| Ashfaq Ahmad |
| ID: | 1451066571 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (101) | ||
| Sequences: | 2233 (1739.9) | ||
| Seq/Len: | 22.109 | ||
| Nf(neff/√len): | 173.1 |
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: 22.109).
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 |
| 43_F | 75_Y | 2.492 | 1.00 |
| 36_I | 80_M | 2.239 | 1.00 |
| 27_A | 90_I | 2.090 | 1.00 |
| 20_I | 98_V | 1.915 | 1.00 |
| 10_F | 14_T | 1.851 | 1.00 |
| 35_M | 83_L | 1.822 | 1.00 |
| 13_A | 103_H | 1.762 | 1.00 |
| 39_V | 79_L | 1.697 | 1.00 |
| 11_S | 14_T | 1.686 | 1.00 |
| 17_T | 21_S | 1.686 | 1.00 |
| 84_I | 88_S | 1.591 | 1.00 |
| 17_T | 102_V | 1.567 | 1.00 |
| 47_D | 72_H | 1.555 | 1.00 |
| 102_V | 105_G | 1.535 | 1.00 |
| 81_N | 85_M | 1.447 | 1.00 |
| 95_V | 99_L | 1.429 | 1.00 |
| 25_I | 91_S | 1.408 | 1.00 |
| 81_N | 84_I | 1.398 | 0.99 |
| 38_S | 82_K | 1.354 | 0.99 |
| 19_F | 101_A | 1.312 | 0.99 |
| 51_L | 55_S | 1.287 | 0.99 |
| 28_F | 86_T | 1.277 | 0.99 |
| 43_F | 46_Q | 1.249 | 0.99 |
| 98_V | 102_V | 1.238 | 0.98 |
| 80_M | 83_L | 1.196 | 0.98 |
| 39_V | 75_Y | 1.163 | 0.97 |
| 33_W | 37_H | 1.157 | 0.97 |
| 24_T | 94_I | 1.157 | 0.97 |
| 16_L | 91_S | 1.151 | 0.97 |
| 43_F | 72_H | 1.145 | 0.97 |
| 55_S | 65_I | 1.127 | 0.97 |
| 49_N | 53_E | 1.122 | 0.97 |
| 48_I | 69_I | 1.115 | 0.96 |
| 36_I | 79_L | 1.107 | 0.96 |
| 19_F | 97_I | 1.106 | 0.96 |
| 90_I | 94_I | 1.103 | 0.96 |
| 49_N | 60_R | 1.079 | 0.95 |
| 32_A | 83_L | 1.067 | 0.95 |
| 21_S | 95_V | 1.065 | 0.95 |
| 24_T | 28_F | 1.064 | 0.95 |
| 68_S | 102_V | 1.064 | 0.95 |
| 36_I | 76_I | 1.062 | 0.95 |
| 94_I | 102_V | 1.060 | 0.95 |
| 55_S | 59_E | 1.056 | 0.95 |
| 10_F | 18_F | 1.052 | 0.95 |
| 10_F | 15_R | 1.043 | 0.94 |
| 45_E | 49_N | 1.021 | 0.93 |
| 65_I | 97_I | 1.016 | 0.93 |
| 26_A | 74_H | 1.011 | 0.93 |
| 14_T | 99_L | 1.009 | 0.93 |
| 34_I | 86_T | 1.007 | 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 | |
| 2kseA | 1 | 0.3679 | 86.4 | 0.668 | Contact Map |
| 2f95B | 1 | 0.5 | 17 | 0.803 | Contact Map |
| 4i5sA | 2 | 0.1038 | 11.5 | 0.818 | Contact Map |
| 4gycB | 1 | 0.5755 | 6.6 | 0.836 | Contact Map |
| 1qleD | 1 | 0.4057 | 5.1 | 0.845 | Contact Map |
| 3pjsK | 4 | 0.8868 | 4.6 | 0.848 | Contact Map |
| 2f93B | 1 | 0.4811 | 4.3 | 0.851 | Contact Map |
| 3rlfG | 1 | 0.8585 | 4.1 | 0.852 | Contact Map |
| 3j1zP | 2 | 0.9623 | 4.1 | 0.852 | Contact Map |
| 2bs2C | 2 | 0.5377 | 3.6 | 0.856 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)