| NS4B -force run |
| ID: | 1414489930 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 248 (245) | ||
| Sequences: | 61 (47.4) | ||
| Seq/Len: | 0.249 | ||
| Nf(neff/√len): | 3.0 |
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: 0.249).
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 |
| 8_K | 239_I | 2.232 | 0.79 |
| 78_L | 130_T | 1.856 | 0.59 |
| 13_L | 108_T | 1.695 | 0.49 |
| 53_R | 78_L | 1.629 | 0.45 |
| 13_L | 190_L | 1.614 | 0.44 |
| 45_T | 118_Y | 1.607 | 0.44 |
| 3_M | 182_L | 1.603 | 0.43 |
| 111_L | 172_M | 1.524 | 0.38 |
| 39_T | 234_G | 1.507 | 0.37 |
| 97_G | 137_A | 1.506 | 0.37 |
| 40_L | 68_I | 1.490 | 0.36 |
| 118_Y | 142_M | 1.464 | 0.35 |
| 183_M | 244_T | 1.456 | 0.34 |
| 165_E | 207_G | 1.455 | 0.34 |
| 69_A | 107_L | 1.411 | 0.32 |
| 32_L | 80_K | 1.410 | 0.32 |
| 182_L | 201_I | 1.382 | 0.30 |
| 115_V | 201_I | 1.379 | 0.30 |
| 97_G | 169_G | 1.369 | 0.30 |
| 110_A | 131_R | 1.363 | 0.29 |
| 49_T | 78_L | 1.358 | 0.29 |
| 137_A | 169_G | 1.349 | 0.28 |
| 220_S | 235_L | 1.319 | 0.27 |
| 32_L | 106_T | 1.316 | 0.27 |
| 40_L | 110_A | 1.309 | 0.26 |
| 52_L | 159_P | 1.299 | 0.26 |
| 47_F | 96_I | 1.295 | 0.26 |
| 47_F | 239_I | 1.283 | 0.25 |
| 97_G | 142_M | 1.280 | 0.25 |
| 122_G | 168_L | 1.275 | 0.25 |
| 75_L | 97_G | 1.273 | 0.25 |
| 86_K | 218_A | 1.272 | 0.25 |
| 125_L | 235_L | 1.267 | 0.24 |
| 157_P | 197_A | 1.251 | 0.24 |
| 171_V | 201_I | 1.244 | 0.23 |
| 56_I | 196_L | 1.241 | 0.23 |
| 51_M | 135_K | 1.238 | 0.23 |
| 48_V | 68_I | 1.234 | 0.23 |
| 135_K | 156_D | 1.232 | 0.23 |
| 63_V | 224_I | 1.230 | 0.23 |
| 141_I | 228_S | 1.230 | 0.23 |
| 156_D | 180_Q | 1.223 | 0.22 |
| 13_L | 150_I | 1.219 | 0.22 |
| 219_V | 234_G | 1.200 | 0.21 |
| 64_S | 214_N | 1.197 | 0.21 |
| 187_T | 221_M | 1.193 | 0.21 |
| 16_G | 178_V | 1.193 | 0.21 |
| 33_R | 228_S | 1.188 | 0.21 |
| 83_P | 124_G | 1.185 | 0.21 |
| 11_K | 112_F | 1.183 | 0.21 |
| 87_M | 218_A | 1.179 | 0.20 |
| 168_L | 174_L | 1.175 | 0.20 |
| 103_N | 198_T | 1.172 | 0.20 |
| 48_V | 52_L | 1.169 | 0.20 |
| 105_I | 239_I | 1.163 | 0.20 |
| 13_L | 179_T | 1.160 | 0.20 |
| 150_I | 216_T | 1.157 | 0.20 |
| 98_C | 170_Q | 1.144 | 0.19 |
| 137_A | 142_M | 1.143 | 0.19 |
| 45_T | 203_T | 1.141 | 0.19 |
| 14_G | 20_T | 1.136 | 0.19 |
| 136_R | 214_N | 1.133 | 0.19 |
| 42_A | 170_Q | 1.125 | 0.18 |
| 21_Q | 33_R | 1.124 | 0.18 |
| 151_T | 201_I | 1.121 | 0.18 |
| 45_T | 114_L | 1.118 | 0.18 |
| 92_P | 114_L | 1.116 | 0.18 |
| 14_G | 23_P | 1.116 | 0.18 |
| 142_M | 169_G | 1.112 | 0.18 |
| 142_M | 203_T | 1.111 | 0.18 |
| 185_R | 237_F | 1.109 | 0.18 |
| 124_G | 162_P | 1.108 | 0.18 |
