| T0836 -force run |
| ID: | 1405445302 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 204 (200) | ||
| Sequences: | 73 (54.6) | ||
| Seq/Len: | 0.365 | ||
| Nf(neff/√len): | 3.9 |
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: 0.365).
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 |
| 60_F | 87_A | 2.591 | 0.95 |
| 99_W | 143_T | 2.099 | 0.83 |
| 176_K | 180_L | 1.915 | 0.74 |
| 59_Y | 64_Q | 1.892 | 0.73 |
| 142_A | 169_D | 1.725 | 0.63 |
| 87_A | 156_N | 1.701 | 0.61 |
| 136_G | 140_W | 1.659 | 0.58 |
| 5_L | 11_T | 1.649 | 0.57 |
| 106_A | 139_M | 1.646 | 0.57 |
| 167_D | 170_A | 1.633 | 0.56 |
| 60_F | 156_N | 1.611 | 0.55 |
| 22_I | 195_T | 1.589 | 0.53 |
| 65_I | 160_A | 1.578 | 0.52 |
| 24_I | 31_H | 1.485 | 0.46 |
| 146_F | 151_V | 1.474 | 0.45 |
| 71_I | 78_A | 1.464 | 0.44 |
| 7_N | 11_T | 1.453 | 0.44 |
| 158_K | 164_V | 1.448 | 0.43 |
| 4_L | 11_T | 1.445 | 0.43 |
| 16_F | 190_I | 1.416 | 0.41 |
| 112_L | 117_T | 1.408 | 0.41 |
| 58_Y | 172_A | 1.363 | 0.38 |
| 45_L | 101_M | 1.348 | 0.37 |
| 60_F | 88_L | 1.348 | 0.37 |
| 152_F | 181_V | 1.344 | 0.36 |
| 65_I | 77_P | 1.324 | 0.35 |
| 61_N | 64_Q | 1.323 | 0.35 |
| 69_P | 75_L | 1.321 | 0.35 |
| 24_I | 142_A | 1.311 | 0.34 |
| 99_W | 103_V | 1.308 | 0.34 |
| 14_V | 18_L | 1.308 | 0.34 |
| 59_Y | 62_F | 1.302 | 0.34 |
| 87_A | 177_T | 1.297 | 0.33 |
| 104_L | 108_N | 1.292 | 0.33 |
| 147_F | 152_F | 1.282 | 0.32 |
| 18_L | 21_V | 1.263 | 0.31 |
| 160_A | 179_M | 1.250 | 0.30 |
| 57_L | 153_I | 1.246 | 0.30 |
| 100_V | 117_T | 1.230 | 0.29 |
| 57_L | 192_M | 1.226 | 0.29 |
| 99_W | 146_F | 1.224 | 0.29 |
| 65_I | 179_M | 1.221 | 0.29 |
| 84_A | 161_L | 1.218 | 0.28 |
| 153_I | 178_A | 1.213 | 0.28 |
| 89_F | 99_W | 1.211 | 0.28 |
| 178_A | 192_M | 1.198 | 0.27 |
| 65_I | 181_V | 1.194 | 0.27 |
| 93_W | 96_L | 1.190 | 0.27 |
| 67_V | 194_A | 1.184 | 0.27 |
| 173_K | 177_T | 1.181 | 0.26 |
| 49_F | 101_M | 1.179 | 0.26 |
| 160_A | 181_V | 1.171 | 0.26 |
| 149_V | 153_I | 1.169 | 0.26 |
| 115_A | 136_G | 1.167 | 0.26 |
| 137_T | 195_T | 1.159 | 0.25 |
| 159_I | 174_A | 1.157 | 0.25 |
| 88_L | 153_I | 1.152 | 0.25 |
| 96_L | 146_F | 1.152 | 0.25 |
| 60_F | 177_T | 1.140 | 0.24 |
| 112_L | 164_V | 1.127 | 0.24 |
| 3_G | 10_N | 1.124 | 0.23 |
| 13_I | 165_E | 1.121 | 0.23 |
| 16_F | 90_W | 1.116 | 0.23 |
| 50_G | 193_L | 1.115 | 0.23 |
| 49_F | 58_Y | 1.103 | 0.22 |
| 60_F | 178_A | 1.102 | 0.22 |
| 64_Q | 84_A | 1.099 | 0.22 |
| 150_W | 161_L | 1.098 | 0.22 |
| 77_P | 160_A | 1.094 | 0.22 |
| 57_L | 87_A | 1.093 | 0.22 |
| 3_G | 12_I | 1.090 | 0.22 |
| 61_N | 192_M | 1.084 | 0.21 |
| 21_V | 167_D | 1.084 | 0.21 |
| 85_P | 153_I | 1.083 | 0.21 |
| 95_A | 98_T | 1.080 | 0.21 |
| 18_L | 90_W | 1.079 | 0.21 |
| 57_L | 178_A | 1.076 | 0.21 |
| 89_F | 94_A | 1.075 | 0.21 |
| 21_V | 170_A | 1.074 | 0.21 |
| 17_V | 20_L | 1.073 | 0.21 |
| 9_R | 105_L | 1.071 | 0.21 |
| 147_F | 151_V | 1.069 | 0.21 |
| 52_L | 73_A | 1.068 | 0.21 |
| 153_I | 192_M | 1.066 | 0.21 |
| 29_S | 32_G | 1.063 | 0.20 |
| 85_P | 149_V | 1.062 | 0.20 |
| 57_L | 149_V | 1.054 | 0.20 |
| 13_I | 21_V | 1.054 | 0.20 |
| 29_S | 130_M | 1.053 | 0.20 |
| 159_I | 166_A | 1.049 | 0.20 |
| 62_F | 135_I | 1.049 | 0.20 |
| 103_V | 146_F | 1.045 | 0.20 |
| 72_P | 139_M | 1.044 | 0.20 |
| 115_A | 140_W | 1.043 | 0.20 |
| 159_I | 170_A | 1.024 | 0.19 |
| 50_G | 149_V | 1.024 | 0.19 |
| 149_V | 178_A | 1.023 | 0.19 |
| 119_G | 131_G | 1.020 | 0.18 |
| 25_G | 28_H | 1.019 | 0.18 |
| 50_G | 98_T | 1.014 | 0.18 |
| 17_V | 26_Y | 1.013 | 0.18 |
| 57_L | 88_L | 1.006 | 0.18 |
| 57_L | 61_N | 1.005 | 0.18 |
| 59_Y | 84_A | 1.004 | 0.18 |
| 26_Y | 31_H | 1.004 | 0.18 |
| 98_T | 149_V | 1.004 | 0.18 |
| 14_V | 186_T | 1.000 | 0.18 |
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 | |
| 3qe7A | 1 | 0.2696 | 2.8 | 0.977 | Contact Map |
| 1fftC | 2 | 0.4902 | 2.6 | 0.977 | Contact Map |
| 3hd7A | 2 | 0.152 | 2.5 | 0.977 | Contact Map |
| 1zxgA | 1 | 0.152 | 1.4 | 0.98 | Contact Map |
| 1n7lA | 1 | 0.1225 | 1.3 | 0.981 | Contact Map |
| 3k8gA | 2 | 0.3039 | 1.3 | 0.981 | Contact Map |
| 1m56C | 2 | 0.4902 | 1.3 | 0.981 | Contact Map |
| 1v54C | 2 | 0.4902 | 1.3 | 0.981 | Contact Map |
| 3zs9C | 2 | 0.1324 | 1.1 | 0.981 | Contact Map |
| 3j01B | 1 | 0.5686 | 1.1 | 0.982 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)