| T0829 |
| ID: | 1505448606 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 67 (67) | ||
| Sequences: | 654 (493) | ||
| Seq/Len: | 9.761 | ||
| Nf(neff/√len): | 60.2 |
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: 9.761).
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 |
| 2_R | 23_E | 2.979 | 1.00 |
| 23_E | 33_Q | 2.731 | 1.00 |
| 44_N | 54_F | 2.304 | 1.00 |
| 39_E | 43_Q | 2.136 | 1.00 |
| 41_A | 54_F | 2.061 | 1.00 |
| 55_F | 60_K | 1.733 | 1.00 |
| 2_R | 12_S | 1.675 | 1.00 |
| 5_V | 13_I | 1.674 | 1.00 |
| 42_H | 46_M | 1.588 | 1.00 |
| 7_S | 52_G | 1.567 | 1.00 |
| 22_L | 59_I | 1.496 | 1.00 |
| 52_G | 60_K | 1.441 | 1.00 |
| 35_L | 64_L | 1.409 | 0.99 |
| 45_F | 54_F | 1.391 | 0.99 |
| 38_P | 63_F | 1.390 | 0.99 |
| 17_P | 39_E | 1.381 | 0.99 |
| 25_Q | 31_T | 1.358 | 0.99 |
| 2_R | 25_Q | 1.339 | 0.99 |
| 21_M | 33_Q | 1.317 | 0.99 |
| 10_I | 55_F | 1.297 | 0.99 |
| 46_M | 51_K | 1.279 | 0.99 |
| 36_G | 64_L | 1.265 | 0.99 |
| 35_L | 66_R | 1.219 | 0.98 |
| 15_Y | 20_R | 1.204 | 0.98 |
| 13_I | 24_I | 1.189 | 0.98 |
| 56_D | 60_K | 1.124 | 0.96 |
| 52_G | 56_D | 1.110 | 0.96 |
| 41_A | 63_F | 1.076 | 0.95 |
| 53_R | 56_D | 1.075 | 0.95 |
| 38_P | 41_A | 1.056 | 0.94 |
| 7_S | 50_S | 1.048 | 0.94 |
| 9_R | 55_F | 1.030 | 0.93 |
| 39_E | 42_H | 1.022 | 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 | |
| 4rgiA | 1 | 1 | 99.9 | 0.035 | Contact Map |
| 3fssA | 1 | 0.7761 | 29.2 | 0.853 | Contact Map |
| 3f5rA | 1 | 0.9701 | 27.9 | 0.855 | Contact Map |
| 4khbD | 4 | 0.9552 | 24.2 | 0.859 | Contact Map |
| 4c5wA | 1 | 0.8955 | 21.8 | 0.862 | Contact Map |
| 3k8rA | 2 | 0.8657 | 17 | 0.868 | Contact Map |
| 2x8nA | 1 | 0.9403 | 14.9 | 0.872 | Contact Map |
| 4hs5A | 2 | 0.9701 | 9 | 0.884 | Contact Map |
| 2xppB | 1 | 0.3582 | 8.3 | 0.886 | Contact Map |
| 2qmeI | 1 | 0.3433 | 7.5 | 0.888 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)