| chey |
| ID: | 1504721032 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 102 (98) | ||
| Sequences: | 200024 (137397) | ||
| Seq/Len: | 2041.061 | ||
| Nf(neff/√len): | 13879.2 |
Jackhmmer Results: (2016_04)
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: 2041.061).
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 |
| 11_A | 28_W | 3.088 | 1.00 |
| 15_Q | 28_W | 2.802 | 1.00 |
| 11_A | 30_D | 2.780 | 1.00 |
| 4_V | 35_T | 2.331 | 1.00 |
| 27_V | 46_F | 2.173 | 1.00 |
| 36_R | 66_L | 2.148 | 1.00 |
| 33_A | 57_D | 2.026 | 1.00 |
| 54_H | 80_D | 2.024 | 1.00 |
| 58_G | 66_L | 1.947 | 1.00 |
| 32_L | 58_G | 1.853 | 1.00 |
| 29_A | 38_H | 1.845 | 1.00 |
| 40_E | 70_H | 1.843 | 1.00 |
| 76_V | 94_V | 1.775 | 1.00 |
| 51_L | 63_V | 1.771 | 1.00 |
| 27_V | 38_H | 1.737 | 1.00 |
| 64_V | 74_A | 1.674 | 1.00 |
| 31_S | 57_D | 1.670 | 1.00 |
| 27_V | 44_H | 1.669 | 1.00 |
| 65_D | 92_K | 1.626 | 1.00 |
| 30_D | 34_Q | 1.538 | 1.00 |
| 53_L | 61_G | 1.512 | 1.00 |
| 66_L | 70_H | 1.469 | 1.00 |
| 68_L | 95_L | 1.412 | 1.00 |
| 15_Q | 19_Q | 1.377 | 0.99 |
| 38_H | 44_H | 1.329 | 0.99 |
| 80_D | 85_M | 1.326 | 0.99 |
| 39_L | 67_V | 1.324 | 0.99 |
| 32_L | 63_V | 1.303 | 0.99 |
| 31_S | 34_Q | 1.295 | 0.99 |
| 61_G | 89_L | 1.289 | 0.99 |
| 33_A | 58_G | 1.287 | 0.99 |
| 38_H | 41_Q | 1.252 | 0.99 |
| 58_G | 62_E | 1.245 | 0.98 |
| 49_A | 72_L | 1.217 | 0.98 |
| 38_H | 46_F | 1.217 | 0.98 |
| 88_Q | 92_K | 1.204 | 0.98 |
| 2_L | 29_A | 1.189 | 0.98 |
| 83_V | 87_T | 1.184 | 0.98 |
| 59_P | 62_E | 1.176 | 0.98 |
| 87_T | 91_K | 1.150 | 0.97 |
| 66_L | 69_Q | 1.133 | 0.97 |
| 8_K | 30_D | 1.106 | 0.96 |
| 3_L | 14_L | 1.096 | 0.96 |
| 36_R | 63_V | 1.094 | 0.96 |
| 76_V | 89_L | 1.089 | 0.96 |
| 6_D | 52_D | 1.073 | 0.95 |
| 82_Q | 85_M | 1.059 | 0.95 |
| 61_G | 88_Q | 1.054 | 0.95 |
| 64_V | 94_V | 1.002 | 0.92 |
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 | |
| 3breA | 2 | 0.9804 | 99.8 | 0.059 | Contact Map |
| 4g97A | 1 | 0.951 | 99.8 | 0.061 | Contact Map |
| 3n0rA | 1 | 0.951 | 99.8 | 0.064 | Contact Map |
| 1w25A | 2 | 0.9706 | 99.8 | 0.065 | Contact Map |
| 3eq2A | 2 | 0.9706 | 99.8 | 0.082 | Contact Map |
| 3dzdA | 2 | 0.9706 | 99.8 | 0.091 | Contact Map |
| 4l4uA | 1 | 0.9706 | 99.8 | 0.107 | Contact Map |
| 2vycA | 10 | 0.9706 | 99.8 | 0.113 | Contact Map |
| 3lufA | 2 | 0.9706 | 99.7 | 0.123 | Contact Map |
| 3rqiA | 1 | 0.9608 | 99.7 | 0.125 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)