| trpv_hmmer_v2 |
| ID: | 1405452580 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 311 (307) | ||
| Sequences: | 1206 (849.8) | ||
| Seq/Len: | 3.928 | ||
| Nf(neff/√len): | 48.5 |
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: 3.928).
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 |
| 104_E | 107_F | 4.331 | 1.00 |
| 103_S | 107_F | 3.456 | 1.00 |
| 101_S | 104_E | 3.408 | 1.00 |
| 83_G | 86_Y | 3.244 | 1.00 |
| 167_D | 276_T | 3.106 | 1.00 |
| 94_L | 97_L | 2.988 | 1.00 |
| 100_D | 104_E | 2.330 | 1.00 |
| 101_S | 107_F | 2.244 | 1.00 |
| 231_F | 235_M | 1.954 | 1.00 |
| 97_L | 104_E | 1.948 | 1.00 |
| 224_T | 228_L | 1.821 | 1.00 |
| 167_D | 171_F | 1.802 | 0.99 |
| 182_F | 256_A | 1.779 | 0.99 |
| 35_Y | 42_A | 1.766 | 0.99 |
| 230_K | 233_I | 1.747 | 0.99 |
| 275_E | 278_N | 1.686 | 0.99 |
| 5_L | 10_N | 1.664 | 0.99 |
| 104_E | 111_S | 1.637 | 0.99 |
| 271_A | 276_T | 1.628 | 0.99 |
| 230_K | 235_M | 1.625 | 0.99 |
| 271_A | 274_G | 1.580 | 0.98 |
| 160_I | 175_Y | 1.577 | 0.98 |
| 160_I | 174_V | 1.565 | 0.98 |
| 218_Y | 224_T | 1.557 | 0.98 |
| 97_L | 101_S | 1.542 | 0.98 |
| 25_F | 36_M | 1.542 | 0.98 |
| 285_K | 289_K | 1.542 | 0.98 |
| 25_F | 35_Y | 1.517 | 0.98 |
| 16_K | 300_E | 1.495 | 0.97 |
| 137_A | 181_G | 1.492 | 0.97 |
| 229_F | 233_I | 1.481 | 0.97 |
| 28_N | 36_M | 1.461 | 0.97 |
| 265_L | 295_T | 1.449 | 0.97 |
| 39_F | 45_Y | 1.445 | 0.97 |
| 271_A | 277_V | 1.441 | 0.97 |
| 32_Y | 36_M | 1.406 | 0.96 |
| 228_L | 231_F | 1.403 | 0.96 |
| 304_L | 307_M | 1.403 | 0.96 |
| 275_E | 279_K | 1.383 | 0.95 |
| 167_D | 272_L | 1.367 | 0.95 |
| 270_I | 274_G | 1.366 | 0.95 |
| 25_F | 32_Y | 1.355 | 0.95 |
| 36_M | 39_F | 1.355 | 0.95 |
| 273_M | 288_W | 1.332 | 0.94 |
| 273_M | 293_A | 1.326 | 0.94 |
| 293_A | 296_I | 1.322 | 0.94 |
| 25_F | 31_V | 1.320 | 0.94 |
| 172_M | 256_A | 1.314 | 0.93 |
| 221_L | 227_E | 1.309 | 0.93 |
| 65_R | 69_E | 1.305 | 0.93 |
| 278_N | 282_Q | 1.305 | 0.93 |
| 100_D | 103_S | 1.298 | 0.93 |
| 144_L | 168_L | 1.285 | 0.92 |
| 167_D | 271_A | 1.264 | 0.92 |
| 273_M | 276_T | 1.262 | 0.92 |
| 31_V | 36_M | 1.253 | 0.91 |
| 163_M | 271_A | 1.249 | 0.91 |
| 36_M | 40_T | 1.248 | 0.91 |
| 27_F | 39_F | 1.247 | 0.91 |
| 107_F | 111_S | 1.228 | 0.90 |
| 104_E | 108_F | 1.227 | 0.90 |
| 145_Y | 156_Y | 1.208 | 0.89 |
| 69_E | 121_Y | 1.206 | 0.89 |
| 35_Y | 45_Y | 1.204 | 0.89 |
| 39_F | 43_A | 1.200 | 0.89 |
| 83_G | 94_L | 1.191 | 0.88 |
| 115_L | 119_V | 1.188 | 0.88 |
| 182_F | 186_V | 1.178 | 0.87 |
| 205_H | 208_R | 1.169 | 0.87 |
| 28_N | 32_Y | 1.163 | 0.86 |
| 155_I | 167_D | 1.158 | 0.86 |
| 33_C | 36_M | 1.157 | 0.86 |
| 275_E | 281_A | 1.153 | 0.86 |
| 134_F | 252_I | 1.136 | 0.85 |
| 264_L | 291_Q | 1.134 | 0.84 |
