| hiv2-gp120 |
| ID: | 1428540931 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 339 (332) | ||
| Sequences: | 5482 (224.2) | ||
| Seq/Len: | 16.512 | ||
| Nf(neff/√len): | 12.3 |
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: 16.512).
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 |
| 159_I | 302_I | 4.555 | 1.00 |
| 87_D | 238_R | 2.751 | 1.00 |
| 46_N | 152_H | 2.601 | 1.00 |
| 63_T | 78_T | 2.346 | 1.00 |
| 16_R | 317_S | 2.297 | 1.00 |
| 184_W | 188_K | 2.277 | 1.00 |
| 16_R | 315_T | 2.267 | 1.00 |
| 169_T | 190_E | 2.208 | 1.00 |
| 74_T | 78_T | 2.139 | 1.00 |
| 16_R | 153_G | 2.138 | 1.00 |
| 6_S | 48_T | 2.137 | 1.00 |
| 108_N | 145_N | 2.090 | 1.00 |
| 313_N | 317_S | 2.038 | 1.00 |
| 153_G | 315_T | 2.010 | 1.00 |
| 314_I | 317_S | 1.960 | 1.00 |
| 228_P | 231_A | 1.914 | 1.00 |
| 201_T | 204_K | 1.881 | 1.00 |
| 153_G | 317_S | 1.878 | 1.00 |
| 106_D | 117_S | 1.825 | 1.00 |
| 152_H | 155_D | 1.784 | 1.00 |
| 3_R | 6_S | 1.774 | 1.00 |
| 146_R | 201_T | 1.771 | 1.00 |
| 63_T | 74_T | 1.770 | 1.00 |
| 3_R | 337_T | 1.764 | 1.00 |
| 166_Y | 190_E | 1.702 | 1.00 |
| 16_R | 313_N | 1.693 | 1.00 |
| 78_T | 274_N | 1.685 | 1.00 |
| 179_R | 268_H | 1.679 | 1.00 |
| 240_E | 244_C | 1.674 | 1.00 |
| 34_I | 281_K | 1.655 | 1.00 |
| 153_G | 316_F | 1.654 | 1.00 |
| 251_N | 316_F | 1.640 | 1.00 |
| 284_Y | 294_C | 1.608 | 1.00 |
| 41_A | 114_P | 1.601 | 1.00 |
| 153_G | 313_N | 1.582 | 1.00 |
| 108_N | 112_F | 1.562 | 1.00 |
| 237_C | 244_C | 1.557 | 1.00 |
| 284_Y | 287_P | 1.554 | 1.00 |
| 270_K | 273_I | 1.547 | 1.00 |
| 16_R | 316_F | 1.529 | 1.00 |
| 313_N | 316_F | 1.518 | 1.00 |
| 287_P | 294_C | 1.508 | 1.00 |
| 16_R | 206_P | 1.501 | 1.00 |
| 274_N | 281_K | 1.491 | 1.00 |
| 107_T | 145_N | 1.475 | 1.00 |
| 169_T | 173_K | 1.456 | 1.00 |
| 267_C | 271_Q | 1.456 | 1.00 |
| 70_K | 278_K | 1.440 | 1.00 |
| 107_T | 144_E | 1.385 | 0.99 |
| 278_K | 281_K | 1.383 | 0.99 |
| 263_N | 315_T | 1.381 | 0.99 |
| 76_V | 231_A | 1.380 | 0.99 |
| 78_T | 281_K | 1.379 | 0.99 |
| 166_Y | 193_E | 1.378 | 0.99 |
| 305_I | 308_G | 1.377 | 0.99 |
| 251_N | 315_T | 1.353 | 0.99 |
| 236_N | 243_Y | 1.346 | 0.99 |
