| 1BGFA |
| ID: | 1411599284 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 124 (121) | ||
| Sequences: | 130 (77.1) | ||
| Seq/Len: | 1.074 | ||
| Nf(neff/√len): | 7.0 |
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: 1.074).
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 |
| 110_L | 113_E | 2.402 | 0.99 |
| 61_L | 79_L | 1.853 | 0.93 |
| 99_P | 113_E | 1.753 | 0.91 |
| 42_Q | 57_L | 1.725 | 0.90 |
| 69_L | 84_L | 1.625 | 0.85 |
| 3_S | 8_V | 1.597 | 0.84 |
| 36_A | 120_A | 1.502 | 0.79 |
| 106_I | 110_L | 1.494 | 0.78 |
| 3_S | 19_V | 1.482 | 0.77 |
| 2_G | 47_A | 1.426 | 0.74 |
| 27_F | 109_C | 1.393 | 0.71 |
| 50_N | 79_L | 1.385 | 0.70 |
| 99_P | 110_L | 1.363 | 0.69 |
| 103_A | 113_E | 1.349 | 0.67 |
| 33_H | 102_V | 1.322 | 0.65 |
| 24_D | 84_L | 1.322 | 0.65 |
| 30_E | 37_Q | 1.320 | 0.65 |
| 91_L | 102_V | 1.309 | 0.64 |
| 54_A | 58_L | 1.297 | 0.63 |
| 95_F | 102_V | 1.295 | 0.63 |
| 31_I | 65_L | 1.273 | 0.61 |
| 36_A | 101_H | 1.272 | 0.61 |
| 9_Q | 16_L | 1.256 | 0.59 |
| 89_K | 95_F | 1.224 | 0.56 |
| 19_V | 26_N | 1.209 | 0.55 |
| 81_I | 87_I | 1.208 | 0.55 |
| 47_A | 68_Q | 1.208 | 0.55 |
| 24_D | 102_V | 1.205 | 0.55 |
| 2_G | 69_L | 1.191 | 0.53 |
| 62_L | 116_I | 1.140 | 0.48 |
| 44_W | 57_L | 1.139 | 0.48 |
| 4_Q | 117_L | 1.139 | 0.48 |
| 14_K | 25_D | 1.139 | 0.48 |
| 31_I | 46_V | 1.132 | 0.48 |
| 23_Y | 36_A | 1.132 | 0.48 |
| 29_M | 117_L | 1.123 | 0.47 |
| 22_F | 98_N | 1.120 | 0.47 |
| 83_N | 86_R | 1.105 | 0.45 |
| 62_L | 68_Q | 1.102 | 0.45 |
| 30_E | 69_L | 1.099 | 0.45 |
| 11_L | 16_L | 1.092 | 0.44 |
| 3_S | 39_I | 1.085 | 0.43 |
| 66_D | 83_N | 1.080 | 0.43 |
| 112_E | 116_I | 1.078 | 0.43 |
| 54_A | 100_M | 1.078 | 0.43 |
| 21_Q | 62_L | 1.077 | 0.43 |
| 5_W | 32_R | 1.074 | 0.42 |
| 33_H | 52_T | 1.074 | 0.42 |
| 18_Q | 108_N | 1.070 | 0.42 |
| 12_E | 58_L | 1.059 | 0.41 |
| 95_F | 104_V | 1.058 | 0.41 |
| 31_I | 95_F | 1.048 | 0.40 |
| 51_E | 106_I | 1.048 | 0.40 |
| 36_A | 118_A | 1.041 | 0.39 |
| 64_Q | 67_E | 1.041 | 0.39 |
| 3_S | 117_L | 1.039 | 0.39 |
| 22_F | 58_L | 1.036 | 0.39 |
| 36_A | 42_Q | 1.036 | 0.39 |
| 17_E | 43_D | 1.032 | 0.38 |
| 10_Q | 107_S | 1.028 | 0.38 |
| 63_I | 114_R | 1.027 | 0.38 |
| 75_E | 79_L | 1.027 | 0.38 |
| 36_A | 91_L | 1.023 | 0.38 |
| 31_I | 35_L | 1.019 | 0.37 |
| 31_I | 93_G | 1.019 | 0.37 |
| 31_I | 106_I | 1.012 | 0.37 |
| 50_N | 80_L | 1.009 | 0.36 |
| 59_Q | 63_I | 1.007 | 0.36 |
| 30_E | 34_L | 1.006 | 0.36 |
| 98_N | 109_C | 1.005 | 0.36 |
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 | |
| 1bgfA | 1 | 1 | 100 | 0.018 | Contact Map |
| 1yvlA | 2 | 0.9839 | 100 | 0.031 | Contact Map |
| 3pyiB | 2 | 0.6774 | 10 | 0.942 | Contact Map |
| 2h8hA | 1 | 0.5806 | 8 | 0.945 | Contact Map |
| 1fmkA | 1 | 0.5806 | 6.5 | 0.947 | Contact Map |
| 3vheA | 1 | 0.5242 | 5.6 | 0.948 | Contact Map |
| 1t46A | 1 | 0.5242 | 5.5 | 0.948 | Contact Map |
| 4aseA | 1 | 0.5161 | 4.4 | 0.951 | Contact Map |
| 4hneA | 2 | 0.7258 | 4.3 | 0.951 | Contact Map |
| 1h99A | 1 | 0.9839 | 4 | 0.952 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)