| 103_S | 111_S | 1.132 | 0.84 |
| 35_Y | 38_I | 1.131 | 0.84 |
| 160_I | 168_L | 1.129 | 0.84 |
| 271_A | 288_W | 1.127 | 0.84 |
| 29_F | 36_M | 1.127 | 0.84 |
| 212_C | 215_G | 1.127 | 0.84 |
| 287_I | 291_Q | 1.126 | 0.84 |
| 155_I | 163_M | 1.126 | 0.84 |
| 94_L | 101_S | 1.122 | 0.84 |
| 223_S | 226_L | 1.119 | 0.83 |
| 215_G | 222_Y | 1.119 | 0.83 |
| 126_K | 129_V | 1.118 | 0.83 |
| 272_L | 277_V | 1.112 | 0.83 |
| 225_C | 228_L | 1.111 | 0.83 |
| 35_Y | 40_T | 1.100 | 0.82 |
| 124_Q | 129_V | 1.100 | 0.82 |
| 276_T | 280_I | 1.097 | 0.82 |
| 32_Y | 35_Y | 1.092 | 0.81 |
| 157_A | 268_M | 1.088 | 0.81 |
| 17_W | 21_V | 1.084 | 0.81 |
| 32_Y | 39_F | 1.083 | 0.81 |
| 163_M | 273_M | 1.080 | 0.80 |
| 124_Q | 127_E | 1.072 | 0.80 |
| 130_A | 174_V | 1.071 | 0.79 |
| 277_V | 290_L | 1.069 | 0.79 |
| 28_N | 35_Y | 1.069 | 0.79 |
| 263_I | 269_L | 1.068 | 0.79 |
| 16_K | 20_F | 1.067 | 0.79 |
| 238_L | 241_T | 1.060 | 0.79 |
| 144_L | 158_V | 1.059 | 0.78 |
| 29_F | 35_Y | 1.054 | 0.78 |
| 222_Y | 225_C | 1.054 | 0.78 |
| 11_R | 14_Q | 1.052 | 0.78 |
| 209_G | 212_C | 1.051 | 0.78 |
| 48_V | 51_L | 1.051 | 0.78 |
| 205_H | 210_S | 1.050 | 0.78 |
| 204_P | 211_A | 1.049 | 0.78 |
| 111_S | 117_S | 1.048 | 0.77 |
| 207_C | 210_S | 1.043 | 0.77 |
| 11_R | 23_R | 1.043 | 0.77 |
| 233_I | 236_G | 1.043 | 0.77 |
| 87_F | 177_V | 1.039 | 0.77 |
| 220_S | 223_S | 1.038 | 0.76 |
| 103_S | 118_V | 1.038 | 0.76 |
| 37_I | 46_R | 1.037 | 0.76 |
| 208_R | 214_P | 1.036 | 0.76 |
| 114_M | 117_S | 1.035 | 0.76 |
| 26_Y | 30_F | 1.029 | 0.76 |
| 77_V | 81_F | 1.028 | 0.75 |
| 182_F | 263_I | 1.026 | 0.75 |
| 274_G | 277_V | 1.025 | 0.75 |
| 79_F | 268_M | 1.023 | 0.75 |
| 97_L | 103_S | 1.021 | 0.75 |
| 124_Q | 128_Y | 1.021 | 0.75 |
| 128_Y | 284_S | 1.019 | 0.75 |
| 25_F | 28_N | 1.017 | 0.74 |
| 204_P | 207_C | 1.017 | 0.74 |
| 235_M | 238_L | 1.013 | 0.74 |
| 163_M | 264_L | 1.013 | 0.74 |
| 100_D | 107_F | 1.012 | 0.74 |
| 170_R | 229_F | 1.012 | 0.74 |
| 26_Y | 43_A | 1.011 | 0.74 |
| 177_V | 262_Y | 1.008 | 0.73 |
| 13_L | 16_K | 1.005 | 0.73 |
| 168_L | 264_L | 1.004 | 0.73 |
| 70_I | 74_S | 1.001 | 0.73 |
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 | |
| 3j5pB | 4 | 0.9068 | 100 | 0.298 | Contact Map |
| 3rvyA | 2 | 0.7042 | 99.7 | 0.721 | Contact Map |
| 4dxwA | 4 | 0.7138 | 99.7 | 0.736 | Contact Map |
| 4bgnA | 2 | 0.6913 | 99.6 | 0.747 | Contact Map |
| 4ltoA | 4 | 0.3923 | 99.3 | 0.798 | Contact Map |
| 2r9rB | 2 | 0.8232 | 99.1 | 0.811 | Contact Map |
| 4cbcA | 4 | 0.2926 | 98.6 | 0.843 | Contact Map |
| 3behA | 4 | 0.7203 | 98.2 | 0.859 | Contact Map |
| 1orqC | 1 | 0.6977 | 95.3 | 0.907 | Contact Map |
| 2a9hA | 4 | 0.3087 | 89.7 | 0.923 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)