| wdcuarenta |
| ID: | 1431614887 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 71 (71) | ||
| Sequences: | 49625 (34878.1) | ||
| Seq/Len: | 698.944 | ||
| Nf(neff/√len): | 4139.3 |
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: 698.944).
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 |
| 14_S | 50_D | 2.604 | 1.00 |
| 48_G | 61_G | 2.562 | 1.00 |
| 59_V | 69_V | 2.497 | 1.00 |
| 12_G | 25_S | 2.494 | 1.00 |
| 11_K | 27_H | 2.470 | 1.00 |
| 47_R | 63_D | 2.342 | 1.00 |
| 23_L | 33_L | 2.250 | 1.00 |
| 23_L | 51_F | 2.182 | 1.00 |
| 16_H | 51_F | 2.039 | 1.00 |
| 6_K | 24_T | 1.885 | 1.00 |
| 31_I | 60_S | 1.826 | 1.00 |
| 23_L | 58_F | 1.805 | 1.00 |
| 32_Q | 38_K | 1.762 | 1.00 |
| 42_H | 60_S | 1.713 | 1.00 |
| 12_G | 48_G | 1.654 | 1.00 |
| 25_S | 49_I | 1.471 | 1.00 |
| 52_H | 57_L | 1.447 | 1.00 |
| 27_H | 45_P | 1.413 | 1.00 |
| 23_L | 49_I | 1.389 | 0.99 |
| 14_S | 49_I | 1.293 | 0.99 |
| 6_K | 26_L | 1.246 | 0.98 |
| 42_H | 62_G | 1.225 | 0.98 |
| 60_S | 68_K | 1.222 | 0.98 |
| 24_T | 32_Q | 1.221 | 0.98 |
| 5_T | 34_W | 1.205 | 0.98 |
| 41_E | 68_K | 1.174 | 0.98 |
| 15_F | 22_I | 1.142 | 0.97 |
| 26_L | 30_V | 1.139 | 0.97 |
| 41_E | 70_W | 1.100 | 0.96 |
| 16_H | 21_W | 1.095 | 0.96 |
| 30_V | 38_K | 1.087 | 0.96 |
| 45_P | 63_D | 1.087 | 0.96 |
| 5_T | 32_Q | 1.077 | 0.95 |
| 24_T | 34_W | 1.039 | 0.94 |
| 57_L | 69_V | 1.029 | 0.94 |
| 62_G | 66_K | 1.017 | 0.93 |
| 25_S | 46_V | 1.004 | 0.93 |
| 12_G | 49_I | 1.003 | 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 | |
| 2ymuA | 2 | 1 | 99.1 | -0.107 | Contact Map |
| 4u1eI | 1 | 1 | 99.1 | -0.103 | Contact Map |
| 4wjsA | 1 | 1 | 99.1 | -0.082 | Contact Map |
| 3f3fA | 4 | 1 | 99 | -0.068 | Contact Map |
| 3sfzA | 1 | 1 | 99 | -0.062 | Contact Map |
| 1vyhC | 10 | 1 | 99 | -0.058 | Contact Map |
| 3dm0A | 1 | 1 | 98.9 | -0.042 | Contact Map |
| 3vu4A | 2 | 1 | 98.9 | -0.033 | Contact Map |
| 3j80g | 1 | 1 | 98.9 | -0.03 | Contact Map |
| 4j87A | 1 | 1 | 98.9 | -0.029 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)