| LAT4 co-evolutionary analysis |
| ID: | 1482144501 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 569 (502) | ||
| Sequences: | 1340 (797.1) | ||
| Seq/Len: | 2.669 | ||
| Nf(neff/√len): | 35.6 |
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: 2.669).
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 |
| 519_V | 523_L | 4.120 | 1.00 |
| 448_P | 452_L | 3.933 | 1.00 |
| 429_A | 533_L | 3.886 | 1.00 |
| 345_M | 454_F | 2.991 | 1.00 |
| 351_F | 508_G | 2.469 | 1.00 |
| 523_L | 527_L | 2.447 | 1.00 |
| 131_L | 135_Y | 2.300 | 1.00 |
| 16_A | 172_F | 2.243 | 1.00 |
| 203_A | 356_D | 2.213 | 1.00 |
| 205_V | 213_V | 2.204 | 1.00 |
| 131_L | 215_A | 2.189 | 1.00 |
| 449_L | 452_L | 2.157 | 1.00 |
| 348_I | 441_T | 2.083 | 1.00 |
| 28_A | 197_I | 2.059 | 1.00 |
| 253_F | 257_I | 2.053 | 1.00 |
| 370_L | 451_I | 1.991 | 0.99 |
| 201_Y | 213_V | 1.966 | 0.99 |
| 145_V | 149_I | 1.939 | 0.99 |
| 538_Y | 541_Q | 1.932 | 0.99 |
| 137_A | 146_L | 1.829 | 0.99 |
| 352_L | 514_P | 1.818 | 0.99 |
| 523_L | 526_L | 1.810 | 0.99 |
| 132_L | 150_A | 1.800 | 0.99 |
| 350_K | 367_F | 1.791 | 0.99 |
| 452_L | 455_I | 1.767 | 0.98 |
| 340_F | 503_F | 1.742 | 0.98 |
| 541_Q | 544_R | 1.724 | 0.98 |
| 540_R | 544_R | 1.679 | 0.98 |
| 111_D | 482_G | 1.674 | 0.98 |
| 349_L | 450_Q | 1.608 | 0.97 |
| 223_L | 226_F | 1.601 | 0.97 |
| 516_W | 523_L | 1.586 | 0.96 |
| 33_W | 91_A | 1.573 | 0.96 |
| 215_A | 219_G | 1.567 | 0.96 |
| 87_M | 90_L | 1.561 | 0.96 |
| 324_L | 472_Y | 1.560 | 0.96 |
| 9_H | 13_W | 1.524 | 0.95 |
| 407_G | 412_K | 1.521 | 0.95 |
| 46_Y | 144_S | 1.503 | 0.95 |
| 201_Y | 205_V | 1.486 | 0.94 |
| 28_A | 214_W | 1.480 | 0.94 |
| 526_L | 529_F | 1.468 | 0.94 |
| 8_A | 11_R | 1.461 | 0.94 |
| 94_V | 148_F | 1.443 | 0.93 |
| 124_A | 222_F | 1.442 | 0.93 |
| 107_G | 498_L | 1.441 | 0.93 |
| 533_L | 537_C | 1.417 | 0.92 |
| 189_S | 375_L | 1.406 | 0.92 |
| 407_G | 410_K | 1.400 | 0.92 |
| 211_L | 214_W | 1.394 | 0.91 |
| 130_C | 154_N | 1.392 | 0.91 |
| 449_L | 453_S | 1.390 | 0.91 |
| 199_L | 368_G | 1.390 | 0.91 |
| 135_Y | 212_V | 1.386 | 0.91 |
| 133_I | 211_L | 1.385 | 0.91 |
| 519_V | 527_L | 1.369 | 0.90 |
| 138_S | 145_V | 1.368 | 0.90 |
| 9_H | 175_L | 1.362 | 0.90 |
| 446_N | 449_L | 1.359 | 0.90 |
| 313_P | 480_Q | 1.351 | 0.90 |
| 534_Y | 544_R | 1.345 | 0.89 |
| 319_V | 325_L | 1.342 | 0.89 |
| 325_L | 329_V | 1.337 | 0.89 |
| 127_A | 219_G | 1.308 | 0.87 |
| 36_L | 40_L | 1.306 | 0.87 |
| 39_M | 357_Q | 1.296 | 0.87 |
| 46_Y | 88_L | 1.294 | 0.87 |
| 393_E | 415_D | 1.288 | 0.86 |
| 326_L | 535_L | 1.281 | 0.86 |
| 324_L | 476_Y | 1.274 | 0.85 |
| 499_Q | 502_L | 1.271 | 0.85 |
| 128_V | 132_L | 1.261 | 0.85 |
| 379_P | 383_Y | 1.259 | 0.85 |
| 201_Y | 340_F | 1.257 | 0.84 |
