| Prasanth Kumar |
| ID: | 1499886867 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 101 (101) | ||
| Sequences: | 587 (431.3) | ||
| Seq/Len: | 5.812 | ||
| Nf(neff/√len): | 42.9 |
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: 5.812).
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 |
| 34_I | 63_M | 3.199 | 1.00 |
| 20_V | 34_I | 2.789 | 1.00 |
| 32_M | 68_M | 2.487 | 1.00 |
| 18_V | 90_I | 2.376 | 1.00 |
| 8_Y | 15_R | 2.372 | 1.00 |
| 32_M | 97_M | 2.135 | 1.00 |
| 51_Y | 66_T | 1.942 | 1.00 |
| 55_H | 60_S | 1.837 | 1.00 |
| 19_D | 31_R | 1.714 | 1.00 |
| 2_Q | 99_W | 1.692 | 1.00 |
| 8_Y | 17_F | 1.609 | 0.99 |
| 2_Q | 22_S | 1.544 | 0.99 |
| 39_A | 60_S | 1.465 | 0.99 |
| 21_Q | 30_R | 1.442 | 0.99 |
| 54_V | 83_L | 1.440 | 0.98 |
| 28_P | 66_T | 1.383 | 0.98 |
| 1_M | 4_K | 1.382 | 0.98 |
| 8_Y | 16_L | 1.363 | 0.98 |
| 86_R | 89_D | 1.358 | 0.98 |
| 34_I | 65_T | 1.340 | 0.97 |
| 4_K | 82_D | 1.308 | 0.97 |
| 2_Q | 67_D | 1.300 | 0.97 |
| 33_V | 76_I | 1.298 | 0.97 |
| 47_S | 51_Y | 1.276 | 0.96 |
| 18_V | 54_V | 1.264 | 0.96 |
| 37_A | 43_S | 1.262 | 0.96 |
| 64_M | 67_D | 1.238 | 0.95 |
| 54_V | 63_M | 1.226 | 0.95 |
| 14_Y | 101_I | 1.225 | 0.95 |
| 20_V | 94_I | 1.216 | 0.95 |
| 2_Q | 8_Y | 1.215 | 0.94 |
| 32_M | 94_I | 1.200 | 0.94 |
| 2_Q | 91_K | 1.126 | 0.91 |
| 1_M | 19_D | 1.114 | 0.90 |
| 56_I | 80_V | 1.103 | 0.90 |
| 12_S | 45_K | 1.098 | 0.90 |
| 2_Q | 14_Y | 1.094 | 0.89 |
| 31_R | 73_V | 1.089 | 0.89 |
| 88_N | 92_N | 1.074 | 0.88 |
| 96_L | 100_G | 1.074 | 0.88 |
| 7_T | 45_K | 1.063 | 0.87 |
| 51_Y | 62_R | 1.057 | 0.87 |
| 91_K | 98_F | 1.050 | 0.87 |
| 46_V | 62_R | 1.044 | 0.86 |
| 75_V | 79_E | 1.038 | 0.86 |
| 36_L | 52_P | 1.036 | 0.86 |
| 17_F | 71_V | 1.026 | 0.85 |
| 5_V | 81_A | 1.020 | 0.84 |
| 49_E | 96_L | 1.018 | 0.84 |
| 7_T | 57_G | 1.015 | 0.84 |
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 | |
| 3vubA | 1 | 1 | 100 | 0.056 | Contact Map |
| 2kmtA | 2 | 1 | 100 | 0.061 | Contact Map |
| 4mzmA | 4 | 0.9604 | 98.6 | 0.628 | Contact Map |
| 1ub4A | 2 | 0.9109 | 98.6 | 0.632 | Contact Map |
| 1m1fA | 2 | 0.9307 | 98.6 | 0.635 | Contact Map |
| 4mdxA | 2 | 0.9604 | 98.5 | 0.644 | Contact Map |
| 4h63H | 1 | 0.3069 | 3.9 | 0.925 | Contact Map |
| 4eu9A | 2 | 0.3366 | 3.4 | 0.927 | Contact Map |
| 3fx7A | 2 | 0.3168 | 3 | 0.929 | Contact Map |
| 3swyA | 3 | 0.2079 | 2.8 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)