| d2i76b1 |
| ID: | 1450281938 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (95) | ||
| Sequences: | 860 (614.7) | ||
| Seq/Len: | 9.053 | ||
| Nf(neff/√len): | 63.1 |
HHblits Results: (2015_06)
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: 9.053).
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 |
| 11_A | 22_S | 3.445 | 1.00 |
| 19_A | 42_M | 3.154 | 1.00 |
| 19_A | 46_A | 2.584 | 1.00 |
| 43_K | 50_K | 2.389 | 1.00 |
| 42_M | 46_A | 2.272 | 1.00 |
| 17_A | 93_L | 1.884 | 1.00 |
| 52_M | 57_S | 1.763 | 1.00 |
| 39_H | 50_K | 1.752 | 1.00 |
| 83_N | 96_E | 1.631 | 1.00 |
| 85_V | 88_D | 1.586 | 1.00 |
| 85_V | 92_K | 1.578 | 1.00 |
| 70_V | 91_V | 1.486 | 1.00 |
| 85_V | 89_E | 1.470 | 1.00 |
| 13_N | 59_T | 1.461 | 1.00 |
| 18_L | 90_I | 1.429 | 0.99 |
| 9_V | 14_F | 1.426 | 0.99 |
| 27_T | 33_E | 1.415 | 0.99 |
| 65_G | 95_R | 1.395 | 0.99 |
| 10_I | 77_Y | 1.377 | 0.99 |
| 12_S | 45_V | 1.368 | 0.99 |
| 15_P | 46_A | 1.302 | 0.99 |
| 10_I | 25_I | 1.299 | 0.99 |
| 10_I | 21_L | 1.285 | 0.99 |
| 16_V | 58_L | 1.245 | 0.98 |
| 86_L | 89_E | 1.227 | 0.98 |
| 6_L | 76_E | 1.194 | 0.97 |
| 70_V | 74_R | 1.187 | 0.97 |
| 73_E | 77_Y | 1.179 | 0.97 |
| 88_D | 92_K | 1.147 | 0.96 |
| 14_F | 17_A | 1.132 | 0.96 |
| 16_V | 48_N | 1.132 | 0.96 |
| 10_I | 18_L | 1.129 | 0.96 |
| 11_A | 42_M | 1.125 | 0.96 |
| 48_N | 52_M | 1.117 | 0.96 |
| 9_V | 44_G | 1.113 | 0.96 |
| 3_A | 76_E | 1.106 | 0.95 |
| 83_N | 92_K | 1.104 | 0.95 |
| 92_K | 95_R | 1.091 | 0.95 |
| 23_K | 27_T | 1.091 | 0.95 |
| 14_F | 62_V | 1.084 | 0.95 |
| 43_K | 47_D | 1.067 | 0.94 |
| 8_A | 25_I | 1.051 | 0.93 |
| 82_G | 88_D | 1.036 | 0.93 |
| 24_R | 27_T | 1.028 | 0.92 |
| 16_V | 62_V | 1.021 | 0.92 |
| 42_M | 49_I | 1.011 | 0.92 |
| 83_N | 93_L | 1.006 | 0.91 |
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 | |
| 2i76A | 2 | 1 | 99.4 | 0.562 | Contact Map |
| 3d1lA | 2 | 0.96 | 99.3 | 0.575 | Contact Map |
| 3dfuA | 2 | 0.83 | 98 | 0.728 | Contact Map |
| 4e12A | 1 | 0.87 | 95.8 | 0.8 | Contact Map |
| 3adoA | 1 | 0.9 | 95.7 | 0.802 | Contact Map |
| 4r1nA | 4 | 0 | 95.4 | 0.806 | Contact Map |
| 3c24A | 2 | 0.9 | 95.2 | 0.809 | Contact Map |
| 1f0yA | 2 | 0.88 | 94.7 | 0.813 | Contact Map |
| 3triA | 2 | 0.93 | 93.6 | 0.823 | Contact Map |
| 4j0eA | 2 | 0.88 | 91 | 0.836 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)