| 1POH |
| ID: | 1429465584 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 85 (85) | ||
| Sequences: | 2156 (1579.1) | ||
| Seq/Len: | 25.365 | ||
| Nf(neff/√len): | 171.3 |
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: 25.365).
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 |
| 5_E | 60_V | 3.168 | 1.00 |
| 31_S | 69_D | 2.551 | 1.00 |
| 65_A | 74_V | 2.536 | 1.00 |
| 4_Q | 78_V | 2.270 | 1.00 |
| 29_F | 76_H | 2.071 | 1.00 |
| 30_T | 68_E | 2.049 | 1.00 |
| 25_E | 28_G | 2.048 | 1.00 |
| 3_Q | 62_T | 2.044 | 1.00 |
| 6_V | 78_V | 1.898 | 1.00 |
| 3_Q | 64_S | 1.823 | 1.00 |
| 30_T | 69_D | 1.812 | 1.00 |
| 79_K | 83_E | 1.777 | 1.00 |
| 78_V | 82_A | 1.763 | 1.00 |
| 22_F | 77_L | 1.752 | 1.00 |
| 34_T | 41_S | 1.723 | 1.00 |
| 37_S | 59_T | 1.672 | 1.00 |
| 71_Q | 75_E | 1.660 | 1.00 |
| 7_T | 60_V | 1.656 | 1.00 |
| 25_E | 76_H | 1.646 | 1.00 |
| 5_E | 62_T | 1.623 | 1.00 |
| 36_T | 64_S | 1.620 | 1.00 |
| 36_T | 62_T | 1.567 | 1.00 |
| 29_F | 73_A | 1.533 | 1.00 |
| 36_T | 41_S | 1.519 | 1.00 |
| 1_M | 70_E | 1.463 | 1.00 |
| 22_F | 44_A | 1.459 | 1.00 |
| 2_F | 71_Q | 1.453 | 1.00 |
| 41_S | 64_S | 1.425 | 1.00 |
| 2_F | 74_V | 1.412 | 1.00 |
| 72_K | 76_H | 1.306 | 0.99 |
| 31_S | 65_A | 1.243 | 0.98 |
| 42_A | 53_L | 1.240 | 0.98 |
| 55_L | 61_V | 1.175 | 0.98 |
| 36_T | 39_G | 1.153 | 0.97 |
| 32_E | 66_E | 1.123 | 0.97 |
| 8_I | 55_L | 1.123 | 0.97 |
| 9_T | 84_L | 1.099 | 0.96 |
| 4_Q | 75_E | 1.096 | 0.96 |
| 75_E | 79_K | 1.092 | 0.96 |
| 9_T | 82_A | 1.080 | 0.95 |
| 11_P | 57_Q | 1.067 | 0.95 |
| 33_I | 73_A | 1.057 | 0.95 |
| 42_A | 48_F | 1.038 | 0.94 |
| 69_D | 72_K | 1.017 | 0.93 |
| 72_K | 75_E | 1.007 | 0.93 |
| 22_F | 35_V | 1.002 | 0.92 |
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 | |
| 3le1A | 2 | 1 | 99.9 | 0.005 | Contact Map |
| 1sphA | 2 | 0.9882 | 99.9 | 0.011 | Contact Map |
| 1y51A | 3 | 0.9882 | 99.9 | 0.012 | Contact Map |
| 1kklH | 3 | 1 | 99.9 | 0.017 | Contact Map |
| 1ka5A | 1 | 1 | 99.9 | 0.024 | Contact Map |
| 1ptfA | 1 | 1 | 99.9 | 0.03 | Contact Map |
| 3ihsA | 2 | 0.9647 | 99.9 | 0.03 | Contact Map |
| 1pchA | 1 | 0.9882 | 99.9 | 0.039 | Contact Map |
| 3ccdA | 2 | 1 | 99.9 | 0.043 | Contact Map |
| 2jpiA | 1 | 0.9059 | 51.9 | 0.849 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)