| pf02326_metagene |
| ID: | 1495004075 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 75 (75) | ||
| Sequences: | 2307 (849.6) | ||
| Seq/Len: | 30.760 | ||
| Nf(neff/√len): | 98.1 |
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: 30.760).
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 |
| 68_K | 72_A | 4.033 | 1.00 |
| 51_S | 54_A | 2.104 | 1.00 |
| 64_E | 68_K | 1.907 | 1.00 |
| 53_A | 56_K | 1.834 | 1.00 |
| 42_A | 46_Q | 1.755 | 1.00 |
| 11_Q | 15_F | 1.734 | 1.00 |
| 3_L | 8_F | 1.702 | 1.00 |
| 61_A | 65_S | 1.651 | 1.00 |
| 5_T | 9_F | 1.641 | 1.00 |
| 57_A | 61_A | 1.607 | 1.00 |
| 59_A | 63_I | 1.544 | 1.00 |
| 64_E | 67_D | 1.526 | 1.00 |
| 65_S | 69_E | 1.515 | 1.00 |
| 51_S | 55_L | 1.442 | 1.00 |
| 67_D | 71_I | 1.425 | 1.00 |
| 54_A | 58_E | 1.365 | 0.99 |
| 12_L | 16_T | 1.338 | 0.99 |
| 29_T | 33_K | 1.337 | 0.99 |
| 43_K | 47_Q | 1.330 | 0.99 |
| 60_T | 64_E | 1.325 | 0.99 |
| 61_A | 64_E | 1.317 | 0.99 |
| 8_F | 37_V | 1.278 | 0.99 |
| 55_L | 59_A | 1.259 | 0.99 |
| 23_Y | 27_L | 1.254 | 0.99 |
| 26_V | 30_I | 1.221 | 0.98 |
| 4_D | 7_T | 1.206 | 0.98 |
| 69_E | 72_A | 1.177 | 0.98 |
| 68_K | 71_I | 1.163 | 0.97 |
| 10_N | 13_F | 1.161 | 0.97 |
| 5_T | 19_F | 1.152 | 0.97 |
| 11_Q | 31_I | 1.147 | 0.97 |
| 52_S | 59_A | 1.138 | 0.97 |
| 53_A | 57_A | 1.122 | 0.97 |
| 21_G | 25_F | 1.115 | 0.96 |
| 44_K | 48_D | 1.111 | 0.96 |
| 56_K | 60_T | 1.068 | 0.95 |
| 65_S | 68_K | 1.048 | 0.94 |
| 7_T | 10_N | 1.003 | 0.93 |
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 | |
| 2khkA | 1 | 0.5467 | 92.4 | 0.744 | Contact Map |
| 1b9uA | 1 | 0.44 | 80.4 | 0.788 | Contact Map |
| 2clyA | 2 | 0.5467 | 42.5 | 0.836 | Contact Map |
| 2rddB | 1 | 0.4933 | 12.5 | 0.873 | Contact Map |
| 1fx0A | 1 | 0.9867 | 5.2 | 0.893 | Contact Map |
| 3qnqA | 4 | 0.6 | 5.2 | 0.894 | Contact Map |
| 4gfqA | 1 | 0.72 | 3.8 | 0.901 | Contact Map |
| 4qinA | 1 | 1 | 3.6 | 0.901 | Contact Map |
| 4phqA | 4 | 1 | 3.6 | 0.901 | Contact Map |
| 4ltoA | 4 | 0.92 | 3.5 | 0.902 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)