| 345_M | 453_S | 1.245 | 0.84 |
| 407_G | 415_D | 1.242 | 0.83 |
| 32_G | 126_F | 1.241 | 0.83 |
| 504_L | 508_G | 1.236 | 0.83 |
| 382_G | 386_D | 1.235 | 0.83 |
| 96_S | 496_A | 1.235 | 0.83 |
| 396_S | 405_N | 1.229 | 0.83 |
| 162_T | 188_A | 1.228 | 0.82 |
| 406_Q | 412_K | 1.228 | 0.82 |
| 220_L | 224_N | 1.228 | 0.82 |
| 351_F | 514_P | 1.227 | 0.82 |
| 40_L | 147_I | 1.220 | 0.82 |
| 101_A | 156_F | 1.219 | 0.82 |
| 395_A | 406_Q | 1.215 | 0.82 |
| 14_W | 228_N | 1.212 | 0.81 |
| 205_V | 220_L | 1.201 | 0.81 |
| 16_A | 179_F | 1.195 | 0.80 |
| 153_L | 496_A | 1.192 | 0.80 |
| 407_G | 411_K | 1.191 | 0.80 |
| 447_L | 451_I | 1.187 | 0.79 |
| 269_V | 272_R | 1.187 | 0.79 |
| 27_S | 99_L | 1.184 | 0.79 |
| 442_C | 518_N | 1.182 | 0.79 |
| 131_L | 441_T | 1.180 | 0.79 |
| 19_A | 167_T | 1.180 | 0.79 |
| 539_R | 543_E | 1.180 | 0.79 |
| 14_W | 21_L | 1.176 | 0.79 |
| 256_K | 527_L | 1.175 | 0.78 |
| 429_A | 536_I | 1.171 | 0.78 |
| 133_I | 147_I | 1.170 | 0.78 |
| 101_A | 125_C | 1.169 | 0.78 |
| 47_S | 535_L | 1.169 | 0.78 |
| 132_L | 514_P | 1.166 | 0.78 |
| 336_L | 496_A | 1.165 | 0.78 |
| 181_A | 382_G | 1.164 | 0.78 |
| 197_I | 213_V | 1.163 | 0.77 |
| 18_T | 228_N | 1.163 | 0.77 |
| 162_T | 485_T | 1.163 | 0.77 |
| 507_M | 518_N | 1.152 | 0.77 |
| 347_N | 508_G | 1.152 | 0.77 |
| 6_A | 396_S | 1.151 | 0.76 |
| 91_A | 99_L | 1.150 | 0.76 |
| 301_L | 306_Q | 1.145 | 0.76 |
| 138_S | 146_L | 1.144 | 0.76 |
| 312_A | 376_L | 1.142 | 0.76 |
| 13_W | 172_F | 1.142 | 0.76 |
| 163_F | 412_K | 1.138 | 0.75 |
| 230_P | 412_K | 1.136 | 0.75 |
| 391_E | 433_L | 1.132 | 0.75 |
| 122_G | 182_L | 1.132 | 0.75 |
| 317_H | 324_L | 1.130 | 0.75 |
| 406_Q | 411_K | 1.129 | 0.75 |
| 396_S | 410_K | 1.127 | 0.74 |
| 11_R | 14_W | 1.127 | 0.74 |
| 15_M | 18_T | 1.123 | 0.74 |
| 380_V | 459_I | 1.123 | 0.74 |
| 272_R | 275_V | 1.123 | 0.74 |
| 537_C | 541_Q | 1.121 | 0.74 |
| 113_Y | 519_V | 1.120 | 0.74 |
| 347_N | 351_F | 1.119 | 0.74 |
| 505_A | 509_P | 1.118 | 0.73 |
| 350_K | 357_Q | 1.112 | 0.73 |
| 295_C | 298_T | 1.112 | 0.73 |
| 383_Y | 394_D | 1.111 | 0.73 |
| 190_S | 522_L | 1.111 | 0.73 |
| 304_K | 308_D | 1.110 | 0.73 |
| 121_L | 529_F | 1.107 | 0.72 |
| 356_D | 535_L | 1.106 | 0.72 |
| 314_S | 317_H | 1.104 | 0.72 |
| 445_P | 515_L | 1.100 | 0.72 |
| 405_N | 408_E | 1.100 | 0.72 |
| 271_R | 275_V | 1.100 | 0.72 |
| 328_L | 491_I | 1.100 | 0.72 |
| 122_G | 160_C | 1.098 | 0.72 |
| 93_T | 358_K | 1.096 | 0.71 |
| 436_V | 444_I | 1.096 | 0.71 |
| 27_S | 494_L | 1.093 | 0.71 |
| 133_I | 197_I | 1.092 | 0.71 |
| 347_N | 514_P | 1.091 | 0.71 |
| 394_D | 406_Q | 1.091 | 0.71 |
| 268_T | 274_S | 1.090 | 0.71 |
| 516_W | 520_G | 1.089 | 0.71 |
| 271_R | 274_S | 1.087 | 0.70 |
| 543_E | 546_L | 1.085 | 0.70 |
| 200_I | 366_I | 1.084 | 0.70 |
