Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102765
Name   oriT_pRspN113d in_silico
Organism   Rhizobium sp. N113
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013521 (712141..712169 [-], 29 nt)
oriT length   29 nt
IRs (inverted repeats)      14..19, 24..29  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 29 nt

>oriT_pRspN113d
AGGGCGCAATATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2040 GenBank   WP_064813248
Name   traA_AMJ96_RS30535_pRspN113d insolico UniProt ID   _
Length   1553 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1553 a.a.        Molecular weight: 171806.03 Da        Isoelectric Point: 6.7399

>WP_064813248.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMMDEQAGTSFSYRGGSRELVHEELALPEQVPGWLRAAIDG
QSVAGASEALWNAVDAFETRADGQLARELIIALPEELTRAENIALVREFVHDNLTSKGMVADWVYHDKDG
NPHIHLMTTLRPLTEDGFGPKKVPVLGEDDKPLRVVTPDRPNGKIVYKVWAGDKETMKGWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELYFAPADLARRHEMADRLLAEPELLLKQ
LGNERSTFDEKDIAKALHRYVDDPSDFANIRARLMASDELVMLKPQEFDGETREVAAPAVFTTREMLRIE
YDMARSARVLSEQAGFGVSARQVDTAIERVETGDPAKPFKLDAEQVDAIRHVTGDSGIAAVVGLAGAGKS
TLLAAARLAWESEGRRVIGAALAGKAAEGLEDSSGIKSRTLTAWELAWANGRDTLHRGDVLVIDEAGMVA
SQQMARVLDIVEEASAKVVLVGDAMQLQPIQAGAAFRAISDRIGFAELAGVRRQREEWAREASRLFARGE
VEKGLEAYAQHGHLAEAGTRAETIDRIVGDWSEARREAIGRSVSEGRDGRLRGDELLVLAHTNDDVRKLN
EALRAVMAGQRALSDSRTFQTARGAREFAVGDRIIFLENARFLEPRARSYGPQYVKNGMLGTVISTGDKR
GEALMSVRLDNGHKVVFSEDSYRNVDHGYAATIHKAQGATVERTLVLATGMMDQHLTYVAMTRHRDRVDL
YAASEDFEPRPEWGRKPRVDHAAGVTGELVETGEAKFRPDDEDADDSPYADVRTDDGTVHRLWGVSLPKA
LEEGGLSEGDTVTLRKDGVERVKVQIAVIDEETGQKRYEEREVDRNVWTARQIETAEARQDRIERESHRP
DLFKPLVERLSRSGAKTTTLDFESEAGYRAYAEDFARRRGFEYLSLAAAEIEGDISRRFAWIAAKREQQE
KLWERASMALGFAIERERRVSYSEARTEARPVPSANAGKAHYLILPTTEFVRSIDEDARLAQLSSPVWKD
RETLLRPVLERIYRDPDGALVALNALASDAGTEPRRLADDLAVSPDRLGRLRGSELIVDGRAARDERNVA
LAAVTELLPMARAHASEFRRNAERFELNEQARRAHMSLSIPALSEGAMARLMEIEAVRHRGGDDAYKTAF
ALAAKDRTVVQEIKAVSEALSARFGWSAFTAKADAVAERNMAERMPEALMAGEREKLVHLFEAVKRFAEA
QHLAERHDRSKIVAAASAVADQEQGMQPGMKSGKENVTVLPMLAAVTEFKTAVDDEARSRVLSAPFYRQQ
RAALANAARTIWRDPAGAVGKIEELIVKGFAAERIAAAVSNDPAAYGALRGSGRLMDKMLASGRERKEAV
QAVPEAAARLRSLGSAYANIFDAERQAIKAERERMAVAIPGLSKVAEEALVRLTAEARKNDRKRGIATAP
LDANIRREFDEISKALDQRFGRNAIIRGDKDLINHVPEPQRQAFVAMQEKLKILQQTVRAESSQQILSER
RQRGFNRGRGIDI

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(391-577)

MobA/MobL family (MobA_MobL)

(17-249)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(1320-1414)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(1057-1127)


  Protein structure



No available structure.




