| hat |
| ID: | 1430261519 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 73 (73) | ||
| Sequences: | 154 (74.8) | ||
| Seq/Len: | 2.110 | ||
| Nf(neff/√len): | 8.8 |
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: 2.110).
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 |
| 9_I | 25_C | 2.272 | 1.00 |
| 38_T | 42_N | 2.064 | 0.99 |
| 58_T | 67_Y | 1.918 | 0.99 |
| 23_A | 46_D | 1.779 | 0.98 |
| 14_F | 23_A | 1.582 | 0.94 |
| 9_I | 22_I | 1.532 | 0.93 |
| 13_P | 27_I | 1.522 | 0.93 |
| 19_F | 57_L | 1.509 | 0.92 |
| 41_M | 67_Y | 1.469 | 0.91 |
| 43_H | 57_L | 1.389 | 0.87 |
| 1_Q | 6_V | 1.371 | 0.86 |
| 33_V | 70_K | 1.363 | 0.86 |
| 28_T | 31_E | 1.361 | 0.86 |
| 23_A | 39_K | 1.265 | 0.80 |
| 22_I | 58_T | 1.221 | 0.76 |
| 6_V | 17_Q | 1.212 | 0.75 |
| 31_E | 34_K | 1.200 | 0.74 |
| 59_Y | 66_G | 1.199 | 0.74 |
| 22_I | 25_C | 1.172 | 0.72 |
| 42_N | 47_Y | 1.156 | 0.70 |
| 1_Q | 44_L | 1.145 | 0.69 |
| 22_I | 41_M | 1.142 | 0.69 |
| 12_R | 33_V | 1.138 | 0.69 |
| 22_I | 67_Y | 1.128 | 0.68 |
| 26_A | 34_K | 1.118 | 0.67 |
| 25_C | 55_R | 1.116 | 0.66 |
| 34_K | 55_R | 1.114 | 0.66 |
| 60_A | 72_G | 1.112 | 0.66 |
| 7_G | 55_R | 1.095 | 0.64 |
| 55_R | 65_I | 1.092 | 0.64 |
| 12_R | 66_G | 1.079 | 0.63 |
| 58_T | 64_A | 1.059 | 0.60 |
| 33_V | 66_G | 1.058 | 0.60 |
| 18_G | 54_Y | 1.050 | 0.59 |
| 3_G | 23_A | 1.046 | 0.59 |
| 1_Q | 11_F | 1.046 | 0.59 |
| 27_I | 33_V | 1.028 | 0.57 |
| 64_A | 67_Y | 1.024 | 0.57 |
| 5_I | 19_F | 1.013 | 0.55 |
| 8_G | 32_Q | 1.013 | 0.55 |
| 24_F | 58_T | 1.008 | 0.55 |
| 59_Y | 63_F | 1.004 | 0.54 |
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 | |
| 1yghA | 2 | 1 | 99 | 0.687 | Contact Map |
| 1qstA | 1 | 1 | 98.7 | 0.712 | Contact Map |
| 4nsqA | 4 | 1 | 98.7 | 0.714 | Contact Map |
| 2r7hA | 2 | 1 | 98.6 | 0.721 | Contact Map |
| 1z4rA | 1 | 1 | 98.6 | 0.725 | Contact Map |
| 2jdcA | 1 | 1 | 98.4 | 0.738 | Contact Map |
| 3d2mA | 1 | 0.9863 | 98.4 | 0.742 | Contact Map |
| 1n71A | 4 | 1 | 98.4 | 0.744 | Contact Map |
| 3e0kA | 1 | 0.9863 | 98.4 | 0.745 | Contact Map |
| 2g3aA | 1 | 0.9726 | 98.4 | 0.745 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)