| 1141 |
| ID: | 1443450285 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 83 (82) | ||
| Sequences: | 282 (232.8) | ||
| Seq/Len: | 3.439 | ||
| Nf(neff/√len): | 25.7 |
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: 3.439).
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 |
| 17_V | 66_V | 3.306 | 1.00 |
| 67_N | 71_Q | 2.100 | 1.00 |
| 37_H | 41_M | 2.073 | 1.00 |
| 61_S | 64_G | 1.932 | 1.00 |
| 75_A | 80_G | 1.899 | 1.00 |
| 71_Q | 75_A | 1.892 | 1.00 |
| 76_N | 80_G | 1.786 | 0.99 |
| 10_E | 70_K | 1.680 | 0.99 |
| 75_A | 83_Q | 1.669 | 0.99 |
| 43_E | 78_K | 1.634 | 0.98 |
| 39_E | 48_S | 1.612 | 0.98 |
| 38_F | 47_G | 1.546 | 0.97 |
| 18_T | 63_S | 1.479 | 0.96 |
| 60_D | 64_G | 1.471 | 0.96 |
| 25_T | 34_L | 1.443 | 0.96 |
| 15_Q | 18_T | 1.393 | 0.94 |
| 21_C | 65_I | 1.376 | 0.94 |
| 27_S | 30_E | 1.357 | 0.93 |
| 58_D | 68_T | 1.334 | 0.93 |
| 19_T | 30_E | 1.321 | 0.92 |
| 49_D | 53_Y | 1.252 | 0.89 |
| 9_T | 12_E | 1.203 | 0.86 |
| 37_H | 40_E | 1.195 | 0.86 |
| 80_G | 83_Q | 1.194 | 0.86 |
| 29_E | 79_S | 1.184 | 0.85 |
| 14_L | 66_V | 1.174 | 0.84 |
| 44_H | 50_L | 1.162 | 0.84 |
| 15_Q | 65_I | 1.135 | 0.82 |
| 47_G | 50_L | 1.130 | 0.81 |
| 23_A | 31_L | 1.112 | 0.80 |
| 20_I | 27_S | 1.104 | 0.79 |
| 29_E | 33_K | 1.088 | 0.78 |
| 19_T | 24_D | 1.061 | 0.75 |
| 28_E | 31_L | 1.054 | 0.74 |
| 56_E | 61_S | 1.037 | 0.73 |
| 46_S | 55_K | 1.034 | 0.72 |
| 9_T | 82_K | 1.031 | 0.72 |
| 74_A | 80_G | 1.028 | 0.72 |
| 13_F | 38_F | 1.027 | 0.72 |
| 56_E | 64_G | 1.015 | 0.70 |
| 21_C | 35_V | 1.012 | 0.70 |
| 67_N | 75_A | 1.009 | 0.70 |
| 59_D | 64_G | 1.009 | 0.70 |
| 69_V | 82_K | 1.008 | 0.70 |
| 13_F | 41_M | 1.008 | 0.70 |
| 32_V | 52_Y | 1.006 | 0.69 |
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 | |
| 4f37A | 2 | 1 | 100 | -0.006 | Contact Map |
| 1fr2A | 1 | 1 | 100 | -0.002 | Contact Map |
| 1unkA | 4 | 1 | 100 | 0.005 | Contact Map |
| 1gxgA | 1 | 0.988 | 100 | 0.01 | Contact Map |
| 4qkoA | 4 | 0 | 100 | 0.011 | Contact Map |
| 3u43A | 1 | 1 | 100 | 0.012 | Contact Map |
| 4uhpB | 4 | 0 | 100 | 0.025 | Contact Map |
| 2k0dX | 1 | 1 | 100 | 0.029 | Contact Map |
| 3or1A | 2 | 0.9036 | 34.6 | 0.89 | Contact Map |
| 3m6zA | 2 | 0.4699 | 23.3 | 0.899 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)