| 4cpv 2-109correct |
| ID: | 1487908086 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (103) | ||
| Sequences: | 7533 (4720) | ||
| Seq/Len: | 73.136 | ||
| Nf(neff/√len): | 465.1 |
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: 73.136).
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 |
| 57_F | 96_K | 4.641 | 1.00 |
| 55_S | 62_E | 2.669 | 1.00 |
| 64_K | 79_D | 2.319 | 1.00 |
| 60_E | 83_K | 2.287 | 1.00 |
| 21_A | 28_A | 2.168 | 1.00 |
| 44_K | 99_V | 2.164 | 1.00 |
| 51_D | 56_G | 2.143 | 1.00 |
| 48_A | 54_K | 1.950 | 1.00 |
| 90_D | 101_E | 1.937 | 1.00 |
| 99_V | 103_T | 1.903 | 1.00 |
| 94_D | 101_E | 1.895 | 1.00 |
| 94_D | 98_G | 1.830 | 1.00 |
| 90_D | 95_G | 1.813 | 1.00 |
| 53_D | 62_E | 1.800 | 1.00 |
| 90_D | 93_G | 1.755 | 1.00 |
| 25_N | 28_A | 1.746 | 1.00 |
| 15_L | 19_K | 1.649 | 1.00 |
| 98_G | 101_E | 1.630 | 1.00 |
| 19_K | 22_D | 1.581 | 1.00 |
| 52_Q | 65_L | 1.557 | 1.00 |
| 13_A | 16_E | 1.520 | 1.00 |
| 55_S | 59_E | 1.506 | 1.00 |
| 26_H | 30_F | 1.493 | 1.00 |
| 44_K | 48_A | 1.472 | 1.00 |
| 97_I | 102_F | 1.464 | 1.00 |
| 15_L | 18_C | 1.412 | 1.00 |
| 40_A | 103_T | 1.392 | 0.99 |
| 78_T | 81_E | 1.381 | 0.99 |
| 103_T | 107_K | 1.373 | 0.99 |
| 26_H | 29_F | 1.275 | 0.99 |
| 41_D | 45_K | 1.238 | 0.98 |
| 48_A | 99_V | 1.233 | 0.98 |
| 90_D | 94_D | 1.227 | 0.98 |
| 58_I | 63_L | 1.197 | 0.98 |
| 92_D | 98_G | 1.162 | 0.97 |
| 51_D | 62_E | 1.156 | 0.97 |
| 91_S | 104_A | 1.135 | 0.97 |
| 51_D | 55_S | 1.115 | 0.96 |
| 64_K | 68_Q | 1.105 | 0.96 |
| 60_E | 64_K | 1.102 | 0.96 |
| 50_I | 66_F | 1.098 | 0.96 |
| 52_Q | 62_E | 1.089 | 0.96 |
| 59_E | 62_E | 1.088 | 0.96 |
| 59_E | 96_K | 1.073 | 0.95 |
| 55_S | 96_K | 1.073 | 0.95 |
| 102_F | 106_V | 1.068 | 0.95 |
| 60_E | 86_L | 1.062 | 0.95 |
| 77_L | 81_E | 1.051 | 0.94 |
| 49_I | 66_F | 1.051 | 0.94 |
| 13_A | 17_A | 1.048 | 0.94 |
| 7_N | 10_D | 1.037 | 0.94 |
| 6_L | 10_D | 1.032 | 0.94 |
| 92_D | 101_E | 1.027 | 0.94 |
| 83_K | 87_K | 1.025 | 0.93 |
| 42_D | 45_K | 1.020 | 0.93 |
| 12_A | 16_E | 1.017 | 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 | |
| 2kycA | 1 | 0.9722 | 99.6 | 0.103 | Contact Map |
| 1bu3A | 1 | 0.9722 | 99.6 | 0.106 | Contact Map |
| 1pvaA | 2 | 0.9722 | 99.6 | 0.11 | Contact Map |
| 1rwyA | 3 | 0.9722 | 99.6 | 0.111 | Contact Map |
| 1rroA | 1 | 0.9722 | 99.6 | 0.111 | Contact Map |
| 3fs7A | 8 | 0.9722 | 99.6 | 0.113 | Contact Map |
| 2pvbA | 1 | 0.963 | 99.6 | 0.116 | Contact Map |
| 5palA | 1 | 0.9722 | 99.5 | 0.129 | Contact Map |
| 3u0kA | 1 | 0.9352 | 99.5 | 0.169 | Contact Map |
| 4ociA | 1 | 0.9722 | 99.5 | 0.175 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)