| T0847 |
| ID: | 1404842590 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (171) | ||
| Sequences: | 261 (180.3) | ||
| Seq/Len: | 1.526 | ||
| Nf(neff/√len): | 13.8 |
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: 1.526).
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 |
| 37_V | 64_C | 2.767 | 1.00 |
| 55_A | 59_R | 2.663 | 1.00 |
| 26_R | 51_D | 2.662 | 1.00 |
| 91_N | 94_I | 1.889 | 0.97 |
| 36_L | 121_S | 1.777 | 0.95 |
| 118_F | 156_F | 1.578 | 0.90 |
| 11_V | 146_S | 1.476 | 0.85 |
| 118_F | 159_E | 1.469 | 0.85 |
| 16_V | 20_N | 1.436 | 0.83 |
| 107_G | 159_E | 1.406 | 0.81 |
| 7_S | 139_H | 1.393 | 0.80 |
| 59_R | 63_V | 1.372 | 0.79 |
| 32_T | 36_L | 1.365 | 0.79 |
| 66_L | 82_V | 1.343 | 0.77 |
| 136_L | 140_V | 1.341 | 0.77 |
| 82_V | 113_Q | 1.339 | 0.77 |
| 67_L | 78_M | 1.326 | 0.76 |
| 12_Y | 16_V | 1.318 | 0.75 |
| 27_R | 169_P | 1.298 | 0.73 |
| 65_V | 90_K | 1.296 | 0.73 |
| 3_L | 6_K | 1.275 | 0.72 |
| 157_D | 161_R | 1.265 | 0.71 |
| 45_D | 135_W | 1.254 | 0.70 |
| 48_I | 56_A | 1.248 | 0.69 |
| 11_V | 83_Q | 1.248 | 0.69 |
| 93_S | 96_S | 1.239 | 0.68 |
| 53_L | 90_K | 1.227 | 0.67 |
| 65_V | 99_G | 1.224 | 0.67 |
| 3_L | 170_V | 1.223 | 0.67 |
| 48_I | 70_G | 1.222 | 0.67 |
| 29_I | 40_M | 1.217 | 0.66 |
| 36_L | 94_I | 1.204 | 0.65 |
| 112_G | 126_V | 1.198 | 0.65 |
| 37_V | 62_F | 1.192 | 0.64 |
| 23_D | 131_Y | 1.170 | 0.62 |
| 45_D | 51_D | 1.156 | 0.61 |
| 40_M | 43_F | 1.155 | 0.60 |
| 20_N | 34_Q | 1.145 | 0.59 |
| 115_R | 132_S | 1.141 | 0.59 |
| 50_C | 53_L | 1.139 | 0.59 |
| 18_H | 61_V | 1.137 | 0.59 |
| 135_W | 140_V | 1.119 | 0.57 |
| 31_R | 61_V | 1.115 | 0.56 |
| 42_V | 71_G | 1.113 | 0.56 |
| 33_S | 87_S | 1.112 | 0.56 |
| 23_D | 173_L | 1.112 | 0.56 |
| 37_V | 157_D | 1.108 | 0.56 |
| 74_L | 88_H | 1.107 | 0.56 |
| 160_F | 164_Y | 1.104 | 0.55 |
| 91_N | 96_S | 1.104 | 0.55 |
| 32_T | 94_I | 1.103 | 0.55 |
| 38_I | 82_V | 1.101 | 0.55 |
| 38_I | 54_E | 1.097 | 0.55 |
| 75_F | 78_M | 1.097 | 0.55 |
| 38_I | 65_V | 1.095 | 0.54 |
| 60_G | 63_V | 1.087 | 0.54 |
| 5_E | 112_G | 1.085 | 0.53 |
| 10_T | 130_S | 1.083 | 0.53 |
| 21_I | 29_I | 1.080 | 0.53 |
| 55_A | 95_R | 1.073 | 0.52 |
| 126_V | 170_V | 1.071 | 0.52 |
| 45_D | 75_F | 1.066 | 0.51 |
| 99_G | 150_G | 1.065 | 0.51 |
| 22_R | 131_Y | 1.063 | 0.51 |
| 26_R | 99_G | 1.063 | 0.51 |
| 58_K | 136_L | 1.060 | 0.51 |
| 130_S | 143_N | 1.057 | 0.50 |
| 41_D | 51_D | 1.051 | 0.50 |
| 33_S | 61_V | 1.051 | 0.50 |
| 36_L | 86_D | 1.050 | 0.50 |
| 36_L | 170_V | 1.050 | 0.50 |
| 17_K | 29_I | 1.048 | 0.50 |
| 77_E | 80_D | 1.047 | 0.49 |
| 56_A | 121_S | 1.047 | 0.49 |
| 99_G | 165_A | 1.045 | 0.49 |
| 127_L | 153_V | 1.044 | 0.49 |
| 5_E | 34_Q | 1.040 | 0.49 |
| 137_C | 143_N | 1.038 | 0.48 |
| 49_F | 63_V | 1.031 | 0.48 |
| 12_Y | 152_A | 1.028 | 0.47 |
| 82_V | 134_T | 1.023 | 0.47 |
| 114_I | 121_S | 1.020 | 0.47 |
| 3_L | 127_L | 1.016 | 0.46 |
| 41_D | 44_T | 1.016 | 0.46 |
| 22_R | 160_F | 1.015 | 0.46 |
| 112_G | 159_E | 1.014 | 0.46 |
| 34_Q | 62_F | 1.012 | 0.46 |
| 116_E | 159_E | 1.006 | 0.45 |
| 45_D | 160_F | 1.005 | 0.45 |
| 131_Y | 138_G | 1.004 | 0.45 |
| 29_I | 151_Q | 1.003 | 0.45 |
| 45_D | 48_I | 1.002 | 0.45 |
| 145_L | 166_S | 1.001 | 0.45 |
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 | |
| 4gelA | 2 | 0.858 | 99.9 | 0.587 | Contact Map |
| 1byrA | 1 | 0.8409 | 99.9 | 0.601 | Contact Map |
| 4ggjA | 1 | 0.7955 | 99.9 | 0.619 | Contact Map |
| 3hsiA | 3 | 0.9886 | 99.8 | 0.631 | Contact Map |
| 1v0wA | 1 | 0.9205 | 99.8 | 0.652 | Contact Map |
| 2o8rA | 2 | 0.8636 | 99.8 | 0.668 | Contact Map |
| 1xdpA | 2 | 0.9034 | 99.7 | 0.673 | Contact Map |
| 2c1lA | 2 | 0.9034 | 99.7 | 0.681 | Contact Map |
| 3qphA | 1 | 0.8182 | 97.7 | 0.855 | Contact Map |
| 2f5tX | 1 | 0.7216 | 97.6 | 0.859 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)