| T0844 |
| ID: | 1404750589 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 145 (135) | ||
| Sequences: | 176 (158.7) | ||
| Seq/Len: | 1.304 | ||
| Nf(neff/√len): | 13.7 |
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: 1.304).
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 |
| 94_K | 102_E | 2.573 | 1.00 |
| 47_I | 86_K | 2.498 | 1.00 |
| 13_E | 48_Y | 1.880 | 0.96 |
| 23_V | 123_R | 1.791 | 0.94 |
| 44_S | 54_L | 1.722 | 0.92 |
| 98_Y | 101_S | 1.686 | 0.91 |
| 43_L | 104_N | 1.663 | 0.90 |
| 56_Q | 95_S | 1.548 | 0.86 |
| 48_Y | 56_Q | 1.537 | 0.85 |
| 119_V | 126_I | 1.520 | 0.84 |
| 40_I | 43_L | 1.460 | 0.81 |
| 39_K | 91_G | 1.438 | 0.79 |
| 103_Q | 121_N | 1.403 | 0.77 |
| 61_I | 112_I | 1.372 | 0.75 |
| 59_S | 71_L | 1.371 | 0.75 |
| 34_Q | 104_N | 1.368 | 0.75 |
| 27_I | 53_I | 1.327 | 0.71 |
| 78_S | 82_I | 1.309 | 0.70 |
| 110_N | 116_A | 1.285 | 0.68 |
| 130_H | 134_G | 1.263 | 0.66 |
| 60_H | 63_A | 1.256 | 0.65 |
| 87_G | 101_S | 1.233 | 0.63 |
| 133_K | 139_Q | 1.228 | 0.63 |
| 37_L | 48_Y | 1.207 | 0.61 |
| 13_E | 144_P | 1.201 | 0.60 |
| 58_I | 111_E | 1.196 | 0.60 |
| 33_I | 121_N | 1.193 | 0.59 |
| 24_I | 33_I | 1.176 | 0.58 |
| 12_A | 142_K | 1.175 | 0.58 |
| 65_P | 116_A | 1.174 | 0.58 |
| 16_P | 45_K | 1.155 | 0.56 |
| 86_K | 101_S | 1.144 | 0.55 |
| 22_E | 126_I | 1.143 | 0.54 |
| 31_A | 40_I | 1.136 | 0.54 |
| 23_V | 95_S | 1.133 | 0.53 |
| 38_E | 125_T | 1.132 | 0.53 |
| 72_S | 119_V | 1.118 | 0.52 |
| 13_E | 16_P | 1.106 | 0.51 |
| 83_G | 118_K | 1.086 | 0.49 |
| 34_Q | 107_I | 1.083 | 0.48 |
| 15_L | 141_V | 1.080 | 0.48 |
| 24_I | 84_R | 1.077 | 0.48 |
| 43_L | 133_K | 1.074 | 0.48 |
| 37_L | 40_I | 1.064 | 0.47 |
| 12_A | 48_Y | 1.056 | 0.46 |
| 75_I | 100_I | 1.056 | 0.46 |
| 33_I | 71_L | 1.054 | 0.46 |
| 70_E | 115_Y | 1.050 | 0.45 |
| 72_S | 113_F | 1.043 | 0.45 |
| 24_I | 89_K | 1.031 | 0.43 |
| 63_A | 74_R | 1.025 | 0.43 |
| 33_I | 72_S | 1.022 | 0.42 |
| 57_D | 81_S | 1.022 | 0.42 |
| 47_I | 93_I | 1.021 | 0.42 |
| 68_G | 116_A | 1.021 | 0.42 |
| 51_P | 93_I | 1.018 | 0.42 |
| 102_E | 143_M | 1.013 | 0.42 |
| 26_K | 136_R | 1.011 | 0.41 |
| 16_P | 136_R | 1.010 | 0.41 |
| 20_E | 40_I | 1.010 | 0.41 |
| 27_I | 110_N | 1.006 | 0.41 |
| 30_D | 125_T | 1.005 | 0.41 |
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 | |
| 2lnmA | 1 | 0.4069 | 43.6 | 0.928 | Contact Map |
| 2llwA | 1 | 0.4897 | 31.2 | 0.934 | Contact Map |
| 2llvA | 1 | 0.4897 | 17.8 | 0.941 | Contact Map |
| 2zbcA | 8 | 0.531 | 12.4 | 0.945 | Contact Map |
| 3hwsA | 6 | 0.6414 | 8.9 | 0.949 | Contact Map |
| 2djwA | 10 | 0.5241 | 8.2 | 0.949 | Contact Map |
| 4o4fA | 1 | 0.9517 | 6.1 | 0.952 | Contact Map |
| 2oeqA | 4 | 0.469 | 5.8 | 0.953 | Contact Map |
| 2lmdA | 1 | 0.469 | 5.8 | 0.953 | Contact Map |
| 2f4mB | 1 | 0.4138 | 5.4 | 0.953 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)