| 4RGI KTSC Domain Protein YPO2434 from Yersinia pestis |
| ID: | 1475964850 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (70) | ||
| Sequences: | 441 (358.7) | ||
| Seq/Len: | 6.300 | ||
| Nf(neff/√len): | 42.9 |
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: 6.300).
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 |
| 3_R | 24_E | 3.340 | 1.00 |
| 24_E | 34_Q | 2.702 | 1.00 |
| 45_N | 55_F | 2.615 | 1.00 |
| 40_E | 44_Q | 1.976 | 1.00 |
| 56_F | 61_K | 1.932 | 1.00 |
| 14_I | 46_F | 1.906 | 1.00 |
| 42_A | 55_F | 1.725 | 1.00 |
| 3_R | 13_S | 1.706 | 1.00 |
| 27_F | 53_G | 1.663 | 1.00 |
| 3_R | 26_Q | 1.600 | 1.00 |
| 11_I | 14_I | 1.565 | 0.99 |
| 13_S | 24_E | 1.549 | 0.99 |
| 37_G | 65_L | 1.547 | 0.99 |
| 23_L | 60_I | 1.453 | 0.99 |
| 36_L | 65_L | 1.415 | 0.99 |
| 18_P | 40_E | 1.413 | 0.99 |
| 39_P | 64_F | 1.382 | 0.98 |
| 43_H | 47_M | 1.369 | 0.98 |
| 11_I | 56_F | 1.344 | 0.98 |
| 6_V | 14_I | 1.316 | 0.97 |
| 26_Q | 32_T | 1.316 | 0.97 |
| 31_G | 68_K | 1.304 | 0.97 |
| 55_F | 59_V | 1.261 | 0.96 |
| 47_M | 52_K | 1.181 | 0.94 |
| 8_S | 51_S | 1.104 | 0.91 |
| 9_S | 51_S | 1.102 | 0.91 |
| 6_V | 15_G | 1.097 | 0.91 |
| 54_R | 57_D | 1.090 | 0.90 |
| 46_F | 55_F | 1.066 | 0.89 |
| 36_L | 67_R | 1.058 | 0.89 |
| 53_G | 61_K | 1.039 | 0.87 |
| 27_F | 51_S | 1.024 | 0.86 |
| 12_L | 28_R | 1.013 | 0.85 |
| 10_R | 61_K | 1.004 | 0.85 |
| 22_M | 34_Q | 1.000 | 0.84 |
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 | 0.074 | Contact Map |
| 2x8nA | 1 | 0.9429 | 29.4 | 0.87 | Contact Map |
| 3f5rA | 1 | 0.9143 | 28.5 | 0.871 | Contact Map |
| 3k8rA | 2 | 0.8571 | 25.8 | 0.874 | Contact Map |
| 4c5wA | 1 | 0.8857 | 24.1 | 0.875 | Contact Map |
| 4khbD | 4 | 0.9571 | 21.7 | 0.878 | Contact Map |
| 3fssA | 1 | 0.7571 | 17.5 | 0.883 | Contact Map |
| 1mhmB | 1 | 0.6286 | 16.2 | 0.885 | Contact Map |
| 4a60A | 1 | 0.7714 | 14.5 | 0.887 | Contact Map |
| 1ej5A | 1 | 0.7143 | 10.2 | 0.895 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)