| SecondMerge_cdhit76_satedit2 |
| ID: | 1509117418 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (104) | ||
| Sequences: | 1254 (814.1) | ||
| Seq/Len: | 12.058 | ||
| Nf(neff/√len): | 79.8 |
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: 12.058).
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 |
| 44_S | 76_F | 3.413 | 1.00 |
| 43_A | 74_S | 3.133 | 1.00 |
| 59_I | 67_L | 2.847 | 1.00 |
| 79_D | 95_S | 2.512 | 1.00 |
| 46_L | 78_I | 2.053 | 1.00 |
| 66_R | 69_E | 1.924 | 1.00 |
| 32_E | 58_H | 1.611 | 1.00 |
| 4_N | 9_F | 1.413 | 1.00 |
| 32_E | 86_S | 1.404 | 0.99 |
| 82_M | 92_T | 1.398 | 0.99 |
| 59_I | 63_E | 1.390 | 0.99 |
| 34_R | 58_H | 1.378 | 0.99 |
| 77_A | 80_G | 1.343 | 0.99 |
| 29_S | 45_L | 1.329 | 0.99 |
| 55_N | 85_V | 1.305 | 0.99 |
| 77_A | 92_T | 1.294 | 0.99 |
| 43_A | 76_F | 1.279 | 0.99 |
| 49_R | 95_S | 1.264 | 0.99 |
| 46_L | 74_S | 1.239 | 0.98 |
| 74_S | 77_A | 1.235 | 0.98 |
| 6_K | 9_F | 1.208 | 0.98 |
| 28_I | 91_L | 1.197 | 0.98 |
| 48_D | 71_L | 1.196 | 0.98 |
| 27_Q | 98_A | 1.189 | 0.98 |
| 7_A | 12_D | 1.185 | 0.98 |
| 45_L | 50_T | 1.161 | 0.97 |
| 54_I | 105_S | 1.157 | 0.97 |
| 36_F | 70_F | 1.156 | 0.97 |
| 4_N | 18_S | 1.141 | 0.97 |
| 68_L | 72_A | 1.136 | 0.97 |
| 4_N | 11_L | 1.127 | 0.97 |
| 11_L | 16_T | 1.127 | 0.97 |
| 36_F | 65_N | 1.121 | 0.97 |
| 3_E | 9_F | 1.114 | 0.96 |
| 47_L | 79_D | 1.102 | 0.96 |
| 51_P | 91_L | 1.096 | 0.96 |
| 61_D | 65_N | 1.091 | 0.96 |
| 28_I | 97_T | 1.084 | 0.96 |
| 40_E | 44_S | 1.083 | 0.96 |
| 33_P | 54_I | 1.056 | 0.95 |
| 6_K | 11_L | 1.056 | 0.95 |
| 85_V | 91_L | 1.054 | 0.95 |
| 5_A | 16_T | 1.045 | 0.94 |
| 55_N | 86_S | 1.045 | 0.94 |
| 39_A | 42_I | 1.044 | 0.94 |
| 2_M | 19_K | 1.034 | 0.94 |
| 33_P | 55_N | 1.024 | 0.93 |
| 56_L | 86_S | 1.023 | 0.93 |
| 54_I | 71_L | 1.008 | 0.93 |
| 38_E | 97_T | 1.004 | 0.93 |
| 31_I | 41_S | 1.001 | 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 | |
| 3p04A | 2 | 0.7358 | 99.9 | 0.204 | Contact Map |
| 3zihA | 2 | 0.7547 | 99.9 | 0.215 | Contact Map |
| 3zieA | 6 | 0.7642 | 99.9 | 0.273 | Contact Map |
| 3zigA | 2 | 0.7642 | 99.9 | 0.284 | Contact Map |
| 1k0wA | 6 | 0.4528 | 16.9 | 0.911 | Contact Map |
| 4pj2A | 2 | 0.5566 | 13.8 | 0.914 | Contact Map |
| 2fk5A | 2 | 0.4434 | 12.8 | 0.915 | Contact Map |
| 4aybF | 1 | 0.5 | 10.2 | 0.919 | Contact Map |
| 2opiA | 2 | 0.4717 | 9.8 | 0.92 | Contact Map |
| 4by7D | 1 | 0.566 | 8.9 | 0.921 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)