| FIBRO_DOMAIN |
| ID: | 1457428246 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 89 (86) | ||
| Sequences: | 686 (433.5) | ||
| Seq/Len: | 7.977 | ||
| Nf(neff/√len): | 46.7 |
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: 7.977).
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_V | 85_I | 2.030 | 1.00 |
| 57_L | 63_Y | 1.709 | 1.00 |
| 9_T | 12_S | 1.699 | 1.00 |
| 3_L | 9_T | 1.515 | 1.00 |
| 5_V | 15_I | 1.511 | 1.00 |
| 7_A | 14_L | 1.506 | 1.00 |
| 27_Y | 69_A | 1.496 | 1.00 |
| 57_L | 61_V | 1.495 | 0.99 |
| 19_A | 27_Y | 1.484 | 0.99 |
| 24_V | 69_A | 1.470 | 0.99 |
| 2_D | 18_D | 1.464 | 0.99 |
| 26_Y | 47_G | 1.457 | 0.99 |
| 21_A | 67_V | 1.436 | 0.99 |
| 17_W | 27_Y | 1.408 | 0.99 |
| 82_P | 85_I | 1.388 | 0.99 |
| 3_L | 15_I | 1.377 | 0.99 |
| 25_R | 70_V | 1.311 | 0.98 |
| 8_A | 13_L | 1.285 | 0.98 |
| 28_R | 36_G | 1.261 | 0.98 |
| 24_V | 67_V | 1.222 | 0.97 |
| 31_Y | 43_F | 1.220 | 0.97 |
| 5_V | 13_L | 1.208 | 0.97 |
| 81_K | 85_I | 1.179 | 0.96 |
| 25_R | 71_T | 1.177 | 0.96 |
| 6_V | 15_I | 1.166 | 0.96 |
| 71_T | 74_G | 1.154 | 0.96 |
| 13_L | 87_Y | 1.130 | 0.95 |
| 10_P | 60_G | 1.129 | 0.95 |
| 70_V | 75_D | 1.094 | 0.94 |
| 69_A | 76_S | 1.083 | 0.93 |
| 39_P | 67_V | 1.080 | 0.93 |
| 24_V | 31_Y | 1.079 | 0.93 |
| 12_S | 32_G | 1.073 | 0.93 |
| 81_K | 84_S | 1.069 | 0.93 |
| 15_I | 65_I | 1.061 | 0.92 |
| 41_Q | 55_S | 1.052 | 0.92 |
| 29_I | 65_I | 1.041 | 0.91 |
| 27_Y | 33_E | 1.039 | 0.91 |
| 27_Y | 76_S | 1.027 | 0.91 |
| 31_Y | 36_G | 1.027 | 0.91 |
| 13_L | 65_I | 1.021 | 0.90 |
| 13_L | 46_P | 1.020 | 0.90 |
| 58_K | 70_V | 1.015 | 0.90 |
| 56_G | 85_I | 1.014 | 0.90 |
| 29_I | 43_F | 1.008 | 0.89 |
| 19_A | 53_T | 1.004 | 0.89 |
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 | |
| 3csgA | 1 | 0.9775 | 99.4 | 0.257 | Contact Map |
| 4jmgA | 1 | 0.9775 | 99.3 | 0.29 | Contact Map |
| 4lxoA | 2 | 1 | 99.3 | 0.293 | Contact Map |
| 2ha1A | 1 | 0.9551 | 99.3 | 0.306 | Contact Map |
| 2ocfD | 1 | 1 | 99.3 | 0.308 | Contact Map |
| 1qr4A | 2 | 0.9438 | 99.3 | 0.312 | Contact Map |
| 3qhtC | 2 | 1 | 99.3 | 0.314 | Contact Map |
| 2h41A | 1 | 0.9438 | 99.3 | 0.317 | Contact Map |
| 3qwqB | 1 | 0.9551 | 99.2 | 0.332 | Contact Map |
| 1fnfA | 1 | 1 | 99.2 | 0.335 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)