| vpr |
| ID: | 1509308077 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 96 (95) | ||
| Sequences: | 745 (64) | ||
| Seq/Len: | 7.842 | ||
| Nf(neff/√len): | 6.6 |
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: 7.842).
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 |
| 65_Q | 69_F | 2.224 | 1.00 |
| 92_G | 95_R | 2.217 | 1.00 |
| 93_A | 96_S | 2.130 | 1.00 |
| 48_E | 55_A | 1.978 | 1.00 |
| 17_E | 21_E | 1.895 | 1.00 |
| 19_T | 22_L | 1.736 | 1.00 |
| 91_N | 95_R | 1.680 | 1.00 |
| 91_N | 96_S | 1.629 | 1.00 |
| 15_Y | 58_E | 1.593 | 1.00 |
| 65_Q | 68_L | 1.582 | 1.00 |
| 35_P | 38_W | 1.476 | 0.99 |
| 64_L | 72_F | 1.474 | 0.99 |
| 60_I | 63_I | 1.450 | 0.99 |
| 19_T | 53_T | 1.387 | 0.99 |
| 3_Q | 11_Q | 1.344 | 0.99 |
| 89_A | 93_A | 1.339 | 0.99 |
| 43_G | 82_G | 1.312 | 0.98 |
| 64_L | 69_F | 1.309 | 0.98 |
| 7_D | 15_Y | 1.309 | 0.98 |
| 75_G | 80_R | 1.304 | 0.98 |
| 10_P | 13_E | 1.300 | 0.98 |
| 90_R | 95_R | 1.286 | 0.98 |
| 21_E | 42_L | 1.266 | 0.98 |
| 77_R | 94_S | 1.246 | 0.97 |
| 7_D | 13_E | 1.244 | 0.97 |
| 55_A | 86_Q | 1.237 | 0.97 |
| 31_V | 37_I | 1.208 | 0.97 |
| 20_L | 31_V | 1.205 | 0.97 |
| 30_A | 33_H | 1.162 | 0.96 |
| 25_E | 43_G | 1.154 | 0.95 |
| 86_Q | 94_S | 1.135 | 0.95 |
| 30_A | 34_F | 1.133 | 0.95 |
| 35_P | 54_W | 1.132 | 0.95 |
| 28_S | 86_Q | 1.131 | 0.95 |
| 38_W | 42_L | 1.129 | 0.95 |
| 21_E | 53_T | 1.126 | 0.95 |
| 31_V | 35_P | 1.121 | 0.94 |
| 5_P | 18_W | 1.118 | 0.94 |
| 4_A | 8_Q | 1.105 | 0.94 |
| 32_R | 85_R | 1.100 | 0.94 |
| 59_A | 66_Q | 1.096 | 0.94 |
| 7_D | 12_R | 1.075 | 0.93 |
| 7_D | 32_R | 1.063 | 0.92 |
| 10_P | 51_G | 1.059 | 0.92 |
| 30_A | 39_L | 1.053 | 0.92 |
| 66_Q | 74_I | 1.046 | 0.91 |
| 52_D | 76_C | 1.038 | 0.91 |
| 28_S | 85_R | 1.032 | 0.91 |
| 22_L | 41_N | 1.026 | 0.90 |
| 47_Y | 50_Y | 1.024 | 0.90 |
| 19_T | 26_L | 1.019 | 0.90 |
| 11_Q | 22_L | 1.019 | 0.90 |
| 45_H | 71_H | 1.002 | 0.89 |
| 44_Q | 54_W | 1.001 | 0.89 |
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 | |
| 1esxA | 1 | 1 | 100 | 0.08 | Contact Map |
| 4z8lB | 2 | 0 | 100 | 0.246 | Contact Map |
| 4cc9B | 1 | 0.8854 | 100 | 0.253 | Contact Map |
| 5ajaB | 1 | 0 | 100 | 0.256 | Contact Map |
| 1ceuA | 1 | 0.5312 | 100 | 0.49 | Contact Map |
| 1bdeA | 1 | 0.3438 | 99.7 | 0.655 | Contact Map |
| 1dskA | 1 | 0.2917 | 99.1 | 0.768 | Contact Map |
| 2qfaC | 1 | 0.3333 | 10.6 | 0.951 | Contact Map |
| 1xkyA | 4 | 0.3646 | 8 | 0.954 | Contact Map |
| 4mlaA | 2 | 0.4792 | 7.4 | 0.954 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)