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Table 3 Domains and motifs of PyVs used in this study

From: Codon usage patterns of LT-Ag genes in polyomaviruses from different host species

No. Abbr. Accession no. DnaJ domain LXCXE motif Helicase domain
Start End nt length Start End a.a. sequence Start End nt length
1 BatPyV4a NC_038556.1 12 67 168 107 111 LRCDE 405 564 480
2 ApanPyV1 NC_019853.1 12 77 198 122 126 LFCNE 441 601 483
3 BatPyV5b-1 NC_026767.1 12 74 189 376 536 483
4 BatPyV5a NC_026768.1 12 67 168 382 546 495
5 OraPyV-Bor NC_013439.1 12 77 198 122 126 LFCDE 422 602 543
6 CardiodermaPyV NC_020067.1 12 77 198 212 216 LYCDE 556 716 483
7 BatPyV4b NC_028120.1 152 156 LLCEE 458 651 582
8 ChPyV NC_014743.1 12 96 255 379 580 606
9 VmPyV1 NC_019844.1 12 80 207 107 111 LHCNE 479 640 486
10 VmPyV3 NC_025898.1 12 75 192 131 135 LFCSE 462 622 483
11 EidolonPyV NC_020068.1 236 240 LRCDE 588 752 495
12 GgorgPyV1 NC_025380.1 200 204 LFCDE 554 714 483
13 HPyV9 NC_015150.1 12 86 225 123 127 LFCSE 446 606 483
14 HPyV12 NC_020890.1 473 635 489
15 MfasPyV1 NC_019851.1 12 86 225 125 129 LFCTE 465 665 603
16 MCPyV NC_010277.2 212 216 LFCDE 567 727 483
17 HaPyV NC_001663.2 130 134 LTCQE 522 682 483
18 BatPyV3b NC_028123.1 107 111 LYCDE 467 630 492
19 MPyV NC_001515.2 142 146 LFCYE 549 709 483
20 NJPyV NC_024118.1 12 80 207 107 111 LHCDE 476 636 483
21 OtomopsPyV NC_020066.1 12 92 243 107 111 LYCDE 483 643 483
22 OtomopsPyV1 NC_020071.1 185 189 LRCDE 520 680 483
23 PtrovPyV2a NC_025370.1 200 204 LFCDE 556 716 483
24 PtrovPyV3 NC_019855.1 12 75 192 486 646 483
25 PtrovPyV4 NC_019856.1 12 75 192 489 646 474
26 PtrovPyV5 NC_019857.1 12 86 225 123 127 LFCSE 439 599 483
27 PtrosPyV2 NC_019858.1 12 85 222 108 112 LYCSE 432 632 603
28 PtrovPyV1a NC_025368.1 203 207 LYCDE 558 718 483
29 PbadPyV2 NC_039051.1 12 92 243 107 111 LHCNE 476 637 486
30 PrufPyV1 NC_019850.1 12 93 246 107 111 LHCNE 476 637 486
31 RacPyV NC_023845.1 167 171 LFCEE 504 685 546
32 RnorPyV1 NC_027531.1 128 132 LYCSE 535 698 492
33 BatPyV3a-B0454 NC_038557.1 107 111 LHCHE 477 637 483
34 OraPyV-Sum NC_028127.1 12 75 192 489 649 483
35 TSPyV NC_014361.1 12 77 198 122 126 LFCHE 445 605 483
36 YbPyV1 NC_025894.1 12 75 192 131 135 LFCSE 463 663 603
37 AelPyV1 NC_022519.1 400 564 495
38 BatPyV2c NC_038558.1 223 227 LLCEE 559 719 483
39 BVPyV NC_028117.1 12 67 168 146 150 LTCHE 383 574 576
40 BatPyV6a NC_026762.1 84 88 LFCHE 395 557 489
41 BatPyV6b NC_026770.1 98 102 LFCHE 407 570 492
42 BatPyV6c NC_026769.1 100 104 LFCRE 426 587 486
