| caATPBD |
| ID: | 1463588014 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 431 (423) | ||
| Sequences: | 9164 (5302.6) | ||
| Seq/Len: | 21.664 | ||
| Nf(neff/√len): | 257.8 |
HHblits Results: (2016_02)
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: 21.664).
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 |
| 27_S | 377_E | 4.139 | 1.00 |
| 46_K | 238_D | 3.642 | 1.00 |
| 97_I | 275_V | 3.536 | 1.00 |
| 192_K | 249_D | 3.440 | 1.00 |
| 370_E | 394_K | 3.394 | 1.00 |
| 344_L | 367_K | 2.840 | 1.00 |
| 317_C | 356_C | 2.831 | 1.00 |
| 348_R | 374_S | 2.784 | 1.00 |
| 340_D | 364_H | 2.754 | 1.00 |
| 39_T | 286_K | 2.693 | 1.00 |
| 176_S | 195_V | 2.688 | 1.00 |
| 195_V | 272_L | 2.673 | 1.00 |
| 343_P | 346_E | 2.666 | 1.00 |
| 176_S | 193_M | 2.572 | 1.00 |
| 190_G | 249_D | 2.548 | 1.00 |
| 97_I | 194_F | 2.484 | 1.00 |
| 93_E | 247_T | 2.389 | 1.00 |
| 294_L | 429_E | 2.377 | 1.00 |
| 246_A | 272_L | 2.373 | 1.00 |
| 247_T | 273_T | 2.367 | 1.00 |
| 284_P | 320_I | 2.367 | 1.00 |
| 290_G | 294_L | 2.350 | 1.00 |
| 219_T | 222_V | 2.345 | 1.00 |
| 287_E | 420_N | 2.322 | 1.00 |
| 13_I | 417_A | 2.312 | 1.00 |
| 117_K | 124_T | 2.303 | 1.00 |
| 10_K | 429_E | 2.285 | 1.00 |
| 400_A | 412_S | 2.274 | 1.00 |
| 314_I | 318_R | 2.269 | 1.00 |
| 301_R | 355_C | 2.260 | 1.00 |
| 10_K | 426_A | 2.240 | 1.00 |
| 373_Q | 394_K | 2.239 | 1.00 |
| 235_T | 279_G | 2.230 | 1.00 |
| 300_I | 428_V | 2.228 | 1.00 |
| 207_N | 271_D | 2.211 | 1.00 |
| 293_Q | 297_D | 2.211 | 1.00 |
| 163_E | 191_N | 2.207 | 1.00 |
| 295_C | 425_V | 2.149 | 1.00 |
| 161_K | 180_S | 2.123 | 1.00 |
| 12_A | 423_T | 2.099 | 1.00 |
| 224_E | 228_S | 2.091 | 1.00 |
| 231_K | 311_G | 2.041 | 1.00 |
| 174_S | 205_R | 1.997 | 1.00 |
| 195_V | 202_V | 1.934 | 1.00 |
| 229_V | 232_E | 1.933 | 1.00 |
| 180_S | 191_N | 1.931 | 1.00 |
| 334_Y | 342_L | 1.912 | 1.00 |
| 103_D | 162_K | 1.902 | 1.00 |
| 226_I | 274_F | 1.897 | 1.00 |
| 176_S | 269_E | 1.884 | 1.00 |
| 303_I | 372_L | 1.884 | 1.00 |
| 426_A | 429_E | 1.861 | 1.00 |
| 28_V | 303_I | 1.811 | 1.00 |
| 392_L | 408_A | 1.782 | 1.00 |
| 128_T | 132_K | 1.765 | 1.00 |
| 245_L | 278_V | 1.765 | 1.00 |
| 175_M | 196_K | 1.759 | 1.00 |
| 335_T | 338_E | 1.756 | 1.00 |
| 287_E | 290_G | 1.749 | 1.00 |
| 380_A | 399_I | 1.739 | 1.00 |
| 97_I | 245_L | 1.725 | 1.00 |
| 122_T | 280_M | 1.705 | 1.00 |
| 248_R | 271_D | 1.690 | 1.00 |
| 244_A | 274_F | 1.680 | 1.00 |
| 48_F | 229_V | 1.665 | 1.00 |
| 240_L | 279_G | 1.665 | 1.00 |
| 161_K | 179_C | 1.663 | 1.00 |
| 192_K | 247_T | 1.663 | 1.00 |
| 45_C | 319_R | 1.644 | 1.00 |
| 247_T | 275_V | 1.618 | 1.00 |
| 208_Y | 273_T | 1.610 | 1.00 |
| 306_T | 313_A | 1.609 | 1.00 |
| 209_V | 222_V | 1.607 | 1.00 |
| 373_Q | 396_E | 1.602 | 1.00 |
| 173_K | 198_A | 1.600 | 1.00 |
| 223_K | 227_L | 1.599 | 1.00 |
| 95_A | 129_L | 1.597 | 1.00 |
| 14_V | 414_M | 1.595 | 1.00 |
| 242_C | 277_V | 1.589 | 1.00 |
| 174_S | 269_E | 1.587 | 1.00 |
| 227_L | 231_K | 1.587 | 1.00 |
| 281_L | 319_R | 1.580 | 1.00 |
| 222_V | 225_K | 1.578 | 1.00 |
| 384_D | 387_N | 1.571 | 1.00 |
| 310_K | 335_T | 1.557 | 1.00 |
| 292_I | 322_I | 1.555 | 1.00 |
| 26_T | 397_I | 1.549 | 1.00 |
| 172_R | 269_E | 1.532 | 1.00 |
| 67_G | 70_Y | 1.530 | 1.00 |
| 202_V | 246_A | 1.526 | 1.00 |
| 370_E | 374_S | 1.525 | 1.00 |
| 178_Y | 250_T | 1.523 | 1.00 |
| 6_R | 430_E | 1.518 | 1.00 |
| 93_E | 96_T | 1.511 | 1.00 |
| 12_A | 427_A | 1.509 | 1.00 |
| 348_R | 371_Y | 1.497 | 1.00 |
| 352_R | 375_Y | 1.489 | 1.00 |
| 163_E | 180_S | 1.489 | 1.00 |
| 26_T | 380_A | 1.482 | 1.00 |
| 11_N | 417_A | 1.466 | 1.00 |
| 99_A | 130_V | 1.456 | 1.00 |
| 287_E | 422_S | 1.454 | 1.00 |
| 310_K | 314_I | 1.452 | 1.00 |
| 193_M | 250_T | 1.431 | 1.00 |
| 289_M | 293_Q | 1.416 | 1.00 |
| 11_N | 423_T | 1.400 | 0.99 |
| 172_R | 176_S | 1.399 | 0.99 |
| 44_V | 126_L | 1.394 | 0.99 |
| 216_V | 222_V | 1.375 | 0.99 |
| 199_P | 230_I | 1.357 | 0.99 |
| 46_K | 240_L | 1.343 | 0.99 |
| 314_I | 323_F | 1.340 | 0.99 |
| 201_G | 205_R | 1.339 | 0.99 |
| 371_Y | 374_S | 1.338 | 0.99 |
| 46_K | 235_T | 1.335 | 0.99 |
| 98_C | 278_V | 1.333 | 0.99 |
| 296_R | 324_G | 1.329 | 0.99 |
| 403_S | 408_A | 1.327 | 0.99 |
| 228_S | 232_E | 1.325 | 0.99 |
| 15_R | 412_S | 1.324 | 0.99 |
| 30_C | 372_L | 1.318 | 0.99 |
| 5_R | 9_K | 1.317 | 0.99 |
| 44_V | 129_L | 1.314 | 0.99 |
| 248_R | 270_T | 1.306 | 0.99 |
| 178_Y | 193_M | 1.305 | 0.99 |
| 202_V | 244_A | 1.304 | 0.99 |
| 129_L | 278_V | 1.302 | 0.99 |
| 235_T | 240_L | 1.295 | 0.99 |
| 304_M | 317_C | 1.292 | 0.99 |
| 11_N | 418_D | 1.289 | 0.99 |
| 369_V | 381_M | 1.276 | 0.99 |
| 295_C | 421_F | 1.262 | 0.99 |
| 220_G | 223_K | 1.257 | 0.99 |
| 32_D | 36_T | 1.248 | 0.99 |
| 281_L | 284_P | 1.247 | 0.99 |
| 304_M | 322_I | 1.243 | 0.98 |
| 72_P | 115_Y | 1.243 | 0.98 |
| 357_F | 372_L | 1.242 | 0.98 |
| 178_Y | 268_Y | 1.238 | 0.98 |
| 294_L | 297_D | 1.233 | 0.98 |
| 37_L | 320_I | 1.230 | 0.98 |
| 204_D | 223_K | 1.224 | 0.98 |
| 305_I | 368_I | 1.223 | 0.98 |
| 347_Q | 367_K | 1.219 | 0.98 |
| 237_R | 311_G | 1.218 | 0.98 |
| 100_L | 179_C | 1.213 | 0.98 |
| 93_E | 194_F | 1.209 | 0.98 |
| 295_C | 302_V | 1.200 | 0.98 |
| 200_E | 309_N | 1.195 | 0.98 |
| 30_C | 305_I | 1.190 | 0.98 |
| 334_Y | 354_A | 1.190 | 0.98 |
| 103_D | 165_T | 1.188 | 0.98 |
| 226_I | 277_V | 1.179 | 0.98 |
| 310_K | 338_E | 1.177 | 0.98 |
| 124_T | 128_T | 1.177 | 0.98 |
