| CytC_bos |
| ID: | 1402323952 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 105 (103) | ||
| Sequences: | 1782 (1243.9) | ||
| Seq/Len: | 17.301 | ||
| Nf(neff/√len): | 122.6 |
Jackhmmer Results: (2014_04_16)
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: 17.301).
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 |
| 62_E | 100_K | 3.476 | 1.00 |
| 66_M | 92_R | 3.159 | 1.00 |
| 11_F | 21_V | 3.083 | 1.00 |
| 41_T | 58_I | 2.535 | 1.00 |
| 71_N | 74_K | 2.485 | 1.00 |
| 39_R | 43_Q | 2.360 | 1.00 |
| 53_N | 68_Y | 2.147 | 1.00 |
| 6_K | 94_D | 2.094 | 1.00 |
| 5_E | 8_K | 2.085 | 1.00 |
| 61_G | 64_T | 1.952 | 1.00 |
| 27_H | 44_A | 1.888 | 1.00 |
| 37_F | 65_L | 1.883 | 1.00 |
| 53_N | 76_I | 1.848 | 1.00 |
| 22_E | 25_G | 1.807 | 1.00 |
| 10_I | 86_I | 1.726 | 1.00 |
| 10_I | 95_L | 1.722 | 1.00 |
| 90_G | 94_D | 1.705 | 1.00 |
| 52_A | 78_G | 1.642 | 1.00 |
| 41_T | 56_K | 1.622 | 1.00 |
| 20_T | 25_G | 1.609 | 1.00 |
| 88_K | 91_E | 1.608 | 1.00 |
| 20_T | 28_K | 1.585 | 1.00 |
| 66_M | 93_E | 1.578 | 1.00 |
| 65_L | 69_L | 1.571 | 1.00 |
| 86_I | 95_L | 1.498 | 1.00 |
| 8_K | 12_V | 1.493 | 1.00 |
| 25_G | 32_N | 1.472 | 1.00 |
| 39_R | 49_Y | 1.431 | 1.00 |
| 58_I | 64_T | 1.410 | 1.00 |
| 70_E | 89_K | 1.346 | 0.99 |
| 66_M | 96_I | 1.325 | 0.99 |
| 67_E | 75_Y | 1.307 | 0.99 |
| 11_F | 33_L | 1.257 | 0.99 |
| 22_E | 34_H | 1.242 | 0.98 |
| 98_Y | 102_A | 1.234 | 0.98 |
| 23_K | 34_H | 1.232 | 0.98 |
| 36_L | 39_R | 1.230 | 0.98 |
| 64_T | 75_Y | 1.214 | 0.98 |
| 10_I | 91_E | 1.214 | 0.98 |
| 47_F | 80_K | 1.182 | 0.98 |
| 14_K | 83_F | 1.182 | 0.98 |
| 20_T | 32_N | 1.099 | 0.96 |
| 25_G | 34_H | 1.092 | 0.96 |
| 10_I | 14_K | 1.080 | 0.95 |
| 37_F | 100_K | 1.076 | 0.95 |
| 89_K | 93_E | 1.076 | 0.95 |
| 21_V | 98_Y | 1.073 | 0.95 |
| 14_K | 91_E | 1.071 | 0.95 |
| 83_F | 86_I | 1.065 | 0.95 |
| 69_L | 96_I | 1.058 | 0.95 |
| 3_D | 6_K | 1.048 | 0.94 |
| 63_E | 67_E | 1.045 | 0.94 |
| 91_E | 94_D | 1.008 | 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 | |
| 1vydA | 2 | 0.9429 | 99.9 | 0.326 | Contact Map |
| 2bh4X | 1 | 0.9619 | 99.9 | 0.363 | Contact Map |
| 155cA | 1 | 0.9619 | 99.9 | 0.386 | Contact Map |
| 3zooA | 4 | 0.9905 | 99.9 | 0.406 | Contact Map |
| 1cxcA | 1 | 0.981 | 99.9 | 0.407 | Contact Map |
| 1co6A | 1 | 0.981 | 99.8 | 0.419 | Contact Map |
| 1hroA | 2 | 0.9714 | 99.8 | 0.43 | Contact Map |
| 1c2nA | 1 | 0.9429 | 99.8 | 0.431 | Contact Map |
| 3m97X | 1 | 0.9524 | 99.8 | 0.433 | Contact Map |
| 1ccrA | 1 | 0.9714 | 99.8 | 0.435 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)