| rdlB |
| ID: | 1510654860 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 133 (131) | ||
| Sequences: | 162 (72.3) | ||
| Seq/Len: | 1.237 | ||
| Nf(neff/√len): | 6.3 |
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: 1.237).
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 |
| 2_I | 6_V | 2.409 | 0.99 |
| 7_A | 14_S | 2.306 | 0.99 |
| 55_N | 61_A | 2.010 | 0.97 |
| 45_Q | 103_E | 1.907 | 0.96 |
| 83_G | 86_P | 1.899 | 0.96 |
| 60_M | 63_I | 1.807 | 0.94 |
| 2_I | 5_V | 1.783 | 0.93 |
| 63_I | 70_P | 1.780 | 0.93 |
| 96_D | 112_G | 1.765 | 0.93 |
| 75_S | 79_V | 1.728 | 0.92 |
| 75_S | 112_G | 1.704 | 0.91 |
| 79_V | 98_N | 1.683 | 0.90 |
| 91_N | 95_D | 1.658 | 0.89 |
| 128_G | 131_G | 1.597 | 0.87 |
| 60_M | 70_P | 1.568 | 0.86 |
| 39_N | 113_A | 1.564 | 0.85 |
| 63_I | 67_F | 1.562 | 0.85 |
| 67_F | 73_A | 1.530 | 0.84 |
| 70_P | 102_A | 1.510 | 0.83 |
| 61_A | 70_P | 1.509 | 0.83 |
| 8_Y | 92_V | 1.451 | 0.79 |
| 77_I | 112_G | 1.438 | 0.78 |
| 29_I | 126_S | 1.415 | 0.77 |
| 70_P | 118_L | 1.402 | 0.76 |
| 19_S | 22_A | 1.358 | 0.72 |
| 1_M | 5_V | 1.323 | 0.69 |
| 77_I | 96_D | 1.304 | 0.68 |
| 19_S | 47_F | 1.296 | 0.67 |
| 30_G | 33_S | 1.276 | 0.65 |
| 66_S | 103_E | 1.272 | 0.65 |
| 92_V | 95_D | 1.248 | 0.63 |
| 65_G | 70_P | 1.242 | 0.62 |
| 98_N | 108_A | 1.235 | 0.62 |
| 55_N | 67_F | 1.234 | 0.62 |
| 83_G | 98_N | 1.230 | 0.61 |
| 122_S | 125_S | 1.224 | 0.61 |
| 31_D | 55_N | 1.210 | 0.59 |
| 75_S | 96_D | 1.206 | 0.59 |
| 19_S | 120_D | 1.194 | 0.58 |
| 60_M | 67_F | 1.183 | 0.57 |
| 27_M | 38_A | 1.180 | 0.56 |
| 80_S | 87_I | 1.170 | 0.56 |
| 29_I | 120_D | 1.159 | 0.54 |
| 61_A | 66_S | 1.153 | 0.54 |
| 55_N | 60_M | 1.147 | 0.53 |
| 45_Q | 56_M | 1.134 | 0.52 |
| 60_M | 65_G | 1.127 | 0.51 |
| 102_A | 118_L | 1.114 | 0.50 |
| 76_D | 112_G | 1.109 | 0.50 |
| 19_S | 130_G | 1.107 | 0.49 |
| 5_V | 60_M | 1.103 | 0.49 |
| 9_A | 22_A | 1.088 | 0.47 |
| 3_K | 8_Y | 1.084 | 0.47 |
| 8_Y | 76_D | 1.083 | 0.47 |
| 110_R | 115_A | 1.075 | 0.46 |
| 59_Q | 64_Q | 1.071 | 0.46 |
| 109_K | 112_G | 1.064 | 0.45 |
| 61_A | 103_E | 1.055 | 0.44 |
| 39_N | 73_A | 1.047 | 0.43 |
| 115_A | 121_V | 1.042 | 0.43 |
| 8_Y | 15_V | 1.035 | 0.42 |
| 79_V | 96_D | 1.017 | 0.41 |
| 86_P | 122_S | 1.016 | 0.41 |
| 79_V | 110_R | 1.016 | 0.41 |
| 19_S | 27_M | 1.013 | 0.40 |
| 95_D | 112_G | 1.006 | 0.40 |
| 50_S | 56_M | 1.004 | 0.39 |
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 | |
| 4oc8A | 4 | 0.3609 | 4.8 | 0.965 | Contact Map |
| 4rknA | 4 | 0.4286 | 3.7 | 0.967 | Contact Map |
| 2vdaB | 1 | 0.1654 | 3.4 | 0.968 | Contact Map |
| 4ujti | 1 | 0 | 2.4 | 0.97 | Contact Map |
| 4ui9T | 1 | 0 | 2.3 | 0.97 | Contact Map |
| 3j3bq | 1 | 0.1353 | 1.7 | 0.972 | Contact Map |
| 2pq4B | 1 | 0.2105 | 1.5 | 0.973 | Contact Map |
| 3j40A | 7 | 0.3835 | 1.5 | 0.973 | Contact Map |
| 4by8A | 1 | 0.0677 | 1.5 | 0.973 | Contact Map |
| 3p7mA | 4 | 0.7669 | 1.2 | 0.975 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)