| 4ku0 |
| ID: | 1500381492 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 96 (93) | ||
| Sequences: | 1933 (1169.9) | ||
| Seq/Len: | 20.785 | ||
| Nf(neff/√len): | 121.3 |
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: 20.785).
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 |
| 75_Q | 78_D | 3.327 | 1.00 |
| 37_V | 40_D | 2.815 | 1.00 |
| 59_T | 74_V | 2.796 | 1.00 |
| 5_Y | 8_C | 2.767 | 1.00 |
| 6_D | 24_T | 2.560 | 1.00 |
| 31_G | 90_S | 2.301 | 1.00 |
| 68_V | 73_A | 2.201 | 1.00 |
| 58_V | 81_S | 2.171 | 1.00 |
| 4_S | 21_V | 2.125 | 1.00 |
| 29_F | 67_Y | 2.106 | 1.00 |
| 25_Q | 69_T | 2.080 | 1.00 |
| 39_G | 71_K | 1.905 | 1.00 |
| 9_V | 89_A | 1.774 | 1.00 |
| 27_K | 69_T | 1.655 | 1.00 |
| 32_G | 70_G | 1.653 | 1.00 |
| 61_P | 78_D | 1.648 | 1.00 |
| 25_Q | 37_V | 1.640 | 1.00 |
| 31_G | 92_K | 1.621 | 1.00 |
| 23_A | 40_D | 1.620 | 1.00 |
| 35_V | 73_A | 1.582 | 1.00 |
| 23_A | 41_P | 1.542 | 1.00 |
| 30_T | 35_V | 1.523 | 1.00 |
| 28_V | 66_V | 1.486 | 1.00 |
| 7_K | 33_I | 1.466 | 1.00 |
| 9_V | 20_V | 1.454 | 1.00 |
| 36_L | 59_T | 1.454 | 1.00 |
| 21_V | 36_L | 1.434 | 1.00 |
| 38_A | 72_K | 1.425 | 1.00 |
| 41_P | 58_V | 1.397 | 0.99 |
| 61_P | 79_P | 1.356 | 0.99 |
| 79_P | 85_T | 1.253 | 0.99 |
| 37_V | 71_K | 1.236 | 0.98 |
| 80_I | 84_D | 1.234 | 0.98 |
| 38_A | 62_R | 1.210 | 0.98 |
| 59_T | 86_V | 1.206 | 0.98 |
| 63_T | 75_Q | 1.194 | 0.98 |
| 28_V | 68_V | 1.179 | 0.98 |
| 74_V | 86_V | 1.152 | 0.97 |
| 76_M | 89_A | 1.101 | 0.96 |
| 24_T | 34_A | 1.093 | 0.96 |
| 6_D | 23_A | 1.092 | 0.96 |
| 22_N | 46_T | 1.085 | 0.96 |
| 13_H | 84_D | 1.084 | 0.96 |
| 5_Y | 90_S | 1.065 | 0.95 |
| 3_L | 73_A | 1.065 | 0.95 |
| 57_G | 81_S | 1.063 | 0.95 |
| 28_V | 35_V | 1.057 | 0.95 |
| 13_H | 80_I | 1.041 | 0.94 |
| 6_D | 34_A | 1.019 | 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 | |
| 4ku0D | 1 | 1 | 99.9 | -0.022 | Contact Map |
| 4jivD | 1 | 0.9688 | 99.9 | 0.057 | Contact Map |
| 4jiwD | 4 | 0.9688 | 99.9 | 0.059 | Contact Map |
| 4zjmA | 1 | 0 | 1.9 | 0.92 | Contact Map |
| 4xinA | 2 | 0.5729 | 1 | 0.931 | Contact Map |
| 1hxrA | 2 | 0.6146 | 1 | 0.932 | Contact Map |
| 2x9aA | 2 | 0.2396 | 0.9 | 0.934 | Contact Map |
| 3oepA | 1 | 0.7708 | 0.8 | 0.937 | Contact Map |
| 3zqjA | 6 | 0.8854 | 0.7 | 0.938 | Contact Map |
| 3u6pA | 1 | 0.3125 | 0.7 | 0.939 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)