| 6_1ifcpdb |
| ID: | 1516869620 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (131) | ||
| Sequences: | 1233 (706.5) | ||
| Seq/Len: | 9.412 | ||
| Nf(neff/√len): | 61.7 |
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: 9.412).
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 |
| 63_E | 66_V | 3.494 | 1.00 |
| 67_D | 79_T | 2.853 | 1.00 |
| 6_W | 108_I | 2.529 | 1.00 |
| 72_L | 76_T | 2.490 | 1.00 |
| 80_G | 91_G | 2.323 | 1.00 |
| 16_K | 19_E | 2.250 | 1.00 |
| 88_K | 107_E | 2.197 | 1.00 |
| 69_A | 77_E | 2.076 | 1.00 |
| 46_K | 63_E | 1.989 | 1.00 |
| 111_N | 130_K | 1.980 | 1.00 |
| 116_T | 125_K | 1.976 | 1.00 |
| 46_K | 61_V | 1.961 | 1.00 |
| 50_K | 59_D | 1.947 | 1.00 |
| 2_F | 108_I | 1.772 | 1.00 |
| 70_Y | 91_G | 1.771 | 1.00 |
| 5_T | 39_T | 1.767 | 1.00 |
| 26_V | 30_L | 1.743 | 1.00 |
| 69_A | 79_T | 1.709 | 1.00 |
| 107_E | 116_T | 1.701 | 1.00 |
| 71_S | 77_E | 1.695 | 1.00 |
| 40_I | 49_V | 1.646 | 1.00 |
| 88_K | 105_V | 1.575 | 1.00 |
| 48_T | 61_V | 1.548 | 1.00 |
| 4_G | 130_K | 1.545 | 1.00 |
| 105_V | 116_T | 1.536 | 1.00 |
| 52_S | 57_N | 1.518 | 1.00 |
| 29_K | 32_A | 1.517 | 1.00 |
| 84_M | 89_L | 1.517 | 1.00 |
| 70_Y | 80_G | 1.487 | 1.00 |
| 18_M | 31_G | 1.449 | 1.00 |
| 14_Y | 18_M | 1.426 | 0.99 |
| 17_F | 102_L | 1.363 | 0.99 |
| 105_V | 118_T | 1.342 | 0.99 |
| 118_T | 123_E | 1.325 | 0.99 |
| 39_T | 52_S | 1.319 | 0.99 |
| 92_K | 96_V | 1.302 | 0.99 |
| 12_E | 125_K | 1.279 | 0.99 |
| 13_N | 17_F | 1.274 | 0.99 |
| 45_N | 63_E | 1.259 | 0.98 |
| 125_K | 129_K | 1.187 | 0.97 |
| 104_A | 115_Q | 1.187 | 0.97 |
| 15_E | 19_E | 1.162 | 0.97 |
| 83_T | 92_K | 1.138 | 0.96 |
| 69_A | 96_V | 1.133 | 0.96 |
| 13_N | 18_M | 1.132 | 0.96 |
| 115_Q | 120_E | 1.124 | 0.96 |
| 8_V | 11_N | 1.104 | 0.96 |
| 42_Q | 47_F | 1.096 | 0.95 |
| 109_S | 114_I | 1.090 | 0.95 |
| 13_N | 16_K | 1.089 | 0.95 |
| 43_E | 46_K | 1.084 | 0.95 |
| 15_E | 18_M | 1.081 | 0.95 |
| 30_L | 34_D | 1.080 | 0.95 |
| 108_I | 111_N | 1.073 | 0.95 |
| 116_T | 127_I | 1.068 | 0.94 |
| 41_T | 48_T | 1.059 | 0.94 |
| 44_G | 65_G | 1.058 | 0.94 |
| 91_G | 95_R | 1.052 | 0.94 |
| 109_S | 112_E | 1.043 | 0.94 |
| 13_N | 122_V | 1.036 | 0.93 |
| 119_Y | 122_V | 1.033 | 0.93 |
| 67_D | 96_V | 1.033 | 0.93 |
| 3_D | 42_Q | 1.032 | 0.93 |
| 7_K | 131_E | 1.028 | 0.93 |
| 23_I | 28_R | 1.023 | 0.93 |
| 46_K | 66_V | 1.017 | 0.92 |
| 8_V | 126_R | 1.016 | 0.92 |
| 6_W | 13_N | 1.011 | 0.92 |
| 123_E | 126_R | 1.003 | 0.92 |
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 | |
| 3q6lA | 1 | 0.9847 | 100 | -0.04 | Contact Map |
| 4aznA | 2 | 0.9847 | 100 | -0.04 | Contact Map |
| 3wbgA | 4 | 0.9847 | 100 | -0.04 | Contact Map |
| 4a60A | 1 | 0.9771 | 100 | -0.038 | Contact Map |
| 3p6dA | 1 | 0.9847 | 100 | -0.03 | Contact Map |
| 4bvmA | 1 | 0.9847 | 100 | -0.03 | Contact Map |
| 4tkbA | 1 | 0.9847 | 100 | -0.028 | Contact Map |
| 1ifcA | 1 | 1 | 100 | -0.028 | Contact Map |
| 1fdqA | 2 | 0.9847 | 100 | -0.028 | Contact Map |
| 1vyfA | 1 | 0.9847 | 100 | -0.026 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)