T4CP

ID   1693 GenBank   WP_064813078
Name   traG_AMJ96_RS30550_pRspN113d insolico UniProt ID   _
Length   638 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 638 a.a.        Molecular weight: 70312.12 Da        Isoelectric Point: 9.0374

>WP_064813078.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTSKKRLHPSLLCVLVPVVVTAISAYVVNWRWPILAHGLTGTTEYWFLRAAPVPALLFGPLAGLLTVWAL
PLHRRRPVAMASLACFLIMAGCYALREYSRLAPFVQAGAVSLNGALSYLDLVAVIGAVMGFMAVAVAARI
SVVVPEAVKRVKGGAFGDADWLSMSAAAKLFPPNGEIVVGERYRVDKEIVHQLPFDPNDHSTWGQGGKAP
LLTYSQDFDSTHMLFFAGSGGYKTTSNVLPTALRYTGPLICLDPSTEVAPMVTEHRTQVLGREVMVLDPN
NPINGFNVLDGIEHSRRKEEEIVGIAHMLLSESVRFESSTGSYFQNQAHNLLTGLLAHVMLSPEYAGRRN
LRSLRQIVSEPEPSVLAMLRDIQEHSKSAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GDAFRPSDIVAGRKDVFLNIPASILRSYPGIARVIIGSLVNAMVQADGDFSRRALFILDEVDLLGYMRVL
EEARDRGRKYGISMMLLYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEVTVEVQG
RSRNIGWDAKGGTRRSESVNVQRRPLILPHEITQAMRKDEQIIIVQGHNPIRCGRAIYFRRKEMDRAAKA
NRFVKPEQ

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(161-633)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 724317..733247

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMJ96_RS30590 (AMJ96_PD00665) 719323..720264 - 942 WP_064813094 DUF2493 domain-containing protein -
AMJ96_RS30595 (AMJ96_PD00666) 720588..721622 - 1035 WP_064813096 toprim domain-containing protein -
AMJ96_RS30605 722003..722239 + 237 WP_064813962 hypothetical protein -
AMJ96_RS30610 (AMJ96_PD00668) 722351..723541 + 1191 WP_064813102 DUF1173 domain-containing protein -
AMJ96_RS30615 (AMJ96_PD00669) 723581..723979 - 399 WP_064813104 type II toxin-antitoxin system VapC family toxin -
AMJ96_RS30620 (AMJ96_PD00670) 723976..724227 - 252 WP_064813105 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
AMJ96_RS30625 (AMJ96_PD00671) 724317..725339 - 1023 WP_064813107 P-type DNA transfer ATPase VirB11 virB11
AMJ96_RS30630 (AMJ96_PD00672) 725348..726523 - 1176 WP_064813109 type IV secretion system protein VirB10 virB10
AMJ96_RS30635 (AMJ96_PD00673) 726532..727389 - 858 WP_064813111 P-type conjugative transfer protein VirB9 virB9
AMJ96_RS30640 (AMJ96_PD00674) 727386..728057 - 672 WP_064813251 virB8 family protein virB8
AMJ96_RS33840 (AMJ96_PD00675) 728051..728344 - 294 WP_082240409 hypothetical protein -
AMJ96_RS30645 (AMJ96_PD00676) 728382..729314 - 933 WP_064813113 type IV secretion system protein virB6
AMJ96_RS30650 (AMJ96_PD00677) 729317..729550 - 234 WP_064813115 EexN family lipoprotein -
AMJ96_RS30655 (AMJ96_PD00678) 729547..730245 - 699 WP_064813117 P-type DNA transfer protein VirB5 virB5
AMJ96_RS30660 (AMJ96_PD00679) 730245..732611 - 2367 WP_097585286 VirB4 family type IV secretion system protein virb4
AMJ96_RS30665 (AMJ96_PD00680) 732604..732942 - 339 WP_064813121 type IV secretion system protein VirB3 virB3
AMJ96_RS30670 (AMJ96_PD00681) 732948..733247 - 300 WP_064813123 TrbC/VirB2 family protein virB2
AMJ96_RS30675 (AMJ96_PD00682) 733244..733910 - 667 Protein_696 lytic transglycosylase domain-containing protein -
AMJ96_RS32115 (AMJ96_PD00683) 733913..734443 - 531 WP_082240410 hypothetical protein -
AMJ96_RS30680 (AMJ96_PD00684) 734545..734916 + 372 WP_064813253 hypothetical protein -
AMJ96_RS30685 (AMJ96_PD00685) 735305..736495 - 1191 WP_064813127 hypothetical protein -

Host bacterium

ID   3208 GenBank   NZ_CP013521
Plasmid name   pRspN113d Incompatibility group   -
Plasmid size   755598 bp Coordinate of oriT [Strand]   712141..712169 [-]
Host baterium   Rhizobium sp. N113

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   hupE2
Degradation gene   -
Symbiosis gene   fixB, fixA
Anti-CRISPR   -