| 56_I | 206_E | 1.102 | 0.17 |
| 24_E | 111_L | 1.102 | 0.17 |
| 30_I | 224_I | 1.098 | 0.17 |
| 22_Q | 201_I | 1.095 | 0.17 |
| 175_V | 183_M | 1.095 | 0.17 |
| 32_L | 107_L | 1.095 | 0.17 |
| 39_T | 231_A | 1.090 | 0.17 |
| 8_K | 244_T | 1.089 | 0.17 |
| 118_Y | 203_T | 1.085 | 0.17 |
| 98_C | 142_M | 1.083 | 0.17 |
| 104_P | 225_F | 1.082 | 0.17 |
| 84_L | 162_P | 1.082 | 0.17 |
| 134_Q | 214_N | 1.078 | 0.17 |
| 19_A | 179_T | 1.075 | 0.16 |
| 78_L | 102_V | 1.074 | 0.16 |
| 207_G | 229_Y | 1.072 | 0.16 |
| 36_S | 97_G | 1.067 | 0.16 |
| 95_A | 200_P | 1.064 | 0.16 |
| 47_F | 58_N | 1.063 | 0.16 |
| 136_R | 204_L | 1.061 | 0.16 |
| 128_K | 237_F | 1.058 | 0.16 |
| 100_S | 223_N | 1.058 | 0.16 |
| 200_P | 212_F | 1.058 | 0.16 |
| 51_M | 74_V | 1.058 | 0.16 |
| 44_A | 180_Q | 1.058 | 0.16 |
| 17_S | 179_T | 1.057 | 0.16 |
| 60_S | 140_G | 1.056 | 0.16 |
| 78_L | 155_L | 1.055 | 0.16 |
| 152_V | 168_L | 1.054 | 0.16 |
| 14_G | 221_M | 1.052 | 0.16 |
| 64_S | 173_L | 1.048 | 0.16 |
| 67_A | 165_E | 1.044 | 0.15 |
| 220_S | 237_F | 1.041 | 0.15 |
| 169_G | 216_T | 1.035 | 0.15 |
| 135_K | 233_A | 1.033 | 0.15 |
| 61_V | 234_G | 1.031 | 0.15 |
| 101_Q | 170_Q | 1.026 | 0.15 |
| 129_A | 140_G | 1.026 | 0.15 |
| 11_K | 16_G | 1.024 | 0.15 |
| 129_A | 133_A | 1.024 | 0.15 |
| 98_C | 118_Y | 1.022 | 0.15 |
| 13_L | 194_L | 1.020 | 0.15 |
| 183_M | 212_F | 1.020 | 0.15 |
| 105_I | 201_I | 1.020 | 0.15 |
| 101_Q | 126_Q | 1.016 | 0.15 |
| 152_V | 196_L | 1.016 | 0.15 |
| 19_A | 174_L | 1.016 | 0.15 |
| 136_R | 140_G | 1.015 | 0.14 |
| 14_G | 189_A | 1.012 | 0.14 |
| 74_V | 107_L | 1.012 | 0.14 |
| 43_V | 119_A | 1.010 | 0.14 |
| 177_C | 184_M | 1.009 | 0.14 |
| 163_K | 172_M | 1.008 | 0.14 |
| 4_G | 83_P | 1.008 | 0.14 |
| 92_P | 210_G | 1.008 | 0.14 |
| 121_I | 125_L | 1.007 | 0.14 |
| 107_L | 135_K | 1.006 | 0.14 |
| 115_V | 182_L | 1.005 | 0.14 |
| 42_A | 216_T | 1.005 | 0.14 |
| 71_Q | 129_A | 1.003 | 0.14 |
| 67_A | 160_Y | 1.002 | 0.14 |
| 18_I | 179_T | 1.002 | 0.14 |
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 | |
| 1q02A | 1 | 0.1008 | 11.8 | 0.974 | Contact Map |
| 1wq6A | 2 | 0.121 | 6.5 | 0.977 | Contact Map |
| 2jtvA | 1 | 0.1089 | 5.2 | 0.978 | Contact Map |
| 1qc6A | 2 | 0.2097 | 3.9 | 0.979 | Contact Map |
| 3hrnA | 1 | 0.125 | 3.1 | 0.98 | Contact Map |
| 4fc5A | 6 | 0.4194 | 2.7 | 0.981 | Contact Map |
| 2i32E | 2 | 0.0565 | 2.6 | 0.981 | Contact Map |
| 3hq9A | 2 | 0.2379 | 2.2 | 0.982 | Contact Map |
| 2ovwA | 4 | 0.1895 | 1.9 | 0.982 | Contact Map |
| 2k9lA | 1 | 0.125 | 1.7 | 0.983 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)