| -CGT Bacillus circulans strain 251 D domain 496-583 10-4-8i |
| ID: | 1510747911 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 88 (85) | ||
| Sequences: | 3461 (2599.5) | ||
| Seq/Len: | 40.718 | ||
| Nf(neff/√len): | 282.0 |
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: 40.718).
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 |
| 44_A | 56_V | 2.785 | 1.00 |
| 19_T | 55_K | 2.273 | 1.00 |
| 14_A | 84_F | 2.236 | 1.00 |
| 21_T | 55_K | 2.200 | 1.00 |
| 15_K | 18_V | 2.059 | 1.00 |
| 8_H | 23_D | 2.024 | 1.00 |
| 19_T | 57_K | 1.950 | 1.00 |
| 14_A | 18_V | 1.874 | 1.00 |
| 5_T | 25_R | 1.846 | 1.00 |
| 67_N | 83_N | 1.827 | 1.00 |
| 18_V | 58_I | 1.827 | 1.00 |
| 35_Y | 71_A | 1.770 | 1.00 |
| 34_V | 56_V | 1.742 | 1.00 |
| 50_E | 53_Q | 1.705 | 1.00 |
| 36_F | 56_V | 1.695 | 1.00 |
| 23_D | 53_Q | 1.684 | 1.00 |
| 45_D | 57_K | 1.674 | 1.00 |
| 21_T | 53_Q | 1.648 | 1.00 |
| 35_Y | 38_T | 1.632 | 1.00 |
| 35_Y | 69_K | 1.615 | 1.00 |
| 20_I | 36_F | 1.439 | 1.00 |
| 9_V | 68_I | 1.396 | 0.99 |
| 22_I | 54_I | 1.381 | 0.99 |
| 54_I | 70_V | 1.377 | 0.99 |
| 6_I | 80_V | 1.362 | 0.99 |
| 80_V | 83_N | 1.344 | 0.99 |
| 6_I | 22_I | 1.339 | 0.99 |
| 58_I | 86_V | 1.331 | 0.99 |
| 33_T | 43_G | 1.306 | 0.99 |
| 24_G | 27_F | 1.299 | 0.99 |
| 14_A | 58_I | 1.279 | 0.99 |
| 32_G | 49_W | 1.271 | 0.99 |
| 28_G | 51_D | 1.250 | 0.99 |
| 61_V | 66_Y | 1.240 | 0.98 |
| 8_H | 12_M | 1.214 | 0.98 |
| 20_I | 56_V | 1.188 | 0.98 |
| 11_P | 14_A | 1.150 | 0.97 |
| 19_T | 47_T | 1.147 | 0.97 |
| 36_F | 44_A | 1.105 | 0.96 |
| 72_N | 75_G | 1.105 | 0.96 |
| 28_G | 49_W | 1.095 | 0.96 |
| 33_T | 71_A | 1.086 | 0.96 |
| 22_I | 34_V | 1.084 | 0.96 |
| 38_T | 69_K | 1.069 | 0.95 |
| 27_F | 54_I | 1.039 | 0.94 |
| 9_V | 82_D | 1.028 | 0.94 |
| 4_P | 26_G | 1.026 | 0.94 |
| 63_G | 66_Y | 1.019 | 0.93 |
| 25_R | 52_T | 1.014 | 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 | |
| 1uadC | 2 | 0.9659 | 99 | 0.095 | Contact Map |
| 2uzxB | 2 | 0.9091 | 98.8 | 0.174 | Contact Map |
| 3mujA | 2 | 0.9432 | 98.7 | 0.18 | Contact Map |
| 4hw6A | 4 | 0.9545 | 98.6 | 0.22 | Contact Map |
| 3hrpA | 1 | 0.9545 | 98.6 | 0.224 | Contact Map |
| 3kyaA | 1 | 0.9545 | 98.5 | 0.24 | Contact Map |
| 3orjA | 1 | 0.9205 | 98.5 | 0.24 | Contact Map |
| 3mlpA | 4 | 0.9545 | 98.4 | 0.254 | Contact Map |
| 2cxkA | 5 | 0.9432 | 98.4 | 0.259 | Contact Map |
| 3brdA | 1 | 0.9545 | 98 | 0.338 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)