43 SLPyV NC_013796.1 12 77 198 113 117 LHCHE 397 556 480
44 CalbPyV1 NC_019854.2 100 104 LFCNE 410 570 483
45 CeryPyV1 NC_025892.1 12 75 192 105 109 LFCHE 402 562 483
46 VmPyV2 NC_025896.1 12 75 192 105 109 LFCHE 402 562 483
47 CVPyV NC_028119.1 12 67 168 145 149 LSCNE 382 573 576
48 BatPyV2a NC_028122.1 12 80 207 406 565 480
49 EPyV NC_017982.1 12 86 225 105 109 LRCDE 402 562 483
50 BKPyV NC_001538.1 12 75 192 105 109 LFCHE 402 562 483
51 KIPyV NC_009238.1 108 112 LRCNE 410 572 489
52 JCPyV NC_001699.1 12 75 192 105 109 LFCHE 401 561 483
53 WsPyV NC_032120.1 12 77 198 113 117 LHCNE 400 561 486
54 SV40 NC_001669.1 12 75 192 103 107 LFCSE 400 560 483
55 MasPyV NC_025895.1 101 105 LFCNE 414 576 489
56 MmelPyV1 NC_026473.1 12 80 207 111 115 LRCDE 365 559 585
57 MiniopterusPyV NC_020069.1 12 75 192 103 107 LHCHE 369 560 576
58 MPtV NC_001505.2 103 107 LFCNE 418 573 468
59 MyPyV NC_011310.1 441 603 489
60 PtrovPyV8 NC_028635.1 12 75 192 105 109 LFCHE 402 562 483
61 PteronotusPyV NC_020070.1 12 80 207 108 112 LRCDE 405 564 480
62 BatPyV2b NC_028121.1 12 80 207 108 112 LRCDE 406 617 636
63 RatPyV2 NC_032005.1 12 79 204 178 182 LHCDE 474 634 483
64 SsciPyV1 NC_038559.1 101 105 LFCHE 410 572 489
65 SquiPyV NC_009951.1 101 105 LFCHE 411 570 480
66 AlPyV NC_034251.1 12 67 168 107 111 LYCNE 407 567 483
67 WUPyV NC_009539.1 12 89 234 108 112 LRCNE 417 579 489
68 YbPyV2 AB767295.2 12 75 192 105 109 LFCHE 402 562 483
69 HPyV6 NC_014406.1 109 113 LYCDE 393 571 537
70 HPyV7 NC_014407.1 109 113 LYCTE 416 576 483
71 MWPyV NC_018102.1 105 109 LSCNE 421 580 480
72 STLPyV NC_020106.1 12 83 216 105 109 LTCNE 406 566 483
73 ADPyV NC_026141.2 8 61 162 69 73 LYCEE 408 582 525
74 BFDV NC_004764.2 6 82 231 372 532 483
75 Butcherbird PyV NC_023008.1 8 67 180 70 74 LFCDE 410 572 489
76 CaPyV NC_017085.1 8 61 162 67 71 LSCNE 390 550 483
77 CpyV NC_007922.1 11 80 210 69 73 LQCEE 405 569 495
78 EgouPyV1 NC_039052.1 8 75 204 70 74 LYCEE 374 572 597
79 FPyV NC_007923.1 6 70 195 60 64 LFCDE 382 543 486
80 GHPV NC_004800.1 8 81 222 65 69 LFCDE 404 599 588
81 HunFPyV NC_039053.1 6 77 216 60 64 LFCDE 382 543 486
82 BassPyV1 NC_025790.1 105 109 LMCGE 338 495 474
83 BPyV NC_001442.1 10 73 192 93 97 LHCDE 391 586 588
84 DPyV NC_025899.1 11 77 201 82 86 LYCDE 357 536 540
85 GfPyV1 NC_026244.1 348 517 510
86 SspPyV NC_026944.1 372 529 474
  1. ScanProsite results together with ProRule-based predicted intra-domain features were used for functional domains retained in LT-Ag of PyVs. LXCXE motifs and their encoding sequences were extracted through the JAVA programming