| Test00 |
| ID: | 1479247833 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 58 (58) | ||
| Sequences: | 101 (101) | ||
| Seq/Len: | 1.741 | ||
| Nf(neff/√len): | 13.3 |
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: 1.741).
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 |
| 8_G | 44_T | 1.542 | 0.91 |
| 23_E | 52_E | 1.469 | 0.88 |
| 54_G | 58_E | 1.461 | 0.87 |
| 25_S | 53_S | 1.435 | 0.86 |
| 8_G | 19_V | 1.397 | 0.84 |
| 12_I | 42_A | 1.357 | 0.81 |
| 8_G | 53_S | 1.349 | 0.81 |
| 15_P | 47_L | 1.349 | 0.81 |
| 12_I | 52_E | 1.342 | 0.80 |
| 17_L | 29_H | 1.335 | 0.80 |
| 18_D | 21_I | 1.237 | 0.72 |
| 44_T | 56_E | 1.182 | 0.67 |
| 4_P | 45_F | 1.176 | 0.67 |
| 27_V | 52_E | 1.171 | 0.66 |
| 2_L | 19_V | 1.165 | 0.65 |
| 4_P | 33_L | 1.161 | 0.65 |
| 18_D | 45_F | 1.158 | 0.65 |
| 11_F | 15_P | 1.156 | 0.65 |
| 16_Q | 46_I | 1.140 | 0.63 |
| 1_S | 25_S | 1.139 | 0.63 |
| 24_A | 52_E | 1.137 | 0.63 |
| 17_L | 35_V | 1.121 | 0.61 |
| 18_D | 37_P | 1.119 | 0.61 |
| 10_F | 14_V | 1.110 | 0.60 |
| 16_Q | 38_V | 1.103 | 0.59 |
| 3_S | 43_L | 1.091 | 0.58 |
| 15_P | 40_L | 1.069 | 0.56 |
| 10_F | 50_V | 1.067 | 0.55 |
| 4_P | 43_L | 1.065 | 0.55 |
| 29_H | 33_L | 1.037 | 0.52 |
| 16_Q | 48_A | 1.026 | 0.51 |
| 33_L | 46_I | 1.021 | 0.51 |
| 23_E | 56_E | 1.017 | 0.50 |
| 1_S | 20_R | 1.012 | 0.50 |
| 37_P | 45_F | 1.009 | 0.49 |
| 13_A | 51_S | 1.004 | 0.49 |
| 9_D | 42_A | 1.002 | 0.48 |
| 10_F | 40_L | 1.002 | 0.48 |
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 | |
| 2hfqA | 1 | 0.9138 | 0.1 | 0.57 | Contact Map |
| 4mxeA | 2 | 0.569 | 0.1 | 0.632 | Contact Map |
| 1vptA | 1 | 0.5517 | 0.1 | 0.64 | Contact Map |
| 3j61R | 1 | 0.1207 | 0.1 | 0.64 | Contact Map |
| 3j3iA | 1 | 0.8621 | 0.1 | 0.64 | Contact Map |
| 1nmbN | 1 | 1 | 0.1 | 0.649 | Contact Map |
| 4r29A | 4 | 1 | 0.1 | 0.667 | Contact Map |
| 1xrsA | 1 | 1 | 0.1 | 0.667 | Contact Map |
| 3iykA | 6 | 0.5517 | 0.1 | 0.675 | Contact Map |
| 4k0mC | 1 | 0.8966 | 0.1 | 0.675 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)