| 4cpv |
| ID: | 1487888185 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 109 (103) | ||
| Sequences: | 7657 (4724.8) | ||
| Seq/Len: | 74.340 | ||
| Nf(neff/√len): | 465.5 |
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: 74.340).
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 |
| 58_F | 97_K | 4.673 | 1.00 |
| 56_S | 63_E | 2.871 | 1.00 |
| 52_D | 57_G | 2.318 | 1.00 |
| 45_K | 100_V | 2.275 | 1.00 |
| 61_E | 84_K | 2.272 | 1.00 |
| 65_K | 80_D | 2.213 | 1.00 |
| 95_D | 102_E | 1.952 | 1.00 |
| 95_D | 99_G | 1.952 | 1.00 |
| 91_D | 96_G | 1.917 | 1.00 |
| 22_A | 29_A | 1.911 | 1.00 |
| 100_V | 104_T | 1.854 | 1.00 |
| 49_A | 55_K | 1.853 | 1.00 |
| 54_D | 63_E | 1.849 | 1.00 |
| 91_D | 102_E | 1.838 | 1.00 |
| 26_N | 29_A | 1.796 | 1.00 |
| 53_Q | 66_L | 1.794 | 1.00 |
| 14_A | 17_E | 1.756 | 1.00 |
| 91_D | 94_G | 1.730 | 1.00 |
| 99_G | 102_E | 1.686 | 1.00 |
| 20_K | 23_D | 1.576 | 1.00 |
| 41_A | 104_T | 1.572 | 1.00 |
| 56_S | 60_E | 1.514 | 1.00 |
| 98_I | 103_F | 1.483 | 1.00 |
| 16_L | 20_K | 1.472 | 1.00 |
| 27_H | 31_F | 1.404 | 0.99 |
| 27_H | 30_F | 1.394 | 0.99 |
| 16_L | 19_C | 1.380 | 0.99 |
| 104_T | 108_K | 1.362 | 0.99 |
| 49_A | 100_V | 1.321 | 0.99 |
| 93_D | 99_G | 1.305 | 0.99 |
| 45_K | 49_A | 1.294 | 0.99 |
| 92_S | 105_A | 1.248 | 0.99 |
| 51_I | 67_F | 1.196 | 0.98 |
| 52_D | 63_E | 1.187 | 0.98 |
| 59_I | 64_L | 1.178 | 0.98 |
| 90_G | 98_I | 1.174 | 0.98 |
| 79_T | 82_E | 1.147 | 0.97 |
| 60_E | 63_E | 1.142 | 0.97 |
| 78_L | 82_E | 1.135 | 0.97 |
| 60_E | 97_K | 1.134 | 0.97 |
| 56_S | 97_K | 1.134 | 0.97 |
| 42_D | 46_K | 1.101 | 0.96 |
| 50_I | 67_F | 1.098 | 0.96 |
| 53_Q | 63_E | 1.090 | 0.96 |
| 64_L | 87_L | 1.086 | 0.96 |
| 61_E | 65_K | 1.079 | 0.95 |
| 91_D | 95_D | 1.078 | 0.95 |
| 43_D | 46_K | 1.077 | 0.95 |
| 92_S | 95_D | 1.061 | 0.95 |
| 103_F | 107_V | 1.045 | 0.94 |
| 13_A | 17_E | 1.001 | 0.92 |
| 7_L | 12_I | 1.001 | 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 | |
| 2kycA | 1 | 0.9633 | 99.6 | 0.121 | Contact Map |
| 1bu3A | 1 | 0.9633 | 99.6 | 0.126 | Contact Map |
| 1rroA | 1 | 0.9633 | 99.6 | 0.128 | Contact Map |
| 1rwyA | 3 | 0.9633 | 99.6 | 0.129 | Contact Map |
| 2pvbA | 1 | 0.9541 | 99.6 | 0.131 | Contact Map |
| 1pvaA | 2 | 0.9633 | 99.6 | 0.131 | Contact Map |
| 3fs7A | 8 | 0.9633 | 99.6 | 0.135 | Contact Map |
| 5palA | 1 | 0.9633 | 99.6 | 0.14 | Contact Map |
| 3u0kA | 1 | 0.9358 | 99.5 | 0.167 | Contact Map |
| 4ociA | 1 | 0.9725 | 99.5 | 0.172 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)