| 1xob |
| ID: | 1515770893 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (105) | ||
| Sequences: | 7509 (4844.9) | ||
| Seq/Len: | 71.514 | ||
| Nf(neff/√len): | 472.8 |
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: 71.514).
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 |
| 86_V | 89_T | 2.869 | 1.00 |
| 44_E | 96_K | 2.472 | 1.00 |
| 59_N | 62_Q | 2.408 | 1.00 |
| 9_D | 65_G | 2.275 | 1.00 |
| 88_A | 102_F | 2.230 | 1.00 |
| 9_D | 66_T | 2.198 | 1.00 |
| 100_K | 104_D | 2.065 | 1.00 |
| 79_L | 86_V | 2.061 | 1.00 |
| 13_D | 69_K | 2.014 | 1.00 |
| 48_E | 100_K | 1.921 | 1.00 |
| 48_E | 96_K | 1.897 | 1.00 |
| 7_L | 56_A | 1.889 | 1.00 |
| 60_I | 75_I | 1.837 | 1.00 |
| 98_Q | 101_E | 1.791 | 1.00 |
| 21_G | 54_T | 1.783 | 1.00 |
| 38_I | 78_L | 1.771 | 1.00 |
| 11_S | 15_D | 1.752 | 1.00 |
| 49_Y | 104_D | 1.744 | 1.00 |
| 42_L | 55_V | 1.742 | 1.00 |
| 80_L | 106_N | 1.717 | 1.00 |
| 79_L | 89_T | 1.685 | 1.00 |
| 95_S | 98_Q | 1.684 | 1.00 |
| 15_D | 54_T | 1.615 | 1.00 |
| 94_L | 98_Q | 1.585 | 1.00 |
| 49_Y | 100_K | 1.557 | 1.00 |
| 30_E | 59_N | 1.541 | 1.00 |
| 13_D | 18_K | 1.537 | 1.00 |
| 41_I | 44_E | 1.445 | 1.00 |
| 90_K | 94_L | 1.374 | 0.99 |
| 78_L | 99_L | 1.361 | 0.99 |
| 31_W | 61_D | 1.361 | 0.99 |
| 102_F | 106_N | 1.335 | 0.99 |
| 70_Y | 81_F | 1.333 | 0.99 |
| 88_A | 106_N | 1.279 | 0.99 |
| 26_D | 57_K | 1.278 | 0.99 |
| 37_M | 93_A | 1.262 | 0.99 |
| 8_T | 11_S | 1.254 | 0.99 |
| 101_E | 105_A | 1.248 | 0.99 |
| 38_I | 99_L | 1.244 | 0.98 |
| 88_A | 105_A | 1.227 | 0.98 |
| 45_I | 55_V | 1.226 | 0.98 |
| 96_K | 100_K | 1.218 | 0.98 |
| 45_I | 100_K | 1.210 | 0.98 |
| 102_F | 105_A | 1.207 | 0.98 |
| 9_D | 63_N | 1.183 | 0.98 |
| 32_C | 35_C | 1.176 | 0.98 |
| 101_E | 104_D | 1.132 | 0.97 |
| 38_I | 93_A | 1.125 | 0.97 |
| 27_F | 60_I | 1.120 | 0.96 |
| 7_L | 15_D | 1.100 | 0.96 |
| 58_L | 67_A | 1.092 | 0.96 |
| 49_Y | 53_L | 1.079 | 0.95 |
| 14_T | 18_K | 1.073 | 0.95 |
| 64_P | 68_P | 1.051 | 0.94 |
| 94_L | 102_F | 1.047 | 0.94 |
| 82_K | 87_A | 1.015 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4kcaA | 2 | 0.9722 | 99.9 | 0.193 | Contact Map |
| 3f8uA | 2 | 0.9815 | 99.9 | 0.196 | Contact Map |
| 3bj5A | 1 | 0.9722 | 99.9 | 0.199 | Contact Map |
| 2qgvA | 10 | 0.9907 | 99.9 | 0.202 | Contact Map |
| 3apoA | 1 | 0.9167 | 99.9 | 0.203 | Contact Map |
| 2av4A | 1 | 0.9815 | 99.9 | 0.203 | Contact Map |
| 4cdoA | 2 | 0.9907 | 99.9 | 0.206 | Contact Map |
| 2r2jA | 1 | 0.9537 | 99.9 | 0.207 | Contact Map |
| 2qsiA | 2 | 0.963 | 99.9 | 0.211 | Contact Map |
| 2b5eA | 1 | 0.9907 | 99.9 | 0.213 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)