| 304_M | 356_C | 1.173 | 0.98 |
| 101_C | 175_M | 1.172 | 0.98 |
| 313_A | 358_A | 1.167 | 0.97 |
| 101_C | 295_C | 1.160 | 0.97 |
| 228_S | 231_K | 1.160 | 0.97 |
| 418_D | 423_T | 1.156 | 0.97 |
| 94_L | 276_G | 1.154 | 0.97 |
| 206_C | 246_A | 1.154 | 0.97 |
| 397_I | 414_M | 1.153 | 0.97 |
| 98_C | 245_L | 1.152 | 0.97 |
| 104_S | 127_T | 1.151 | 0.97 |
| 239_T | 315_A | 1.146 | 0.97 |
| 30_C | 369_V | 1.145 | 0.97 |
| 310_K | 333_A | 1.144 | 0.97 |
| 179_C | 194_F | 1.141 | 0.97 |
| 44_V | 280_M | 1.137 | 0.97 |
| 97_I | 101_C | 1.131 | 0.97 |
| 220_G | 224_E | 1.130 | 0.97 |
| 336_G | 339_F | 1.127 | 0.97 |
| 193_M | 272_L | 1.125 | 0.97 |
| 290_G | 293_Q | 1.121 | 0.97 |
| 317_C | 322_I | 1.119 | 0.96 |
| 92_V | 96_T | 1.115 | 0.96 |
| 208_Y | 217_P | 1.115 | 0.96 |
| 202_V | 206_C | 1.115 | 0.96 |
| 408_A | 411_A | 1.113 | 0.96 |
| 224_E | 227_L | 1.100 | 0.96 |
| 126_L | 278_V | 1.096 | 0.96 |
| 314_I | 333_A | 1.096 | 0.96 |
| 174_S | 195_V | 1.093 | 0.96 |
| 45_C | 281_L | 1.089 | 0.96 |
| 231_K | 237_R | 1.086 | 0.96 |
| 209_V | 216_V | 1.085 | 0.96 |
| 369_V | 379_T | 1.085 | 0.96 |
| 53_V | 235_T | 1.080 | 0.95 |
| 334_Y | 339_F | 1.078 | 0.95 |
| 236_G | 311_G | 1.076 | 0.95 |
| 162_K | 165_T | 1.075 | 0.95 |
| 339_F | 364_H | 1.074 | 0.95 |
| 98_C | 129_L | 1.073 | 0.95 |
| 178_Y | 191_N | 1.071 | 0.95 |
| 342_L | 350_A | 1.070 | 0.95 |
| 406_A | 409_K | 1.061 | 0.95 |
| 288_V | 421_F | 1.053 | 0.95 |
| 48_F | 226_I | 1.049 | 0.94 |
| 48_F | 235_T | 1.044 | 0.94 |
| 42_M | 123_E | 1.044 | 0.94 |
| 44_V | 278_V | 1.042 | 0.94 |
| 171_D | 363_S | 1.035 | 0.94 |
| 354_A | 357_F | 1.030 | 0.94 |
| 10_K | 430_E | 1.026 | 0.94 |
| 264_R | 267_E | 1.026 | 0.94 |
| 208_Y | 271_D | 1.026 | 0.94 |
| 332_R | 353_R | 1.023 | 0.93 |
| 239_T | 281_L | 1.022 | 0.93 |
| 230_I | 242_C | 1.020 | 0.93 |
| 284_P | 289_M | 1.018 | 0.93 |
| 173_K | 201_G | 1.016 | 0.93 |
| 102_N | 127_T | 1.016 | 0.93 |
| 180_S | 252_P | 1.015 | 0.93 |
| 169_S | 173_K | 1.013 | 0.93 |
| 35_G | 38_T | 1.006 | 0.93 |
| 227_L | 230_I | 1.001 | 0.92 |
| 101_C | 177_V | 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 | |
| 3ar4A | 1 | 1 | 100 | 0.198 | Contact Map |
| 3ixzA | 1 | 0.9142 | 100 | 0.234 | Contact Map |
| 2zxeA | 1 | 0.9142 | 100 | 0.234 | Contact Map |
| 1mhsA | 2 | 0.7773 | 100 | 0.292 | Contact Map |
| 3b8cA | 2 | 0.7819 | 100 | 0.303 | Contact Map |
| 4bbjA | 1 | 0.6404 | 100 | 0.519 | Contact Map |
| 3j09A | 2 | 0.6334 | 100 | 0.556 | Contact Map |
| 4umwA | 1 | 0.6288 | 100 | 0.559 | Contact Map |
| 3j08A | 2 | 0.6334 | 100 | 0.569 | Contact Map |
| 3a1cA | 2 | 0.6172 | 100 | 0.735 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)