| 1C9O |
| ID: | 1471612555 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 66 (65) | ||
| Sequences: | 6041 (3469.8) | ||
| Seq/Len: | 92.938 | ||
| Nf(neff/√len): | 430.4 |
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: 92.938).
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 |
| 50_E | 62_N | 2.874 | 1.00 |
| 52_V | 61_A | 2.653 | 1.00 |
| 45_Q | 65_K | 2.522 | 1.00 |
| 28_V | 63_V | 2.495 | 1.00 |
| 7_K | 25_D | 2.494 | 1.00 |
| 20_V | 49_F | 2.204 | 1.00 |
| 3_R | 48_S | 2.165 | 1.00 |
| 48_S | 64_V | 2.066 | 1.00 |
| 21_E | 46_E | 1.800 | 1.00 |
| 7_K | 19_E | 1.716 | 1.00 |
| 3_R | 46_E | 1.635 | 1.00 |
| 26_V | 51_I | 1.588 | 1.00 |
| 20_V | 26_V | 1.568 | 1.00 |
| 60_A | 63_V | 1.548 | 1.00 |
| 17_F | 27_F | 1.544 | 1.00 |
| 3_R | 21_E | 1.498 | 1.00 |
| 4_G | 18_I | 1.492 | 1.00 |
| 5_K | 46_E | 1.484 | 1.00 |
| 42_E | 45_Q | 1.463 | 1.00 |
| 2_Q | 20_V | 1.446 | 1.00 |
| 30_F | 39_K | 1.399 | 0.99 |
| 8_W | 25_D | 1.327 | 0.99 |
| 32_A | 61_A | 1.301 | 0.99 |
| 6_V | 47_V | 1.265 | 0.99 |
| 26_V | 49_F | 1.243 | 0.98 |
| 18_I | 47_V | 1.195 | 0.98 |
| 51_I | 58_P | 1.156 | 0.97 |
| 34_Q | 64_V | 1.154 | 0.97 |
| 11_N | 40_T | 1.148 | 0.97 |
| 34_Q | 62_N | 1.148 | 0.97 |
| 4_G | 49_F | 1.128 | 0.97 |
| 6_V | 28_V | 1.094 | 0.96 |
| 53_Q | 58_P | 1.040 | 0.94 |
| 19_E | 25_D | 1.033 | 0.94 |
| 52_V | 59_Q | 1.028 | 0.94 |
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 | |
| 1c9oA | 2 | 1 | 99.6 | -0.093 | Contact Map |
| 2lxjA | 1 | 1 | 99.6 | -0.089 | Contact Map |
| 3a0jA | 2 | 1 | 99.6 | -0.078 | Contact Map |
| 3camA | 2 | 1 | 99.6 | -0.072 | Contact Map |
| 3i2zB | 2 | 1 | 99.6 | -0.062 | Contact Map |
| 1g6pA | 1 | 0.9848 | 99.6 | -0.06 | Contact Map |
| 2kcmA | 1 | 0.9848 | 99.6 | -0.055 | Contact Map |
| 2lssA | 1 | 1 | 99.5 | -0.042 | Contact Map |
| 3uljA | 2 | 1 | 99.5 | -0.03 | Contact Map |
| 2mqhA | 1 | 0 | 99.5 | -0.028 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)