| 228_P | 232_Y | 1.340 | 0.99 |
| 333_L | 338_P | 1.335 | 0.99 |
| 237_C | 240_E | 1.314 | 0.99 |
| 323_L | 326_L | 1.312 | 0.99 |
| 207_R | 214_T | 1.310 | 0.99 |
| 226_S | 229_E | 1.309 | 0.99 |
| 327_E | 334_I | 1.306 | 0.99 |
| 86_W | 91_F | 1.304 | 0.99 |
| 232_Y | 247_T | 1.280 | 0.99 |
| 166_Y | 197_E | 1.259 | 0.99 |
| 311_Q | 315_T | 1.256 | 0.99 |
| 312_T | 315_T | 1.255 | 0.99 |
| 227_D | 235_T | 1.248 | 0.99 |
| 271_Q | 279_V | 1.245 | 0.98 |
| 153_G | 263_N | 1.241 | 0.98 |
| 289_E | 293_T | 1.237 | 0.98 |
| 95_A | 101_L | 1.233 | 0.98 |
| 275_T | 282_N | 1.232 | 0.98 |
| 251_N | 313_N | 1.229 | 0.98 |
| 89_M | 92_R | 1.226 | 0.98 |
| 4_N | 190_E | 1.220 | 0.98 |
| 187_F | 221_A | 1.214 | 0.98 |
| 251_N | 317_S | 1.211 | 0.98 |
| 187_F | 231_A | 1.209 | 0.98 |
| 99_F | 163_N | 1.207 | 0.98 |
| 237_C | 243_Y | 1.201 | 0.98 |
| 110_S | 114_P | 1.199 | 0.98 |
| 286_P | 294_C | 1.198 | 0.98 |
| 15_N | 153_G | 1.195 | 0.98 |
| 251_N | 263_N | 1.193 | 0.98 |
| 331_Y | 334_I | 1.193 | 0.98 |
| 324_Y | 328_L | 1.191 | 0.98 |
| 148_Y | 167_N | 1.186 | 0.98 |
| 108_N | 117_S | 1.185 | 0.98 |
| 263_N | 317_S | 1.185 | 0.98 |
| 15_N | 84_H | 1.176 | 0.98 |
| 202_L | 313_N | 1.171 | 0.98 |
| 311_Q | 317_S | 1.170 | 0.97 |
| 51_E | 321_A | 1.168 | 0.97 |
| 147_T | 163_N | 1.167 | 0.97 |
| 201_T | 278_K | 1.165 | 0.97 |
| 106_D | 112_F | 1.165 | 0.97 |
| 311_Q | 314_I | 1.163 | 0.97 |
| 87_D | 129_E | 1.160 | 0.97 |
| 99_F | 335_E | 1.155 | 0.97 |
| 195_M | 199_K | 1.155 | 0.97 |
| 285_L | 288_R | 1.155 | 0.97 |
| 63_T | 281_K | 1.152 | 0.97 |
| 67_P | 71_L | 1.150 | 0.97 |
| 236_N | 240_E | 1.149 | 0.97 |
| 68_C | 71_L | 1.147 | 0.97 |
| 153_G | 206_P | 1.144 | 0.97 |
| 189_G | 192_K | 1.142 | 0.97 |
| 199_K | 252_W | 1.140 | 0.97 |
| 325_R | 328_L | 1.136 | 0.97 |
| 16_R | 263_N | 1.134 | 0.97 |
| 73_N | 81_C | 1.130 | 0.97 |
| 16_R | 251_N | 1.125 | 0.97 |
| 147_T | 193_E | 1.114 | 0.96 |
| 3_R | 74_T | 1.109 | 0.96 |
| 87_D | 99_F | 1.109 | 0.96 |
| 118_K | 122_A | 1.106 | 0.96 |
| 108_N | 146_R | 1.103 | 0.96 |
| 99_F | 252_W | 1.102 | 0.96 |
| 169_T | 179_R | 1.099 | 0.96 |
| 87_D | 205_H | 1.096 | 0.96 |
| 228_P | 281_K | 1.095 | 0.96 |
