| Hetunandan Munisharan Kamichetty 60-226 |
| ID: | 1489349672 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 167 (158) | ||
| Sequences: | 1321 (772.4) | ||
| Seq/Len: | 8.361 | ||
| Nf(neff/√len): | 61.4 |
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: 8.361).
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 |
| 99_K | 103_D | 3.942 | 1.00 |
| 40_Y | 99_K | 3.475 | 1.00 |
| 55_H | 80_G | 3.276 | 1.00 |
| 52_L | 85_I | 2.854 | 1.00 |
| 96_F | 102_F | 2.654 | 1.00 |
| 18_A | 62_V | 2.594 | 1.00 |
| 96_F | 101_R | 2.278 | 1.00 |
| 43_A | 74_M | 2.171 | 1.00 |
| 58_Q | 77_F | 2.044 | 1.00 |
| 57_N | 78_G | 2.027 | 1.00 |
| 43_A | 63_A | 1.889 | 1.00 |
| 54_L | 81_L | 1.800 | 1.00 |
| 12_I | 16_T | 1.759 | 1.00 |
| 57_N | 90_Y | 1.757 | 1.00 |
| 41_G | 105_F | 1.755 | 1.00 |
| 50_F | 87_G | 1.638 | 1.00 |
| 19_D | 64_V | 1.588 | 1.00 |
| 162_L | 165_T | 1.584 | 1.00 |
| 53_M | 85_I | 1.566 | 1.00 |
| 66_R | 71_H | 1.532 | 1.00 |
| 94_I | 135_M | 1.520 | 1.00 |
| 22_L | 26_F | 1.512 | 1.00 |
| 45_F | 61_G | 1.493 | 1.00 |
| 36_F | 95_L | 1.439 | 0.99 |
| 121_G | 138_Y | 1.437 | 0.99 |
| 85_I | 147_L | 1.415 | 0.99 |
| 22_L | 44_V | 1.414 | 0.99 |
| 36_F | 42_Y | 1.356 | 0.99 |
| 78_G | 154_S | 1.354 | 0.99 |
| 40_Y | 102_F | 1.353 | 0.99 |
| 18_A | 44_V | 1.336 | 0.99 |
| 13_A | 17_M | 1.263 | 0.98 |
| 81_L | 84_G | 1.254 | 0.98 |
| 41_G | 63_A | 1.239 | 0.98 |
| 161_D | 164_E | 1.234 | 0.98 |
| 48_R | 89_F | 1.232 | 0.98 |
| 94_I | 137_I | 1.229 | 0.98 |
| 26_F | 36_F | 1.203 | 0.97 |
| 76_M | 156_Y | 1.184 | 0.97 |
| 104_A | 108_Q | 1.162 | 0.96 |
| 9_E | 12_I | 1.161 | 0.96 |
| 21_A | 24_R | 1.156 | 0.96 |
| 46_D | 84_G | 1.145 | 0.96 |
| 41_G | 65_N | 1.136 | 0.96 |
| 102_F | 106_V | 1.130 | 0.95 |
| 45_F | 140_I | 1.115 | 0.95 |
| 78_G | 90_Y | 1.114 | 0.95 |
| 39_A | 110_W | 1.092 | 0.94 |
| 35_L | 136_A | 1.089 | 0.94 |
| 22_L | 93_V | 1.080 | 0.94 |
| 63_A | 96_F | 1.079 | 0.94 |
| 39_A | 66_R | 1.067 | 0.93 |
| 45_F | 76_M | 1.058 | 0.93 |
| 105_F | 156_Y | 1.056 | 0.93 |
| 35_L | 95_L | 1.051 | 0.92 |
| 110_W | 155_K | 1.043 | 0.92 |
| 80_G | 152_S | 1.039 | 0.92 |
| 37_D | 40_Y | 1.039 | 0.92 |
| 10_A | 49_K | 1.037 | 0.92 |
| 75_K | 159_D | 1.033 | 0.92 |
| 53_M | 81_L | 1.026 | 0.91 |
| 85_I | 150_N | 1.024 | 0.91 |
| 132_N | 150_N | 1.016 | 0.91 |
| 45_F | 74_M | 1.012 | 0.90 |
| 43_A | 96_F | 1.011 | 0.90 |
| 15_N | 73_Y | 1.007 | 0.90 |
| 34_L | 38_K | 1.006 | 0.90 |
| 118_V | 147_L | 1.005 | 0.90 |
| 119_V | 133_G | 1.004 | 0.90 |
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 | |
| 1r89A | 1 | 0.6826 | 5.4 | 0.944 | Contact Map |
| 2wscL | 1 | 0.3772 | 4.9 | 0.946 | Contact Map |
| 1px5A | 2 | 0.7425 | 4.9 | 0.946 | Contact Map |
| 4xq7A | 1 | 0 | 3 | 0.951 | Contact Map |
| 2marA | 1 | 0.2754 | 3 | 0.951 | Contact Map |
| 1yo3A | 3 | 0.491 | 2.9 | 0.951 | Contact Map |
| 3rjsA | 1 | 0.491 | 2.8 | 0.952 | Contact Map |
| 2g5xA | 1 | 0.3353 | 2.7 | 0.952 | Contact Map |
| 2qklA | 1 | 0.6766 | 2.7 | 0.952 | Contact Map |
| 2ervA | 2 | 0.5329 | 2.6 | 0.953 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)