| Brucella suis 1330 |
| ID: | 1401101488 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 287 (273) | ||
| Sequences: | 978 (737.6) | ||
| Seq/Len: | 3.582 | ||
| Nf(neff/√len): | 44.6 |
HHblits Results: (2013_03)
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: 3.582).
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 |
| 99_N | 102_E | 3.509 | 1.00 |
| 111_N | 124_Y | 2.645 | 1.00 |
| 67_A | 93_T | 2.436 | 1.00 |
| 87_L | 114_Y | 2.274 | 1.00 |
| 221_A | 256_S | 2.249 | 1.00 |
| 149_I | 172_I | 2.079 | 1.00 |
| 188_R | 218_E | 2.072 | 1.00 |
| 128_G | 152_M | 2.007 | 1.00 |
| 187_G | 203_F | 2.001 | 1.00 |
| 191_L | 226_A | 1.975 | 1.00 |
| 104_I | 130_S | 1.936 | 1.00 |
| 108_K | 127_I | 1.896 | 1.00 |
| 204_R | 208_E | 1.872 | 1.00 |
| 62_R | 65_E | 1.854 | 1.00 |
| 91_A | 126_I | 1.809 | 0.99 |
| 228_Y | 236_A | 1.802 | 0.99 |
| 107_A | 130_S | 1.782 | 0.99 |
| 110_Y | 117_S | 1.758 | 0.99 |
| 203_F | 222_R | 1.746 | 0.99 |
| 54_G | 70_F | 1.728 | 0.99 |
| 111_N | 120_S | 1.727 | 0.99 |
| 91_A | 107_A | 1.720 | 0.99 |
| 155_V | 162_S | 1.720 | 0.99 |
| 205_G | 208_E | 1.663 | 0.99 |
| 187_G | 222_R | 1.614 | 0.98 |
| 153_Q | 157_D | 1.607 | 0.98 |
| 94_N | 102_E | 1.591 | 0.98 |
| 21_V | 24_P | 1.586 | 0.98 |
| 224_V | 240_A | 1.585 | 0.98 |
| 205_G | 209_E | 1.580 | 0.98 |
| 88_V | 123_A | 1.516 | 0.97 |
| 18_T | 21_V | 1.488 | 0.97 |
| 92_F | 126_I | 1.485 | 0.97 |
| 70_F | 90_A | 1.465 | 0.96 |
| 94_N | 99_N | 1.464 | 0.96 |
| 183_E | 202_R | 1.445 | 0.96 |
| 120_S | 159_F | 1.429 | 0.96 |
| 243_L | 250_S | 1.427 | 0.96 |
| 125_Y | 167_D | 1.408 | 0.95 |
| 154_E | 158_R | 1.406 | 0.95 |
| 70_F | 89_M | 1.377 | 0.94 |
| 188_R | 192_E | 1.366 | 0.94 |
| 55_L | 70_F | 1.364 | 0.94 |
| 94_N | 106_M | 1.362 | 0.94 |
| 239_A | 243_L | 1.352 | 0.94 |
| 127_I | 151_A | 1.350 | 0.94 |
| 232_L | 235_E | 1.307 | 0.92 |
| 73_I | 77_H | 1.304 | 0.92 |
| 191_L | 225_E | 1.294 | 0.92 |
| 258_K | 262_S | 1.288 | 0.91 |
| 272_N | 276_A | 1.279 | 0.91 |
| 26_A | 237_Q | 1.278 | 0.91 |
| 247_F | 250_S | 1.270 | 0.91 |
| 90_A | 106_M | 1.261 | 0.90 |
| 100_Y | 130_S | 1.260 | 0.90 |
| 273_S | 276_A | 1.235 | 0.89 |
| 95_Y | 179_L | 1.233 | 0.89 |
| 108_K | 112_T | 1.228 | 0.88 |
| 270_N | 276_A | 1.227 | 0.88 |
| 54_G | 69_K | 1.219 | 0.88 |
| 29_A | 44_I | 1.215 | 0.88 |
| 104_I | 108_K | 1.213 | 0.88 |
| 244_G | 253_Y | 1.207 | 0.87 |
| 273_S | 277_K | 1.205 | 0.87 |
| 177_D | 215_Q | 1.203 | 0.87 |
| 107_A | 127_I | 1.201 | 0.87 |
| 268_R | 272_N | 1.197 | 0.87 |
| 207_V | 219_A | 1.191 | 0.86 |
| 266_Q | 273_S | 1.191 | 0.86 |
| 65_E | 69_K | 1.191 | 0.86 |
| 92_F | 107_A | 1.187 | 0.86 |
| 121_A | 162_S | 1.177 | 0.85 |
