| test_pinA |
| ID: | 1484082639 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 92 (91) | ||
| Sequences: | 9604 (6538.8) | ||
| Seq/Len: | 105.538 | ||
| Nf(neff/√len): | 685.5 |
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: 105.538).
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 |
| 22_Q | 26_K | 3.671 | 1.00 |
| 8_S | 91_L | 2.835 | 1.00 |
| 57_G | 64_E | 2.269 | 1.00 |
| 6_K | 50_S | 2.262 | 1.00 |
| 8_S | 89_K | 2.125 | 1.00 |
| 70_L | 76_S | 2.072 | 1.00 |
| 72_V | 92_G | 1.957 | 1.00 |
| 6_K | 53_Y | 1.915 | 1.00 |
| 13_K | 40_I | 1.903 | 1.00 |
| 24_R | 29_E | 1.879 | 1.00 |
| 6_K | 91_L | 1.811 | 1.00 |
| 21_V | 38_L | 1.807 | 1.00 |
| 53_Y | 92_G | 1.794 | 1.00 |
| 30_K | 33_K | 1.793 | 1.00 |
| 5_I | 68_F | 1.752 | 1.00 |
| 22_Q | 77_E | 1.752 | 1.00 |
| 71_Q | 74_E | 1.730 | 1.00 |
| 54_F | 59_M | 1.699 | 1.00 |
| 29_E | 34_L | 1.655 | 1.00 |
| 20_A | 24_R | 1.646 | 1.00 |
| 9_H | 86_H | 1.592 | 1.00 |
| 6_K | 92_G | 1.549 | 1.00 |
| 61_K | 65_D | 1.531 | 1.00 |
| 24_R | 38_L | 1.521 | 1.00 |
| 4_K | 53_Y | 1.511 | 1.00 |
| 56_R | 68_F | 1.475 | 1.00 |
| 70_L | 90_R | 1.472 | 1.00 |
| 22_Q | 87_V | 1.457 | 1.00 |
| 80_K | 85_Y | 1.446 | 1.00 |
| 12_V | 21_V | 1.369 | 0.99 |
| 55_G | 58_K | 1.358 | 0.99 |
| 23_E | 27_A | 1.331 | 0.99 |
| 14_K | 17_E | 1.245 | 0.98 |
| 81_S | 86_H | 1.231 | 0.98 |
| 19_L | 23_E | 1.220 | 0.98 |
| 15_Q | 19_L | 1.220 | 0.98 |
| 33_K | 37_E | 1.210 | 0.98 |
| 41_D | 44_S | 1.203 | 0.98 |
| 81_S | 84_G | 1.165 | 0.97 |
| 21_V | 34_L | 1.134 | 0.97 |
| 72_V | 90_R | 1.132 | 0.97 |
| 56_R | 64_E | 1.119 | 0.96 |
| 60_V | 83_F | 1.101 | 0.96 |
| 64_E | 68_F | 1.101 | 0.96 |
| 25_L | 34_L | 1.093 | 0.96 |
| 7_C | 67_A | 1.093 | 0.96 |
| 78_P | 85_Y | 1.070 | 0.95 |
| 22_Q | 78_P | 1.069 | 0.95 |
| 5_I | 67_A | 1.066 | 0.95 |
| 66_A | 79_V | 1.043 | 0.94 |
| 50_S | 91_L | 1.042 | 0.94 |
| 70_L | 74_E | 1.035 | 0.94 |
| 4_K | 55_G | 1.026 | 0.94 |
| 23_E | 26_K | 1.012 | 0.93 |
| 17_E | 38_L | 1.012 | 0.93 |
| 75_V | 89_K | 1.011 | 0.93 |
| 8_S | 32_G | 1.004 | 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 | |
| 2m08A | 1 | 1 | 99.7 | -0.076 | Contact Map |
| 1jnsA | 1 | 0.9783 | 99.7 | -0.054 | Contact Map |
| 3gpkA | 2 | 0.9891 | 99.7 | -0.05 | Contact Map |
| 2jzvA | 1 | 1 | 99.7 | -0.035 | Contact Map |
| 2lj4A | 1 | 0.9891 | 99.7 | -0.03 | Contact Map |
| 2pv1A | 1 | 0.9674 | 99.6 | -0.027 | Contact Map |
| 2kgjA | 1 | 0.9783 | 99.6 | -0.022 | Contact Map |
| 2mntA | 1 | 0.9783 | 99.6 | -0.015 | Contact Map |
| 3ui4A | 1 | 0.9783 | 99.6 | -0.015 | Contact Map |
| 1j6yA | 1 | 0.9891 | 99.6 | -0.013 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)