| d3lx2c1 |
| ID: | 1448552756 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (116) | ||
| Sequences: | 641 (432.1) | ||
| Seq/Len: | 5.526 | ||
| Nf(neff/√len): | 40.1 |
HHblits Results: (2015_06)
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: 5.526).
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 |
| 30_V | 60_Y | 2.117 | 1.00 |
| 12_F | 88_L | 1.869 | 1.00 |
| 44_R | 47_L | 1.819 | 1.00 |
| 70_F | 98_L | 1.771 | 1.00 |
| 28_F | 37_M | 1.771 | 1.00 |
| 90_L | 100_V | 1.721 | 1.00 |
| 25_E | 71_D | 1.674 | 1.00 |
| 3_E | 91_R | 1.635 | 0.99 |
| 75_F | 100_V | 1.602 | 0.99 |
| 41_D | 69_A | 1.564 | 0.99 |
| 81_L | 108_T | 1.564 | 0.99 |
| 24_D | 73_K | 1.523 | 0.99 |
| 23_F | 27_V | 1.509 | 0.99 |
| 9_A | 115_I | 1.472 | 0.99 |
| 90_L | 98_L | 1.425 | 0.98 |
| 40_I | 44_R | 1.421 | 0.98 |
| 41_D | 45_V | 1.380 | 0.98 |
| 16_I | 28_F | 1.367 | 0.97 |
| 30_V | 35_I | 1.339 | 0.97 |
| 19_L | 37_M | 1.319 | 0.97 |
| 27_V | 67_A | 1.316 | 0.97 |
| 12_F | 82_A | 1.306 | 0.96 |
| 31_N | 60_Y | 1.256 | 0.95 |
| 35_I | 98_L | 1.253 | 0.95 |
| 26_A | 72_L | 1.236 | 0.95 |
| 9_A | 88_L | 1.228 | 0.94 |
| 32_M | 42_P | 1.205 | 0.94 |
| 31_N | 36_Q | 1.185 | 0.93 |
| 26_A | 37_M | 1.174 | 0.92 |
| 80_K | 86_D | 1.166 | 0.92 |
| 60_Y | 93_G | 1.166 | 0.92 |
| 72_L | 86_D | 1.158 | 0.92 |
| 22_F | 49_D | 1.158 | 0.92 |
| 47_L | 77_K | 1.148 | 0.91 |
| 8_S | 13_E | 1.145 | 0.91 |
| 91_R | 94_G | 1.141 | 0.91 |
| 29_Q | 40_I | 1.139 | 0.91 |
| 15_L | 53_P | 1.138 | 0.91 |
| 62_V | 66_E | 1.136 | 0.91 |
| 40_I | 45_V | 1.130 | 0.90 |
| 31_N | 70_F | 1.130 | 0.90 |
| 39_A | 50_L | 1.115 | 0.90 |
| 45_V | 72_L | 1.106 | 0.89 |
| 23_F | 39_A | 1.103 | 0.89 |
| 105_D | 108_T | 1.092 | 0.88 |
| 30_V | 62_V | 1.088 | 0.88 |
| 98_L | 114_L | 1.082 | 0.88 |
| 56_L | 79_L | 1.071 | 0.87 |
| 66_E | 92_K | 1.065 | 0.87 |
| 23_F | 26_A | 1.052 | 0.86 |
| 25_E | 42_P | 1.052 | 0.86 |
| 3_E | 115_I | 1.048 | 0.85 |
| 41_D | 44_R | 1.045 | 0.85 |
| 3_E | 59_K | 1.045 | 0.85 |
| 58_S | 78_V | 1.043 | 0.85 |
| 59_K | 110_F | 1.036 | 0.85 |
| 74_R | 96_N | 1.025 | 0.84 |
| 36_Q | 51_N | 1.017 | 0.83 |
| 70_F | 111_K | 1.009 | 0.82 |
| 38_R | 47_L | 1.008 | 0.82 |
| 7_D | 107_N | 1.005 | 0.82 |
| 33_E | 55_M | 1.005 | 0.82 |
| 108_T | 113_P | 1.003 | 0.82 |
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 | |
| 3k4xA | 1 | 0.9914 | 99.9 | 0.175 | Contact Map |
| 3a1jA | 1 | 1 | 99.9 | 0.239 | Contact Map |
| 3g65A | 1 | 0.9397 | 99.9 | 0.24 | Contact Map |
| 3a1jC | 1 | 0.9828 | 99.9 | 0.269 | Contact Map |
| 3a1jB | 1 | 0.9828 | 99.9 | 0.291 | Contact Map |
| 3fdsC | 1 | 0.9914 | 99.8 | 0.372 | Contact Map |
| 1plqA | 1 | 1 | 99.7 | 0.395 | Contact Map |
| 1u7bA | 1 | 1 | 99.7 | 0.402 | Contact Map |
| 3lx2A | 3 | 1 | 99.7 | 0.403 | Contact Map |
| 3aizA | 2 | 0.9914 | 99.7 | 0.403 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)