Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100278
Name   oriT_pYR1 in_silico
Organism   Yersinia ruckeri
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_009139 (54664..55214 [+], 551 nt)
oriT length   551 nt
IRs (inverted repeats)      IR1: 62..70, 71..79  (AACCCTTTC..GACAGGGTT)
  IR2: 143..150, 154..161  (TGGCCTGC..GGAGGCCA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 551 nt

>oriT_pYR1
GAGCAGAGCTATGTGTGACAAGAAGTATAGAGATTACGAGGTAGCCATCATGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAAGGCTAATCAGGAGCCTGTGATTTACCCGATCATTGAAGAAGCTCTGCATCGCTACAGCCAGCTCGTGTTTCATGAGCAGAGAGAGAAATATGAAGACCCGGCCAGAATTGGGGCATTTCTGGAAACCCTGATCACCGAAACCTGCCGGGCGTTGGAAGTGCAAATTGTCGATAGTGGCGGTGATTCATGGTCTGTCGATTCAGGAGAGTCGTTCTCACTGTGGCTTTCTTCCCATCCAGGAGAACTATCCATTAACCCGCAGCCCCATGAGGATGAGACCTCTTTGCGTGGCTTGCTGTATGAGCTCATCACCTGTGAGAGCGTGAAAACTGTTTTAAGGAGAACCGACT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   349 GenBank   YP_001101767
Name   TraI_pYR1 insolico UniProt ID   A4IUA1
Length   992 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 992 a.a.        Molecular weight: 109595.88 Da        Isoelectric Point: 4.8967

>YP_001101767.1 type IV conjugative transfer system protein TraI (plasmid) [Yersinia ruckeri]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB A4IUA1


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 52798..77989

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
YR71PYR1_RS00395 48823..49056 - 234 WP_001191892 hypothetical protein -
YR71PYR1_RS00400 (YR71pYR1_0072) 49038..49655 - 618 WP_001249396 hypothetical protein -
YR71PYR1_RS00405 (YR71pYR1_0073) 49823..52801 + 2979 WP_011872892 MobH family relaxase -
YR71PYR1_RS00410 (YR71pYR1_0074) 52798..54663 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
YR71PYR1_RS00415 (YR71pYR1_0075) 54674..55258 + 585 WP_000332866 hypothetical protein -
YR71PYR1_RS00420 (YR71pYR1_0076) 55215..55844 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
YR71PYR1_RS00425 (YR71pYR1_0077) 55854..56300 + 447 WP_000122506 hypothetical protein -
YR71PYR1_RS00430 (YR71pYR1_0078) 56310..56687 + 378 WP_000869261 hypothetical protein -
YR71PYR1_RS00435 (YR71pYR1_0079) 56687..57349 + 663 WP_001231463 hypothetical protein -
YR71PYR1_RS00440 57530..57673 + 144 WP_001275801 hypothetical protein -
YR71PYR1_RS00445 (YR71pYR1_0080) 57685..58050 + 366 WP_001052531 hypothetical protein -
YR71PYR1_RS00450 (YR71pYR1_0081) 58195..58476 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
YR71PYR1_RS00455 (YR71pYR1_0082) 58473..59099 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
YR71PYR1_RS00460 (YR71pYR1_0083) 59083..60000 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
YR71PYR1_RS00465 (YR71pYR1_0084) 60000..61313 + 1314 WP_024131605 TraB/VirB10 family protein traB
YR71PYR1_RS00470 (YR71pYR1_0085) 61310..61888 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
YR71PYR1_RS00475 (YR71pYR1_0086) 61892..62284 + 393 WP_000479535 TraA family conjugative transfer protein -
YR71PYR1_RS00480 (YR71pYR1_0087) 62485..68016 + 5532 WP_000606833 Ig-like domain-containing protein -
YR71PYR1_RS00485 (YR71pYR1_0088) 68165..68872 + 708 WP_001259347 DsbC family protein -
YR71PYR1_RS00490 (YR71pYR1_0089) 68869..71316 + 2448 WP_011872839 type IV secretion system protein TraC virb4
YR71PYR1_RS00495 (YR71pYR1_0090) 71331..71648 + 318 WP_011872858 hypothetical protein -
YR71PYR1_RS00500 (YR71pYR1_0091) 71645..72175 + 531 WP_011872856 S26 family signal peptidase -
YR71PYR1_RS00505 (YR71pYR1_0092) 72138..73403 + 1266 WP_011872896 TrbC family F-type conjugative pilus assembly protein traW
YR71PYR1_RS00510 (YR71pYR1_0093) 73400..74071 + 672 WP_001337754 EAL domain-containing protein -
YR71PYR1_RS00515 (YR71pYR1_0094) 74071..75075 + 1005 WP_043940352 TraU family protein traU
YR71PYR1_RS00520 (YR71pYR1_0095) 75191..77989 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
YR71PYR1_RS00525 (YR71pYR1_0096) 78028..78888 - 861 WP_000709517 hypothetical protein -
YR71PYR1_RS00530 (YR71pYR1_0097) 79011..79652 - 642 WP_000796664 hypothetical protein -
YR71PYR1_RS00535 (YR71pYR1_0098) 79946..80266 + 321 WP_000547566 hypothetical protein -
YR71PYR1_RS00540 (YR71pYR1_0099) 80570..80755 + 186 WP_001186917 hypothetical protein -
YR71PYR1_RS00545 (YR71pYR1_0100) 80975..81943 + 969 WP_000085162 AAA family ATPase -
YR71PYR1_RS00550 (YR71pYR1_0101) 81954..82862 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   740 GenBank   NC_009139
Plasmid name   pYR1 Incompatibility group   IncA/C2
Plasmid size   158038 bp Coordinate of oriT [Strand]   54664..55214 [+]
Host baterium   Yersinia ruckeri

Cargo genes

Drug resistance gene   sul2, tet(B), aph(3'')-Ib, aph(6)-Id
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -