Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102763
Name   oriT_pRspN621d in_silico
Organism   Rhizobium sp. N621
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013499 (699024..699052 [-], 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_pRspN621d
AGGGCGCAATATACGTCGCTGCCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2038 GenBank   WP_064813248
Name   traA_AMK00_RS30220_pRspN621d 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   1691 GenBank   WP_064813078
Name   traG_AMK00_RS30235_pRspN621d 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: 711200..720130

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMK00_RS30275 (AMK00_PD00649) 706206..707147 - 942 WP_064813094 DUF2493 domain-containing protein -
AMK00_RS30280 (AMK00_PD00650) 707471..708505 - 1035 WP_064813096 toprim domain-containing protein -
AMK00_RS30290 708886..709122 + 237 WP_064813962 hypothetical protein -
AMK00_RS30295 (AMK00_PD00652) 709234..710424 + 1191 WP_064813102 DUF1173 domain-containing protein -
AMK00_RS30300 (AMK00_PD00653) 710464..710862 - 399 WP_064813104 type II toxin-antitoxin system VapC family toxin -
AMK00_RS30305 (AMK00_PD00654) 710859..711110 - 252 WP_064813105 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
AMK00_RS30310 (AMK00_PD00655) 711200..712222 - 1023 WP_064813107 P-type DNA transfer ATPase VirB11 virB11
AMK00_RS30315 (AMK00_PD00656) 712231..713406 - 1176 WP_064813109 type IV secretion system protein VirB10 virB10
AMK00_RS30320 (AMK00_PD00657) 713415..714272 - 858 WP_064813111 P-type conjugative transfer protein VirB9 virB9
AMK00_RS30325 (AMK00_PD00658) 714269..714940 - 672 WP_064813251 virB8 family protein virB8
AMK00_RS33400 714934..715227 - 294 WP_082240409 hypothetical protein -
AMK00_RS30330 (AMK00_PD00659) 715265..716197 - 933 WP_064813113 type IV secretion system protein virB6
AMK00_RS30335 (AMK00_PD00660) 716200..716433 - 234 WP_064813115 EexN family lipoprotein -
AMK00_RS30340 (AMK00_PD00661) 716430..717128 - 699 WP_064813117 P-type DNA transfer protein VirB5 virB5
AMK00_RS30345 (AMK00_PD00662) 717128..719494 - 2367 WP_097585286 VirB4 family type IV secretion system protein virb4
AMK00_RS30350 (AMK00_PD00663) 719487..719825 - 339 WP_064813121 type IV secretion system protein VirB3 virB3
AMK00_RS30355 (AMK00_PD00664) 719831..720130 - 300 WP_064813123 TrbC/VirB2 family protein virB2
AMK00_RS30360 (AMK00_PD00665) 720127..720793 - 667 Protein_687 lytic transglycosylase domain-containing protein -
AMK00_RS31765 (AMK00_PD00666) 720796..721326 - 531 WP_082240410 hypothetical protein -
AMK00_RS30365 (AMK00_PD00667) 721428..721799 + 372 WP_064813253 hypothetical protein -
AMK00_RS30370 (AMK00_PD00668) 722206..723396 - 1191 WP_064813127 hypothetical protein -

Host bacterium

ID   3206 GenBank   NZ_CP013499
Plasmid name   pRspN621d Incompatibility group   -
Plasmid size   742499 bp Coordinate of oriT [Strand]   699024..699052 [-]
Host baterium   Rhizobium sp. N621

Cargo genes

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