| 298_V | 303_A | 1.092 | 0.96 |
| 165_F | 197_E | 1.091 | 0.96 |
| 16_R | 311_Q | 1.089 | 0.96 |
| 6_S | 281_K | 1.081 | 0.95 |
| 237_C | 242_L | 1.081 | 0.95 |
| 206_P | 317_S | 1.071 | 0.95 |
| 184_W | 264_Y | 1.070 | 0.95 |
| 2_W | 5_A | 1.070 | 0.95 |
| 226_S | 239_G | 1.068 | 0.95 |
| 3_R | 78_T | 1.067 | 0.95 |
| 296_S | 300_S | 1.067 | 0.95 |
| 320_V | 325_R | 1.060 | 0.95 |
| 234_W | 238_R | 1.059 | 0.95 |
| 207_R | 215_E | 1.056 | 0.95 |
| 228_P | 274_N | 1.056 | 0.95 |
| 60_L | 71_L | 1.051 | 0.94 |
| 283_V | 292_L | 1.048 | 0.94 |
| 161_S | 302_I | 1.047 | 0.94 |
| 53_A | 58_W | 1.046 | 0.94 |
| 271_Q | 280_G | 1.046 | 0.94 |
| 153_G | 311_Q | 1.043 | 0.94 |
| 331_Y | 336_V | 1.042 | 0.94 |
| 48_T | 51_E | 1.039 | 0.94 |
| 145_N | 165_F | 1.038 | 0.94 |
| 193_E | 197_E | 1.037 | 0.94 |
| 88_T | 91_F | 1.035 | 0.94 |
| 87_D | 199_K | 1.032 | 0.94 |
| 16_R | 264_Y | 1.030 | 0.94 |
| 334_I | 339_I | 1.028 | 0.94 |
| 127_M | 130_T | 1.025 | 0.93 |
| 240_E | 243_Y | 1.024 | 0.93 |
| 206_P | 313_N | 1.021 | 0.93 |
| 53_A | 56_D | 1.021 | 0.93 |
| 76_V | 252_W | 1.020 | 0.93 |
| 6_S | 34_I | 1.019 | 0.93 |
| 153_G | 314_I | 1.017 | 0.93 |
| 323_L | 330_D | 1.013 | 0.93 |
| 229_E | 235_T | 1.013 | 0.93 |
| 206_P | 315_T | 1.013 | 0.93 |
| 263_N | 316_F | 1.013 | 0.93 |
| 75_S | 283_V | 1.012 | 0.93 |
| 148_Y | 187_F | 1.008 | 0.93 |
| 198_V | 248_W | 1.006 | 0.93 |
| 272_I | 279_V | 1.005 | 0.93 |
| 229_E | 243_Y | 1.005 | 0.93 |
| 153_G | 251_N | 1.003 | 0.93 |
| 237_C | 245_N | 1.001 | 0.92 |
| 56_D | 64_S | 1.000 | 0.92 |
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 | |
| 4r4hA | 1 | 0.9381 | 100 | 0.01 | Contact Map |
| 4jzzA | 1 | 0.9558 | 100 | 0.018 | Contact Map |
| 4tvpG | 1 | 0.9646 | 100 | 0.02 | Contact Map |
| 3lqaG | 1 | 0.8171 | 100 | 0.146 | Contact Map |
| 2bf1A | 1 | 0.8319 | 100 | 0.152 | Contact Map |
| 4i3sG | 1 | 0.4926 | 100 | 0.585 | Contact Map |
| 3tygA | 1 | 0.4248 | 100 | 0.665 | Contact Map |
| 4jpkA | 1 | 0.4602 | 100 | 0.712 | Contact Map |
| 3u2sG | 2 | 0.2271 | 99.4 | 0.919 | Contact Map |
| 4r61A | 1 | 0.177 | 79.6 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)