Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102783
Name   oriT_pRspN871d in_silico
Organism   Rhizobium sp. N871
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013594 (709465..709493 [-], 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_pRspN871d
AGGGCGCAATATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2055 GenBank   WP_064813248
Name   traA_AMK04_RS30620_pRspN871d 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   1711 GenBank   WP_064813078
Name   traG_AMK04_RS30635_pRspN871d 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: 721641..730571

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMK04_RS30675 (AMK04_PD00657) 716647..717588 - 942 WP_064813094 DUF2493 domain-containing protein -
AMK04_RS30680 (AMK04_PD00658) 717912..718946 - 1035 WP_064813096 toprim domain-containing protein -
AMK04_RS30690 719363..719563 + 201 WP_145924266 hypothetical protein -
AMK04_RS30695 (AMK04_PD00660) 719675..720865 + 1191 WP_064813102 DUF1173 domain-containing protein -
AMK04_RS30700 (AMK04_PD00661) 720905..721303 - 399 WP_064813104 type II toxin-antitoxin system VapC family toxin -
AMK04_RS30705 (AMK04_PD00662) 721300..721551 - 252 WP_064813105 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
AMK04_RS30710 (AMK04_PD00663) 721641..722663 - 1023 WP_064813107 P-type DNA transfer ATPase VirB11 virB11
AMK04_RS30715 (AMK04_PD00664) 722672..723847 - 1176 WP_064813109 type IV secretion system protein VirB10 virB10
AMK04_RS30720 (AMK04_PD00665) 723856..724713 - 858 WP_064813111 P-type conjugative transfer protein VirB9 virB9
AMK04_RS30725 (AMK04_PD00666) 724710..725381 - 672 WP_064813251 virB8 family protein virB8
AMK04_RS33880 725375..725668 - 294 WP_082240409 hypothetical protein -
AMK04_RS30730 (AMK04_PD00667) 725706..726638 - 933 WP_064813113 type IV secretion system protein virB6
AMK04_RS30735 (AMK04_PD00668) 726641..726874 - 234 WP_064813115 EexN family lipoprotein -
AMK04_RS30740 (AMK04_PD00669) 726871..727569 - 699 WP_064813117 P-type DNA transfer protein VirB5 virB5
AMK04_RS30745 (AMK04_PD00670) 727569..729935 - 2367 WP_097585286 VirB4 family type IV secretion system protein virb4
AMK04_RS30750 (AMK04_PD00671) 729928..730266 - 339 WP_064813121 type IV secretion system protein VirB3 virB3
AMK04_RS30755 (AMK04_PD00672) 730272..730571 - 300 WP_064813123 TrbC/VirB2 family protein virB2
AMK04_RS30760 (AMK04_PD00673) 730568..731234 - 667 Protein_695 lytic transglycosylase domain-containing protein -
AMK04_RS32165 (AMK04_PD00674) 731237..731767 - 531 WP_082240410 hypothetical protein -
AMK04_RS30765 (AMK04_PD00675) 731869..732240 + 372 WP_064813253 hypothetical protein -
AMK04_RS30770 (AMK04_PD00676) 732647..733837 - 1191 WP_064813127 hypothetical protein -

Host bacterium

ID   3226 GenBank   NZ_CP013594
Plasmid name   pRspN871d Incompatibility group   -
Plasmid size   752940 bp Coordinate of oriT [Strand]   709465..709493 [-]
Host baterium   Rhizobium sp. N871

Cargo genes

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