| T0780 |
| ID: | 1400182026 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 259 (229) | ||
| Sequences: | 1081 (977.4) | ||
| Seq/Len: | 4.721 | ||
| Nf(neff/√len): | 64.6 |
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: 4.721).
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 |
| 132_G | 174_E | 3.847 | 1.00 |
| 206_D | 210_V | 2.627 | 1.00 |
| 74_G | 79_S | 2.533 | 1.00 |
| 4_N | 8_I | 2.474 | 1.00 |
| 158_E | 226_T | 2.470 | 1.00 |
| 137_K | 140_V | 2.445 | 1.00 |
| 167_V | 218_P | 2.366 | 1.00 |
| 140_V | 182_I | 2.310 | 1.00 |
| 192_I | 196_Y | 2.197 | 1.00 |
| 203_Q | 211_V | 2.142 | 1.00 |
| 138_D | 166_E | 2.133 | 1.00 |
| 184_A | 202_L | 2.128 | 1.00 |
| 197_S | 222_I | 2.065 | 1.00 |
| 93_V | 109_L | 2.026 | 1.00 |
| 173_Q | 177_D | 1.963 | 1.00 |
| 184_A | 200_V | 1.962 | 1.00 |
| 164_D | 221_T | 1.957 | 1.00 |
| 195_N | 226_T | 1.954 | 1.00 |
| 95_A | 109_L | 1.952 | 1.00 |
| 142_I | 167_V | 1.947 | 1.00 |
| 11_S | 15_A | 1.901 | 1.00 |
| 51_D | 92_K | 1.842 | 1.00 |
| 171_S | 176_L | 1.830 | 1.00 |
| 182_I | 204_A | 1.805 | 1.00 |
| 100_A | 105_I | 1.798 | 1.00 |
| 133_K | 173_Q | 1.757 | 1.00 |
| 182_I | 202_L | 1.756 | 1.00 |
| 100_A | 131_I | 1.724 | 1.00 |
| 202_L | 221_T | 1.719 | 0.99 |
| 145_E | 183_I | 1.708 | 0.99 |
| 204_A | 216_I | 1.703 | 0.99 |
| 142_I | 202_L | 1.682 | 0.99 |
| 140_V | 179_I | 1.679 | 0.99 |
| 162_V | 221_T | 1.670 | 0.99 |
| 195_N | 224_K | 1.661 | 0.99 |
| 199_S | 220_D | 1.645 | 0.99 |
| 157_I | 226_T | 1.632 | 0.99 |
| 7_Y | 11_S | 1.617 | 0.99 |
| 8_I | 11_S | 1.587 | 0.99 |
| 136_Q | 170_T | 1.584 | 0.99 |
| 152_D | 193_T | 1.552 | 0.99 |
| 162_V | 223_M | 1.543 | 0.99 |
| 171_S | 214_A | 1.528 | 0.99 |
| 204_A | 214_A | 1.462 | 0.98 |
| 141_K | 144_P | 1.449 | 0.98 |
| 54_Y | 96_D | 1.442 | 0.98 |
| 143_V | 181_K | 1.442 | 0.98 |
| 72_L | 90_K | 1.432 | 0.98 |
| 132_G | 172_D | 1.430 | 0.97 |
| 142_I | 164_D | 1.414 | 0.97 |
| 186_L | 189_S | 1.407 | 0.97 |
| 94_T | 110_S | 1.393 | 0.97 |
| 144_P | 162_V | 1.355 | 0.96 |
| 160_V | 226_T | 1.352 | 0.96 |
| 104_T | 128_T | 1.352 | 0.96 |
| 50_I | 109_L | 1.337 | 0.96 |
| 140_V | 169_I | 1.331 | 0.96 |
| 136_Q | 168_S | 1.303 | 0.95 |
