| Ance_R5all |
| ID: | 1510607168 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 65 (63) | ||
| Sequences: | 8403 (3604.9) | ||
| Seq/Len: | 133.381 | ||
| Nf(neff/√len): | 454.2 |
Jackhmmer Results: (2016_04)
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: 133.381).
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 |
| 51_G | 60_E | 3.627 | 1.00 |
| 27_V | 62_V | 3.432 | 1.00 |
| 49_S | 61_N | 3.192 | 1.00 |
| 7_K | 24_D | 2.512 | 1.00 |
| 52_S | 57_P | 2.195 | 1.00 |
| 20_D | 45_R | 2.076 | 1.00 |
| 3_Q | 47_S | 1.915 | 1.00 |
| 53_G | 56_G | 1.877 | 1.00 |
| 3_Q | 45_R | 1.865 | 1.00 |
| 5_T | 45_R | 1.783 | 1.00 |
| 19_T | 48_Y | 1.777 | 1.00 |
| 25_M | 50_V | 1.675 | 1.00 |
| 41_Q | 44_Q | 1.654 | 1.00 |
| 19_T | 23_Q | 1.645 | 1.00 |
| 19_T | 22_G | 1.612 | 1.00 |
| 33_D | 61_N | 1.576 | 1.00 |
| 50_V | 57_P | 1.565 | 1.00 |
| 31_N | 60_E | 1.535 | 1.00 |
| 3_Q | 20_D | 1.440 | 1.00 |
| 27_V | 40_L | 1.423 | 1.00 |
| 53_G | 58_R | 1.392 | 0.99 |
| 33_D | 63_R | 1.343 | 0.99 |
| 29_C | 38_E | 1.342 | 0.99 |
| 47_S | 63_R | 1.260 | 0.99 |
| 29_C | 32_I | 1.232 | 0.98 |
| 17_I | 46_V | 1.190 | 0.98 |
| 19_T | 25_M | 1.183 | 0.98 |
| 51_G | 58_R | 1.165 | 0.97 |
| 23_Q | 57_P | 1.159 | 0.97 |
| 31_N | 58_R | 1.151 | 0.97 |
| 48_Y | 59_A | 1.146 | 0.97 |
| 7_K | 18_A | 1.030 | 0.94 |
| 32_I | 40_L | 1.029 | 0.94 |
| 17_I | 48_Y | 1.001 | 0.92 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2lxjA | 1 | 1 | 99.7 | 0.111 | Contact Map |
| 1c9oA | 2 | 1 | 99.7 | 0.118 | Contact Map |
| 3camA | 2 | 1 | 99.7 | 0.121 | Contact Map |
| 3a0jA | 2 | 1 | 99.7 | 0.128 | Contact Map |
| 3i2zB | 2 | 1 | 99.7 | 0.139 | Contact Map |
| 1g6pA | 1 | 0.9846 | 99.7 | 0.152 | Contact Map |
| 1wfqA | 1 | 0.9692 | 99.7 | 0.156 | Contact Map |
| 2mqhA | 1 | 0 | 99.7 | 0.158 | Contact Map |
| 2ytxA | 1 | 0.9692 | 99.7 | 0.164 | Contact Map |
| 1h95A | 1 | 1 | 99.7 | 0.166 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)