -0.019 | Contact Map |
| 3w5kB | 1 | 0.9529 | 99.5 | -0.007 | Contact Map |
| 2jp9A | 1 | 0.9765 | 99.5 | -0.005 | Contact Map |
| 2kmkA | 1 | 0.9647 | 99.5 | -0.005 | Contact Map |
| 2dmdA | 1 | 0.9765 | 99.4 | 0.021 | Contact Map |
| 2ee8A | 1 | 0.9765 | 99.4 | 0.025 | Contact Map |
| 2ebtA | 1 | 1 | 99.4 | 0.031 | Contact Map |
| 2wbsA | 1 | 0.9882 | 99.4 | 0.045 | Contact Map |
| 2yt9A | 1 | 0.9765 | 99.4 | 0.046 | Contact Map |
| 2i13A | 2 | 0.9529 | 99.4 | 0.056 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)