| pduN |
| ID: | 1438819717 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 91 (86) | ||
| Sequences: | 370 (271) | ||
| Seq/Len: | 4.302 | ||
| Nf(neff/√len): | 29.2 |
HHblits Results: (2013_03)
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: 4.302).
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 |
| 3_L | 86_V | 3.581 | 1.00 |
| 31_S | 35_E | 1.986 | 1.00 |
| 15_K | 21_G | 1.954 | 1.00 |
| 46_V | 60_L | 1.788 | 1.00 |
| 58_L | 86_V | 1.776 | 1.00 |
| 25_L | 82_V | 1.680 | 0.99 |
| 51_V | 81_A | 1.558 | 0.98 |
| 67_A | 79_D | 1.477 | 0.98 |
| 64_G | 68_R | 1.461 | 0.97 |
| 47_A | 82_V | 1.435 | 0.97 |
| 23_K | 51_V | 1.434 | 0.97 |
| 3_L | 46_V | 1.407 | 0.97 |
| 30_V | 34_G | 1.399 | 0.96 |
| 54_G | 57_E | 1.373 | 0.96 |
| 2_H | 29_R | 1.369 | 0.96 |
| 52_G | 57_E | 1.350 | 0.95 |
| 46_V | 79_D | 1.330 | 0.95 |
| 6_V | 25_L | 1.318 | 0.95 |
| 62_S | 66_S | 1.247 | 0.92 |
| 78_I | 81_A | 1.230 | 0.91 |
| 27_V | 47_A | 1.185 | 0.89 |
| 6_V | 27_V | 1.162 | 0.88 |
| 29_R | 45_E | 1.150 | 0.87 |
| 79_D | 85_I | 1.150 | 0.87 |
| 63_S | 80_L | 1.140 | 0.87 |
| 6_V | 47_A | 1.135 | 0.86 |
| 23_K | 54_G | 1.133 | 0.86 |
| 5_R | 27_V | 1.128 | 0.86 |
| 65_S | 68_R | 1.123 | 0.86 |
| 57_E | 85_I | 1.115 | 0.85 |
| 51_V | 85_I | 1.108 | 0.85 |
| 30_V | 58_L | 1.102 | 0.84 |
| 7_T | 20_I | 1.096 | 0.84 |
| 20_I | 55_V | 1.092 | 0.83 |
| 23_K | 53_A | 1.083 | 0.83 |
| 62_S | 70_V | 1.071 | 0.82 |
| 27_V | 61_L | 1.056 | 0.80 |
| 16_S | 70_V | 1.055 | 0.80 |
| 33_D | 75_N | 1.053 | 0.80 |
| 26_L | 33_D | 1.044 | 0.79 |
| 10_V | 45_E | 1.041 | 0.79 |
| 24_L | 66_S | 1.036 | 0.79 |
| 11_V | 22_K | 1.025 | 0.78 |
| 2_H | 77_A | 1.017 | 0.77 |
| 53_A | 85_I | 1.014 | 0.77 |
| 18_S | 77_A | 1.010 | 0.76 |
| 2_H | 14_Q | 1.005 | 0.76 |
| 11_V | 48_V | 1.000 | 0.75 |
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 | |
| 4n8fA | 5 | 0.956 | 100 | 0.031 | Contact Map |
| 4jw0B | 5 | 0.956 | 100 | 0.033 | Contact Map |
| 2hd3A | 12 | 0.956 | 100 | 0.034 | Contact Map |
| 4i7aA | 5 | 0.9121 | 100 | 0.034 | Contact Map |
| 2qw7A | 10 | 0.956 | 100 | 0.041 | Contact Map |
| 2rcfA | 5 | 0.9011 | 100 | 0.158 | Contact Map |
| 1ok8A | 1 | 0.5714 | 7.2 | 0.922 | Contact Map |
| 4d2iA | 2 | 0.7692 | 6.5 | 0.924 | Contact Map |
| 2yvkA | 4 | 0.7143 | 4.6 | 0.929 | Contact Map |
| 3b8cA | 2 | 0.7912 | 4.4 | 0.929 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)