| frataxin |
| ID: | 1431426096 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (106) | ||
| Sequences: | 473 (339.3) | ||
| Seq/Len: | 4.462 | ||
| Nf(neff/√len): | 33.0 |
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: 4.462).
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 |
| 59_Q | 72_D | 2.969 | 1.00 |
| 3_D | 58_H | 2.388 | 1.00 |
| 6_F | 55_E | 2.051 | 1.00 |
| 9_L | 73_L | 2.041 | 1.00 |
| 85_E | 93_Q | 1.819 | 1.00 |
| 86_T | 89_D | 1.804 | 1.00 |
| 93_Q | 97_Q | 1.681 | 0.99 |
| 64_T | 94_A | 1.577 | 0.99 |
| 2_N | 5_E | 1.573 | 0.99 |
| 3_D | 55_E | 1.572 | 0.99 |
| 66_Q | 94_A | 1.559 | 0.99 |
| 37_G | 59_Q | 1.552 | 0.99 |
| 10_A | 14_W | 1.545 | 0.98 |
| 63_A | 68_G | 1.535 | 0.98 |
| 71_F | 83_S | 1.530 | 0.98 |
| 71_F | 85_E | 1.504 | 0.98 |
| 7_H | 53_R | 1.456 | 0.98 |
| 7_H | 11_D | 1.455 | 0.98 |
| 12_Q | 31_D | 1.389 | 0.96 |
| 39_L | 43_F | 1.388 | 0.96 |
| 54_Q | 57_L | 1.379 | 0.96 |
| 34_I | 80_C | 1.364 | 0.96 |
| 6_F | 44_E | 1.309 | 0.95 |
| 44_E | 47_S | 1.278 | 0.94 |
| 80_C | 83_S | 1.274 | 0.94 |
| 1_M | 5_E | 1.261 | 0.93 |
| 62_L | 87_F | 1.247 | 0.93 |
| 57_L | 70_H | 1.242 | 0.92 |
| 40_T | 48_K | 1.241 | 0.92 |
| 64_T | 67_G | 1.218 | 0.91 |
| 38_V | 67_G | 1.214 | 0.91 |
| 59_Q | 81_D | 1.213 | 0.91 |
| 30_I | 39_L | 1.203 | 0.91 |
| 73_L | 79_I | 1.189 | 0.90 |
| 64_T | 98_Q | 1.161 | 0.89 |
| 51_I | 90_L | 1.141 | 0.87 |
| 92_E | 105_F | 1.125 | 0.86 |
| 6_F | 58_H | 1.122 | 0.86 |
| 72_D | 81_D | 1.119 | 0.86 |
| 37_G | 53_R | 1.107 | 0.85 |
| 71_F | 90_L | 1.104 | 0.85 |
| 54_Q | 68_G | 1.101 | 0.85 |
| 37_G | 57_L | 1.094 | 0.84 |
| 71_F | 100_G | 1.090 | 0.84 |
| 21_L | 33_E | 1.071 | 0.83 |
| 77_E | 86_T | 1.059 | 0.82 |
| 38_V | 50_I | 1.045 | 0.80 |
| 15_L | 89_D | 1.045 | 0.80 |
| 39_L | 82_R | 1.040 | 0.80 |
| 13_L | 88_W | 1.036 | 0.80 |
| 69_Y | 80_C | 1.035 | 0.79 |
| 2_N | 35_N | 1.028 | 0.79 |
| 21_L | 24_W | 1.028 | 0.79 |
| 95_A | 99_A | 1.021 | 0.78 |
| 41_I | 93_Q | 1.019 | 0.78 |
| 54_Q | 62_L | 1.018 | 0.78 |
| 22_D | 32_C | 1.012 | 0.77 |
| 38_V | 48_K | 1.006 | 0.77 |
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 | |
| 1ew4A | 1 | 1 | 100 | -0.001 | Contact Map |
| 4jpdA | 1 | 1 | 100 | 0.004 | Contact Map |
| 4hs5A | 2 | 0.9811 | 100 | 0.011 | Contact Map |
| 3t3lA | 1 | 1 | 100 | 0.029 | Contact Map |
| 3oeqA | 1 | 0.9528 | 100 | 0.088 | Contact Map |
| 4da2A | 2 | 0.9057 | 17.6 | 0.92 | Contact Map |
| 4n4uA | 2 | 0.8679 | 16.3 | 0.921 | Contact Map |
| 4ux3B | 1 | 0.2547 | 14.5 | 0.923 | Contact Map |
| 3aabA | 2 | 0.5094 | 13.4 | 0.924 | Contact Map |
| 2fkbA | 3 | 0.8585 | 11 | 0.927 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)