| T0806 |
| ID: | 1461796934 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 110 (109) | ||
| Sequences: | 194 (163.4) | ||
| Seq/Len: | 1.780 | ||
| Nf(neff/√len): | 15.7 |
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: 1.780).
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 |
| 24_D | 78_R | 3.653 | 1.00 |
| 34_C | 63_W | 2.072 | 0.99 |
| 67_M | 96_L | 1.951 | 0.98 |
| 59_D | 86_R | 1.848 | 0.97 |
| 63_W | 107_F | 1.702 | 0.95 |
| 92_V | 107_F | 1.674 | 0.95 |
| 21_H | 76_S | 1.661 | 0.94 |
| 45_R | 66_A | 1.622 | 0.93 |
| 62_E | 89_G | 1.547 | 0.91 |
| 61_D | 89_G | 1.495 | 0.89 |
| 17_E | 81_S | 1.442 | 0.87 |
| 2_A | 9_Y | 1.373 | 0.83 |
| 2_A | 110_Q | 1.339 | 0.81 |
| 3_R | 110_Q | 1.333 | 0.80 |
| 3_R | 6_D | 1.308 | 0.78 |
| 47_E | 50_K | 1.288 | 0.77 |
| 2_A | 107_F | 1.275 | 0.76 |
| 4_Y | 39_S | 1.274 | 0.76 |
| 37_E | 57_G | 1.233 | 0.72 |
| 61_D | 66_A | 1.224 | 0.72 |
| 62_E | 66_A | 1.212 | 0.71 |
| 39_S | 46_Q | 1.195 | 0.69 |
| 12_A | 23_S | 1.191 | 0.69 |
| 28_A | 78_R | 1.189 | 0.68 |
| 35_T | 70_E | 1.187 | 0.68 |
| 24_D | 27_K | 1.181 | 0.68 |
| 41_A | 70_E | 1.152 | 0.65 |
| 2_A | 6_D | 1.146 | 0.64 |
| 4_Y | 106_L | 1.140 | 0.64 |
| 19_G | 23_S | 1.138 | 0.63 |
| 2_A | 5_D | 1.138 | 0.63 |
| 32_D | 110_Q | 1.138 | 0.63 |
| 80_V | 84_D | 1.138 | 0.63 |
| 11_P | 31_A | 1.123 | 0.62 |
| 65_M | 68_C | 1.122 | 0.62 |
| 4_Y | 109_V | 1.109 | 0.61 |
| 40_G | 47_E | 1.097 | 0.59 |
| 2_A | 73_K | 1.095 | 0.59 |
| 2_A | 47_E | 1.094 | 0.59 |
| 27_K | 109_V | 1.084 | 0.58 |
| 99_Y | 103_T | 1.083 | 0.58 |
| 34_C | 68_C | 1.069 | 0.56 |
| 60_R | 65_M | 1.064 | 0.56 |
| 18_T | 84_D | 1.056 | 0.55 |
| 72_G | 75_A | 1.052 | 0.54 |
| 100_A | 103_T | 1.046 | 0.54 |
| 5_D | 106_L | 1.045 | 0.54 |
| 45_R | 75_A | 1.041 | 0.53 |
| 66_A | 102_G | 1.037 | 0.53 |
| 3_R | 9_Y | 1.037 | 0.53 |
| 31_A | 39_S | 1.029 | 0.52 |
| 82_S | 88_A | 1.026 | 0.52 |
| 32_D | 51_G | 1.024 | 0.51 |
| 3_R | 47_E | 1.010 | 0.50 |
| 7_V | 73_K | 1.007 | 0.50 |
| 3_R | 39_S | 1.006 | 0.50 |
| 84_D | 90_S | 1.005 | 0.49 |
| 62_E | 85_N | 1.003 | 0.49 |
| 74_G | 86_R | 1.002 | 0.49 |
| 21_H | 88_A | 1.000 | 0.49 |
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 | |
| 2cmyB | 1 | 0.1909 | 7.4 | 0.933 | Contact Map |
| 2plxB | 1 | 0.2364 | 2.8 | 0.946 | Contact Map |
| 2a1kA | 2 | 0.4636 | 2.6 | 0.946 | Contact Map |
| 2gkwB | 1 | 0.1545 | 2.4 | 0.947 | Contact Map |
| 1sa3A | 2 | 0.4636 | 2.3 | 0.947 | Contact Map |
| 3a0rA | 1 | 0.8909 | 1.9 | 0.95 | Contact Map |
| 3bdlA | 1 | 0.2091 | 1.8 | 0.951 | Contact Map |
| 4pp4A | 1 | 0.1727 | 1.6 | 0.952 | Contact Map |
| 2dgyA | 1 | 0.3636 | 1.6 | 0.952 | Contact Map |
| 1lshB | 1 | 0 | 1.6 | 0.952 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)