| 1D4OA |
| ID: | 1411607109 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 177 (176) | ||
| Sequences: | 539 (227.5) | ||
| Seq/Len: | 3.062 | ||
| Nf(neff/√len): | 17.1 |
HHblits Results: (2013_03)
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: 3.062).
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 |
| 91_F | 124_L | 3.797 | 1.00 |
| 111_Q | 125_E | 2.830 | 1.00 |
| 111_Q | 127_W | 2.784 | 1.00 |
| 53_R | 90_D | 2.688 | 1.00 |
| 97_V | 129_S | 2.586 | 1.00 |
| 24_T | 126_V | 2.511 | 1.00 |
| 22_I | 91_F | 2.421 | 1.00 |
| 135_M | 166_T | 2.397 | 1.00 |
| 94_T | 124_L | 2.387 | 1.00 |
| 46_S | 80_I | 2.327 | 1.00 |
| 11_A | 133_I | 2.050 | 1.00 |
| 21_I | 50_K | 1.954 | 1.00 |
| 123_V | 127_W | 1.953 | 1.00 |
| 67_L | 108_S | 1.888 | 0.99 |
| 22_I | 87_I | 1.805 | 0.99 |
| 139_L | 160_L | 1.775 | 0.99 |
| 22_I | 94_T | 1.769 | 0.99 |
| 125_E | 128_K | 1.732 | 0.99 |
| 108_S | 150_I | 1.725 | 0.99 |
| 91_F | 94_T | 1.717 | 0.99 |
| 53_R | 82_L | 1.692 | 0.98 |
| 106_V | 151_F | 1.644 | 0.98 |
| 140_G | 160_L | 1.610 | 0.98 |
| 22_I | 124_L | 1.552 | 0.97 |
| 94_T | 97_V | 1.550 | 0.97 |
| 6_I | 133_I | 1.534 | 0.96 |
| 161_G | 166_T | 1.529 | 0.96 |
| 67_L | 150_I | 1.501 | 0.96 |
| 20_S | 51_K | 1.484 | 0.95 |
| 83_E | 143_Y | 1.474 | 0.95 |
| 112_E | 153_K | 1.465 | 0.95 |
| 2_T | 5_E | 1.449 | 0.95 |
| 133_I | 159_L | 1.445 | 0.95 |
| 29_L | 38_I | 1.443 | 0.95 |
| 170_L | 174_V | 1.422 | 0.94 |
| 165_K | 169_A | 1.407 | 0.94 |
| 53_R | 94_T | 1.401 | 0.93 |
| 66_Q | 108_S | 1.400 | 0.93 |
| 147_D | 152_Y | 1.380 | 0.93 |
| 6_I | 11_A | 1.370 | 0.92 |
| 159_L | 170_L | 1.357 | 0.92 |
| 53_R | 87_I | 1.346 | 0.91 |
| 42_V | 54_F | 1.338 | 0.91 |
| 89_H | 125_E | 1.338 | 0.91 |
| 39_A | 43_K | 1.338 | 0.91 |
| 46_S | 81_V | 1.331 | 0.91 |
| 123_V | 126_V | 1.315 | 0.90 |
| 138_S | 160_L | 1.289 | 0.89 |
| 131_Q | 157_A | 1.281 | 0.88 |
| 10_N | 13_D | 1.280 | 0.88 |
| 37_P | 168_D | 1.246 | 0.87 |
| 82_L | 85_D | 1.245 | 0.86 |
| 66_Q | 150_I | 1.235 | 0.86 |
| 13_D | 17_E | 1.227 | 0.85 |
| 134_V | 156_T | 1.225 | 0.85 |
| 87_I | 94_T | 1.213 | 0.85 |
| 18_A | 96_L | 1.191 | 0.83 |
| 87_I | 91_F | 1.161 | 0.81 |
| 12_I | 48_Q | 1.142 | 0.79 |
| 81_V | 143_Y | 1.126 | 0.78 |
| 113_D | 116_S | 1.113 | 0.77 |
| 159_L | 166_T | 1.110 | 0.77 |
| 15_I | 96_L | 1.107 | 0.76 |
| 92_P | 128_K | 1.105 | 0.76 |
| 1_G | 112_E | 1.096 | 0.75 |
| 20_S | 53_R | 1.092 | 0.75 |
| 116_S | 151_F | 1.069 | 0.73 |
| 1_G | 134_V | 1.068 | 0.73 |
| 151_F | 158_M | 1.051 | 0.71 |
| 3_H | 138_S | 1.050 | 0.71 |
| 20_S | 90_D | 1.044 | 0.70 |
| 12_I | 174_V | 1.040 | 0.70 |
| 87_I | 90_D | 1.033 | 0.69 |
| 123_V | 155_N | 1.032 | 0.69 |
| 1_G | 152_Y | 1.026 | 0.68 |
| 67_L | 145_A | 1.022 | 0.68 |
| 81_V | 86_E | 1.022 | 0.68 |
| 17_E | 50_K | 1.018 | 0.67 |
| 24_T | 97_V | 1.016 | 0.67 |
| 29_L | 123_V | 1.013 | 0.67 |
| 66_Q | 75_G | 1.007 | 0.66 |
| 138_S | 147_D | 1.000 | 0.65 |
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 | |
| 1djlA | 2 | 1 | 100 | -0.013 | Contact Map |
| 2fsvC | 1 | 0.9831 | 100 | -0.01 | Contact Map |
| 1pnoA | 2 | 0.9887 | 100 | 0.001 | Contact Map |
| 1d4oA | 1 | 1 | 100 | 0.002 | Contact Map |
| 2bruC | 1 | 0.9435 | 100 | 0.005 | Contact Map |
| 4j1tC | 2 | 0.9944 | 100 | 0.008 | Contact Map |
| 1q6zA | 1 | 0.8249 | 96.8 | 0.92 | Contact Map |
| 4k9qA | 2 | 0.8249 | 96.8 | 0.92 | Contact Map |
| 2uz1A | 2 | 0.8362 | 96.7 | 0.921 | Contact Map |
| 2c31A | 2 | 0.8079 | 96.7 | 0.921 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)