| test 170-310 |
| ID: | 1383361478 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (136) | ||
| Sequences: | 150 (87.9) | ||
| Seq/Len: | 1.103 | ||
| Nf(neff/√len): | 7.5 |
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: 1.103).
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 |
| 13_L | 19_S | 2.370 | 0.99 |
| 46_E | 129_H | 1.666 | 0.88 |
| 23_L | 106_S | 1.607 | 0.85 |
| 111_S | 114_Q | 1.588 | 0.84 |
| 21_G | 106_S | 1.581 | 0.84 |
| 24_V | 106_S | 1.508 | 0.80 |
| 55_P | 67_S | 1.486 | 0.78 |
| 105_L | 130_I | 1.482 | 0.78 |
| 120_L | 129_H | 1.481 | 0.78 |
| 52_Q | 56_Q | 1.465 | 0.77 |
| 7_E | 11_Q | 1.421 | 0.74 |
| 24_V | 109_P | 1.376 | 0.70 |
| 19_S | 111_S | 1.342 | 0.68 |
| 9_T | 24_V | 1.325 | 0.66 |
| 68_A | 74_I | 1.317 | 0.66 |
| 38_L | 101_V | 1.308 | 0.65 |
| 122_L | 137_I | 1.307 | 0.65 |
| 106_S | 118_K | 1.303 | 0.64 |
| 29_Y | 32_E | 1.303 | 0.64 |
| 24_V | 114_Q | 1.295 | 0.64 |
| 38_L | 139_R | 1.277 | 0.62 |
| 68_A | 71_L | 1.256 | 0.60 |
| 91_F | 104_F | 1.256 | 0.60 |
| 37_K | 92_L | 1.253 | 0.60 |
| 124_D | 133_G | 1.251 | 0.60 |
| 109_P | 114_Q | 1.235 | 0.58 |
| 20_Y | 24_V | 1.208 | 0.56 |
| 22_L | 118_K | 1.197 | 0.55 |
| 118_K | 131_Y | 1.190 | 0.54 |
| 4_D | 92_L | 1.186 | 0.54 |
| 9_T | 17_E | 1.172 | 0.52 |
| 68_A | 72_G | 1.169 | 0.52 |
| 120_L | 141_S | 1.166 | 0.52 |
| 54_R | 71_L | 1.164 | 0.52 |
| 15_E | 43_V | 1.153 | 0.50 |
| 34_C | 140_A | 1.152 | 0.50 |
| 24_V | 111_S | 1.151 | 0.50 |
| 119_V | 124_D | 1.128 | 0.48 |
| 41_D | 100_P | 1.126 | 0.48 |
| 47_F | 117_K | 1.125 | 0.48 |
| 122_L | 141_S | 1.125 | 0.48 |
| 56_Q | 63_N | 1.118 | 0.47 |
| 14_H | 24_V | 1.106 | 0.46 |
| 20_Y | 140_A | 1.102 | 0.46 |
| 106_S | 111_S | 1.098 | 0.45 |
| 18_G | 26_S | 1.083 | 0.44 |
| 14_H | 99_M | 1.081 | 0.44 |
| 63_N | 71_L | 1.076 | 0.43 |
| 63_N | 66_T | 1.076 | 0.43 |
| 32_E | 96_D | 1.072 | 0.43 |
| 114_Q | 140_A | 1.069 | 0.43 |
| 119_V | 133_G | 1.063 | 0.42 |
| 52_Q | 69_A | 1.062 | 0.42 |
| 66_T | 71_L | 1.060 | 0.42 |
| 78_P | 88_S | 1.058 | 0.41 |
| 41_D | 83_L | 1.058 | 0.41 |
| 53_H | 56_Q | 1.056 | 0.41 |
| 6_N | 114_Q | 1.055 | 0.41 |
| 7_E | 19_S | 1.055 | 0.41 |
| 29_Y | 121_F | 1.053 | 0.41 |
| 21_G | 118_K | 1.049 | 0.41 |
| 88_S | 93_S | 1.048 | 0.41 |
| 56_Q | 62_H | 1.040 | 0.40 |
| 65_A | 73_F | 1.038 | 0.40 |
| 69_A | 73_F | 1.038 | 0.40 |
| 57_Q | 73_F | 1.037 | 0.40 |
| 9_T | 114_Q | 1.032 | 0.39 |
| 66_T | 73_F | 1.029 | 0.39 |
| 15_E | 98_P | 1.028 | 0.39 |
| 37_K | 93_S | 1.026 | 0.39 |
| 125_D | 138_H | 1.024 | 0.38 |
| 19_S | 24_V | 1.023 | 0.38 |
| 111_S | 115_H | 1.021 | 0.38 |
| 75_P | 80_E | 1.011 | 0.37 |
| 34_C | 43_V | 1.004 | 0.37 |
| 117_K | 120_L | 1.004 | 0.37 |
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 | |
| 2bplA | 3 | 0.6312 | 98.1 | 0.843 | Contact Map |
| 1xffA | 2 | 0.6312 | 97.1 | 0.872 | Contact Map |
| 1ecfA | 2 | 0.6738 | 93.8 | 0.9 | Contact Map |
| 1ea0A | 2 | 0.6383 | 87.5 | 0.914 | Contact Map |
| 1ao0A | 4 | 0.6312 | 86.8 | 0.915 | Contact Map |
| 1ofdA | 2 | 0.6383 | 84.1 | 0.918 | Contact Map |
| 3mdnA | 4 | 0.6454 | 80.1 | 0.922 | Contact Map |
| 1ct9A | 4 | 0.6383 | 56.2 | 0.934 | Contact Map |
| 1jgtA | 2 | 0.6312 | 47.9 | 0.937 | Contact Map |
| 1umuA | 2 | 0.4752 | 7.6 | 0.957 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)