| 44_G | 147_I | 1.083 | 0.70 |
| 35_S | 202_D | 1.083 | 0.70 |
| 443_L | 519_V | 1.082 | 0.70 |
| 184_I | 386_D | 1.078 | 0.70 |
| 439_G | 443_L | 1.076 | 0.69 |
| 270_G | 300_D | 1.074 | 0.69 |
| 273_L | 278_S | 1.074 | 0.69 |
| 341_Y | 374_C | 1.074 | 0.69 |
| 408_E | 411_K | 1.073 | 0.69 |
| 24_L | 190_S | 1.070 | 0.69 |
| 345_M | 441_T | 1.070 | 0.69 |
| 253_F | 263_Y | 1.068 | 0.69 |
| 174_D | 394_D | 1.067 | 0.68 |
| 393_E | 406_Q | 1.067 | 0.68 |
| 392_C | 415_D | 1.066 | 0.68 |
| 370_L | 373_L | 1.066 | 0.68 |
| 17_C | 394_D | 1.065 | 0.68 |
| 321_S | 476_Y | 1.063 | 0.68 |
| 95_G | 154_N | 1.060 | 0.68 |
| 334_T | 496_A | 1.060 | 0.68 |
| 21_L | 217_C | 1.060 | 0.68 |
| 185_G | 382_G | 1.057 | 0.67 |
| 297_S | 300_D | 1.056 | 0.67 |
| 324_L | 475_V | 1.055 | 0.67 |
| 25_L | 214_W | 1.055 | 0.67 |
| 52_E | 83_A | 1.054 | 0.67 |
| 304_K | 544_R | 1.053 | 0.67 |
| 503_F | 517_V | 1.052 | 0.67 |
| 205_V | 216_G | 1.052 | 0.67 |
| 119_R | 164_T | 1.050 | 0.67 |
| 216_G | 220_L | 1.048 | 0.66 |
| 378_A | 462_G | 1.048 | 0.66 |
| 96_S | 466_S | 1.047 | 0.66 |
| 168_L | 457_H | 1.043 | 0.66 |
| 217_C | 221_V | 1.042 | 0.66 |
| 528_G | 531_L | 1.040 | 0.66 |
| 40_L | 46_Y | 1.039 | 0.65 |
| 336_L | 495_F | 1.038 | 0.65 |
| 406_Q | 415_D | 1.034 | 0.65 |
| 109_V | 537_C | 1.033 | 0.65 |
| 269_V | 512_G | 1.033 | 0.65 |
| 214_W | 379_P | 1.031 | 0.65 |
| 144_S | 182_L | 1.028 | 0.64 |
| 28_A | 31_L | 1.024 | 0.64 |
| 406_Q | 409_K | 1.024 | 0.64 |
| 391_E | 438_F | 1.022 | 0.64 |
| 26_F | 378_A | 1.020 | 0.63 |
| 440_V | 453_S | 1.019 | 0.63 |
| 146_L | 150_A | 1.017 | 0.63 |
| 316_M | 320_F | 1.016 | 0.63 |
| 472_Y | 484_L | 1.010 | 0.62 |
| 388_R | 392_C | 1.010 | 0.62 |
| 261_Q | 264_K | 1.010 | 0.62 |
| 116_R | 229_W | 1.009 | 0.62 |
| 211_L | 378_A | 1.008 | 0.62 |
| 28_A | 32_G | 1.008 | 0.62 |
| 129_S | 348_I | 1.007 | 0.62 |
| 411_K | 415_D | 1.006 | 0.62 |
| 31_L | 195_P | 1.006 | 0.62 |
| 122_G | 229_W | 1.006 | 0.62 |
| 415_D | 442_C | 1.005 | 0.62 |
| 173_G | 193_T | 1.005 | 0.62 |
| 33_W | 100_S | 1.004 | 0.62 |
| 153_L | 228_N | 1.003 | 0.61 |
| 374_C | 463_F | 1.002 | 0.61 |
| 393_E | 407_G | 1.001 | 0.61 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1pw4A | 1 | 0.7206 | 100 | 0.675 | Contact Map |
| 4j05A | 2 | 0.6749 | 100 | 0.693 | Contact Map |
| 4pypA | 1 | 0.7469 | 100 | 0.693 | Contact Map |
| 3wdoA | 1 | 0.7293 | 100 | 0.703 | Contact Map |
| 2cfqA | 1 | 0.7206 | 100 | 0.711 | Contact Map |
| 3o7qA | 1 | 0.6696 | 100 | 0.716 | Contact Map |
| 2gfpA | 2 | 0.6503 | 100 | 0.719 | Contact Map |
| 4ldsA | 2 | 0.7241 | 100 | 0.72 | Contact Map |
| 4zw9A | 1 | 0 | 100 | 0.722 | Contact Map |
| 4xnjA | 1 | 0 | 100 | 0.73 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)