| T0764_missing |
| ID: | 1400797745 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (130) | ||
| Sequences: | 138 (91.8) | ||
| Seq/Len: | 1.062 | ||
| Nf(neff/√len): | 8.1 |
Jackhmmer Results: (2014_04_16)
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: 1.062).
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 |
| 6_A | 34_T | 2.557 | 0.99 |
| 49_V | 114_M | 2.409 | 0.99 |
| 118_A | 128_V | 2.340 | 0.99 |
| 78_V | 81_E | 2.295 | 0.99 |
| 9_F | 15_G | 2.266 | 0.98 |
| 118_A | 130_V | 2.102 | 0.97 |
| 121_L | 128_V | 2.072 | 0.97 |
| 2_S | 33_K | 1.881 | 0.94 |
| 23_G | 26_V | 1.800 | 0.92 |
| 19_T | 27_G | 1.626 | 0.85 |
| 22_Q | 26_V | 1.624 | 0.85 |
| 2_S | 22_Q | 1.609 | 0.84 |
| 50_P | 113_L | 1.607 | 0.84 |
| 16_V | 39_A | 1.541 | 0.81 |
| 55_Q | 124_Q | 1.483 | 0.77 |
| 60_A | 109_R | 1.442 | 0.74 |
| 90_Y | 131_I | 1.404 | 0.72 |
| 25_P | 47_G | 1.356 | 0.68 |
| 28_W | 83_T | 1.348 | 0.67 |
| 36_N | 40_I | 1.339 | 0.66 |
| 26_V | 32_L | 1.308 | 0.64 |
| 7_A | 35_R | 1.300 | 0.63 |
| 74_V | 96_P | 1.287 | 0.62 |
| 23_G | 42_S | 1.268 | 0.60 |
| 71_G | 115_K | 1.220 | 0.56 |
| 88_V | 131_I | 1.201 | 0.54 |
| 8_L | 12_I | 1.197 | 0.53 |
| 48_A | 67_K | 1.197 | 0.53 |
| 23_G | 71_G | 1.196 | 0.53 |
| 47_G | 91_Y | 1.192 | 0.53 |
| 80_M | 84_K | 1.191 | 0.53 |
| 66_S | 128_V | 1.188 | 0.53 |
| 60_A | 112_R | 1.174 | 0.51 |
| 117_W | 128_V | 1.132 | 0.47 |
| 118_A | 121_L | 1.123 | 0.47 |
| 23_G | 37_I | 1.122 | 0.46 |
| 59_E | 105_Y | 1.118 | 0.46 |
| 47_G | 67_K | 1.114 | 0.46 |
| 105_Y | 114_M | 1.113 | 0.46 |
| 14_P | 61_K | 1.112 | 0.45 |
| 105_Y | 108_T | 1.111 | 0.45 |
| 22_Q | 25_P | 1.109 | 0.45 |
| 89_I | 130_V | 1.102 | 0.45 |
| 95_L | 108_T | 1.095 | 0.44 |
| 101_R | 131_I | 1.094 | 0.44 |
| 53_E | 100_E | 1.084 | 0.43 |
| 120_M | 130_V | 1.084 | 0.43 |
| 53_E | 73_E | 1.077 | 0.42 |
| 103_E | 106_E | 1.075 | 0.42 |
| 22_Q | 91_Y | 1.068 | 0.41 |
| 122_N | 125_G | 1.062 | 0.41 |
| 43_Y | 81_E | 1.054 | 0.40 |
| 60_A | 69_M | 1.054 | 0.40 |
| 45_P | 57_P | 1.053 | 0.40 |
| 120_M | 123_D | 1.047 | 0.39 |
| 106_E | 110_R | 1.043 | 0.39 |
| 47_G | 69_M | 1.025 | 0.38 |
| 49_V | 83_T | 1.020 | 0.37 |
| 30_T | 40_I | 1.011 | 0.36 |
| 18_I | 43_Y | 1.010 | 0.36 |
| 49_V | 89_I | 1.008 | 0.36 |
| 31_L | 37_I | 1.006 | 0.36 |
| 83_T | 122_N | 1.003 | 0.36 |
| 18_I | 101_R | 1.001 | 0.35 |
| 32_L | 78_V | 1.001 | 0.35 |
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 | |
| 1qlwA | 2 | 0.7634 | 99.6 | 0.75 | Contact Map |
| 3b5eA | 2 | 0.7176 | 97.9 | 0.866 | Contact Map |
| 2h1iA | 3 | 0.7252 | 97.9 | 0.867 | Contact Map |
| 2r8bA | 2 | 0.7252 | 97.8 | 0.867 | Contact Map |
| 2zyrA | 2 | 0.6412 | 97.7 | 0.87 | Contact Map |
| 3og9A | 2 | 0.7252 | 97.7 | 0.872 | Contact Map |
| 4h0cA | 2 | 0.7557 | 97.6 | 0.873 | Contact Map |
| 3azoA | 2 | 0.9008 | 97.6 | 0.874 | Contact Map |
| 1fj2A | 2 | 0.7634 | 97.6 | 0.875 | Contact Map |
| 3lp5A | 1 | 0.8702 | 97.6 | 0.875 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)