| 74_D | 109_R | 1.175 | 0.85 |
| 87_L | 109_R | 1.163 | 0.84 |
| 275_L | 278_A | 1.158 | 0.84 |
| 120_S | 124_Y | 1.157 | 0.84 |
| 268_R | 276_A | 1.157 | 0.84 |
| 270_N | 275_L | 1.154 | 0.84 |
| 144_A | 147_R | 1.154 | 0.84 |
| 204_R | 223_L | 1.153 | 0.84 |
| 207_V | 211_S | 1.152 | 0.84 |
| 152_M | 155_V | 1.146 | 0.83 |
| 167_D | 171_K | 1.143 | 0.83 |
| 125_Y | 129_L | 1.142 | 0.83 |
| 217_E | 250_S | 1.136 | 0.83 |
| 189_Y | 202_R | 1.132 | 0.82 |
| 48_D | 52_N | 1.127 | 0.82 |
| 191_L | 196_Y | 1.117 | 0.81 |
| 266_Q | 269_E | 1.114 | 0.81 |
| 199_A | 206_V | 1.112 | 0.81 |
| 72_A | 75_R | 1.111 | 0.81 |
| 92_F | 246_N | 1.110 | 0.81 |
| 268_R | 271_G | 1.107 | 0.80 |
| 200_I | 226_A | 1.102 | 0.80 |
| 71_A | 94_N | 1.102 | 0.80 |
| 224_V | 243_L | 1.100 | 0.80 |
| 220_L | 243_L | 1.096 | 0.79 |
| 54_G | 73_I | 1.091 | 0.79 |
| 265_L | 275_L | 1.090 | 0.79 |
| 266_Q | 272_N | 1.085 | 0.78 |
| 265_L | 273_S | 1.083 | 0.78 |
| 75_R | 235_E | 1.080 | 0.78 |
| 57_N | 62_R | 1.074 | 0.77 |
| 122_Y | 202_R | 1.068 | 0.77 |
| 207_V | 216_V | 1.065 | 0.77 |
| 277_K | 281_L | 1.062 | 0.76 |
| 47_A | 78_P | 1.060 | 0.76 |
| 175_A | 211_S | 1.058 | 0.76 |
| 278_A | 281_L | 1.047 | 0.75 |
| 124_Y | 155_V | 1.044 | 0.75 |
| 267_P | 272_N | 1.043 | 0.74 |
| 51_Y | 89_M | 1.041 | 0.74 |
| 63_L | 93_T | 1.040 | 0.74 |
| 269_E | 276_A | 1.038 | 0.74 |
| 25_L | 28_C | 1.036 | 0.74 |
| 168_A | 219_A | 1.035 | 0.74 |
| 141_D | 190_Y | 1.035 | 0.74 |
| 110_Y | 202_R | 1.031 | 0.73 |
| 187_G | 243_L | 1.029 | 0.73 |
| 79_Y | 116_T | 1.029 | 0.73 |
| 84_R | 139_T | 1.028 | 0.73 |
| 174_V | 178_Q | 1.028 | 0.73 |
| 46_P | 49_K | 1.021 | 0.72 |
| 67_A | 97_K | 1.017 | 0.72 |
| 275_L | 279_G | 1.014 | 0.71 |
| 269_E | 272_N | 1.013 | 0.71 |
| 188_R | 225_E | 1.012 | 0.71 |
| 121_A | 155_V | 1.011 | 0.71 |
| 267_P | 270_N | 1.011 | 0.71 |
| 132_F | 159_F | 1.010 | 0.71 |
| 158_R | 161_N | 1.006 | 0.71 |
| 155_V | 167_D | 1.005 | 0.70 |
| 179_L | 190_Y | 1.003 | 0.70 |
| 86_A | 114_Y | 1.003 | 0.70 |
| 61_G | 98_G | 1.002 | 0.70 |
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 | |
| 2yhcA | 1 | 0.7178 | 100 | 0.518 | Contact Map |
| 3qkyA | 1 | 0.8362 | 99.9 | 0.573 | Contact Map |
| 3iegA | 2 | 0.7596 | 99.9 | 0.611 | Contact Map |
| 2y4tA | 3 | 0.7735 | 99.9 | 0.624 | Contact Map |
| 3vtxA | 2 | 0.6411 | 99.9 | 0.628 | Contact Map |
| 3as5A | 2 | 0.6376 | 99.9 | 0.629 | Contact Map |
| 3uq3A | 1 | 0.784 | 99.9 | 0.629 | Contact Map |
| 2pl2A | 2 | 0.6585 | 99.9 | 0.631 | Contact Map |
| 2q7fA | 2 | 0.669 | 99.9 | 0.632 | Contact Map |
| 4gywA | 2 | 0.7317 | 99.9 | 0.637 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)