| 42_T | 73_T | 1.283 | 0.94 |
| 167_V | 182_I | 1.271 | 0.94 |
| 97_L | 107_V | 1.270 | 0.94 |
| 183_I | 205_I | 1.261 | 0.94 |
| 157_I | 160_V | 1.256 | 0.94 |
| 175_T | 213_P | 1.240 | 0.93 |
| 167_V | 216_I | 1.235 | 0.93 |
| 135_A | 173_Q | 1.229 | 0.93 |
| 175_T | 178_R | 1.214 | 0.92 |
| 5_S | 8_I | 1.209 | 0.92 |
| 157_I | 225_V | 1.201 | 0.91 |
| 50_I | 127_I | 1.197 | 0.91 |
| 114_L | 120_A | 1.171 | 0.90 |
| 13_F | 17_V | 1.168 | 0.90 |
| 155_V | 227_T | 1.168 | 0.90 |
| 184_A | 189_S | 1.163 | 0.90 |
| 196_Y | 225_V | 1.155 | 0.89 |
| 70_V | 91_F | 1.145 | 0.89 |
| 41_Y | 76_N | 1.143 | 0.89 |
| 124_P | 218_P | 1.142 | 0.89 |
| 192_I | 227_T | 1.142 | 0.89 |
| 35_Q | 38_T | 1.128 | 0.88 |
| 204_A | 212_L | 1.110 | 0.87 |
| 55_N | 59_Y | 1.100 | 0.86 |
| 106_E | 126_K | 1.100 | 0.86 |
| 35_Q | 39_E | 1.099 | 0.86 |
| 169_I | 214_A | 1.098 | 0.86 |
| 108_P | 111_I | 1.098 | 0.86 |
| 142_I | 162_V | 1.094 | 0.85 |
| 86_E | 91_F | 1.093 | 0.85 |
| 47_N | 67_E | 1.092 | 0.85 |
| 76_N | 80_L | 1.091 | 0.85 |
| 48_V | 70_V | 1.090 | 0.85 |
| 178_R | 206_D | 1.088 | 0.85 |
| 138_D | 168_S | 1.077 | 0.84 |
| 228_K | 231_A | 1.076 | 0.84 |
| 204_A | 218_P | 1.072 | 0.84 |
| 12_L | 16_C | 1.064 | 0.83 |
| 188_T | 192_I | 1.055 | 0.83 |
| 134_K | 170_T | 1.053 | 0.82 |
| 58_K | 133_K | 1.052 | 0.82 |
| 73_T | 119_T | 1.039 | 0.81 |
| 50_I | 68_V | 1.039 | 0.81 |
| 61_I | 79_S | 1.031 | 0.81 |
| 17_V | 70_V | 1.019 | 0.79 |
| 161_M | 224_K | 1.017 | 0.79 |
| 33_A | 38_T | 1.017 | 0.79 |
| 199_S | 222_I | 1.007 | 0.78 |
| 33_A | 36_V | 1.006 | 0.78 |
| 102_V | 173_Q | 1.002 | 0.78 |
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 | |
| 2kq1A | 1 | 0.4517 | 99.7 | 0.671 | Contact Map |
| 2kpsA | 1 | 0.3784 | 99.4 | 0.726 | Contact Map |
| 2kxyA | 1 | 0.3861 | 99.3 | 0.748 | Contact Map |
| 3lywA | 1 | 0.3243 | 99.2 | 0.764 | Contact Map |
| 2xwxA | 2 | 0.4903 | 9.5 | 0.953 | Contact Map |
| 2m59A | 2 | 0.1351 | 7.5 | 0.955 | Contact Map |
| 2dibA | 1 | 0.4595 | 5.7 | 0.957 | Contact Map |
| 3j1rA | 21 | 0.0888 | 5.3 | 0.958 | Contact Map |
| 2di9A | 1 | 0.4479 | 5.1 | 0.958 | Contact Map |
| 3sd2A | 1 | 0.305 | 3.6 | 0.961 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)