| 5pti |
| ID: | 1408344119 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 58 (56) | ||
| Sequences: | 1771 (1355.4) | ||
| Seq/Len: | 31.625 | ||
| Nf(neff/√len): | 181.1 |
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: 31.625).
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_C | 38_C | 5.399 | 1.00 |
| 20_R | 44_N | 3.653 | 1.00 |
| 24_N | 31_Q | 3.308 | 1.00 |
| 48_A | 52_M | 2.742 | 1.00 |
| 27_A | 31_Q | 2.303 | 1.00 |
| 17_R | 34_V | 2.187 | 1.00 |
| 9_P | 22_F | 1.798 | 1.00 |
| 52_M | 56_G | 1.627 | 1.00 |
| 21_Y | 48_A | 1.608 | 1.00 |
| 20_R | 46_K | 1.556 | 1.00 |
| 13_P | 36_G | 1.496 | 1.00 |
| 47_S | 50_D | 1.318 | 0.99 |
| 7_E | 42_R | 1.303 | 0.99 |
| 7_E | 45_F | 1.300 | 0.99 |
| 11_T | 36_G | 1.294 | 0.99 |
| 40_A | 44_N | 1.278 | 0.99 |
| 13_P | 39_R | 1.261 | 0.99 |
| 22_F | 31_Q | 1.243 | 0.98 |
| 37_G | 40_A | 1.239 | 0.98 |
| 51_C | 55_C | 1.203 | 0.98 |
| 19_I | 32_T | 1.193 | 0.98 |
| 4_F | 54_T | 1.177 | 0.98 |
| 41_K | 44_N | 1.137 | 0.97 |
| 10_Y | 40_A | 1.130 | 0.97 |
| 46_K | 50_D | 1.045 | 0.94 |
| 4_F | 45_F | 1.010 | 0.93 |
| 12_G | 44_N | 1.010 | 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 | |
| 1g6xA | 1 | 1 | 99.5 | -0.005 | Contact Map |
| 3aubA | 2 | 1 | 99.5 | -0.004 | Contact Map |
| 4dtgK | 1 | 1 | 99.5 | 0.001 | Contact Map |
| 2ddiA | 1 | 1 | 99.5 | 0.01 | Contact Map |
| 4bqdA | 2 | 1 | 99.5 | 0.01 | Contact Map |
| 1co7I | 1 | 0.7069 | 99.5 | 0.011 | Contact Map |
| 3augA | 2 | 1 | 99.5 | 0.012 | Contact Map |
| 1bf0A | 1 | 1 | 99.5 | 0.015 | Contact Map |
| 2m99A | 1 | 0.9828 | 99.5 | 0.023 | Contact Map |
| 1jc6A | 1 | 1 | 99.5 | 0.025 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)