Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120829
Name   oriT_pRlX4 in_silico
Organism   Rhizobium beringeri strain TP13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140877 (995218..995246 [+], 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_pRlX4
AGGGCGCAATATACGTCGCTATCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13139 GenBank   WP_327212794
Name   traA_U8Q06_RS36050_pRlX4 insolico UniProt ID   _
Length   1535 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1535 a.a.        Molecular weight: 169991.82 Da        Isoelectric Point: 7.1785

>WP_327212794.1 Ti-type conjugative transfer relaxase TraA [Rhizobium beringeri]
MAIMFVRAQVISRGAGRSIVSAAAYRHRTRMMDEQAGTSFSYRGGASELVHEELALPDQMPTWLRTAIDG
RSVAGASEALWNAVDAFEKRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDRDG
NPHIHLMTTLRPLTEEGFGQKKVAVTGDDGAPLRVVTPDRPKGRIVYRLWAGDKETMKAWKIAWADTANR
HLALAGHEVRLDGRSYAEQGLDGIAQTHLGPEKAALVRKGRELHFAPADLARRQEMADRLLAEPELLLKQ
LSNERSTFDERDIAKALHRYVDDPAVFANIRARLMVSDDLIMLKPQQLDAETGKASEPAIFTTRQILRIE
YDMARSAQVLAEYRGFAVSDRVVAAAISNVETRDPQKSFHLDPEQVDAVRHVTRDNGIAAVVGLAGAGKS
TLLAAARVAWESDGRRVIGAALAGKAAEGLEDSSGIRSRTLAAWELTWASGRELLERGNVLVIDEAGMVS
SQQMARVLDIAEQAEAKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQRQQWAREASRLFARGE
VEQGLDAYARHGHLVEAGTRDEVIARIVGDWSEARKLAIETSVRQGNDGRLRGDELLVLAHTNEDVKRLN
EALRSVMSQEGALSENRTFRTERGARDFAAGDRIIFLENARFIEPRAPRLGPQHVKNGMLGTVVSTGDKR
GDTLLSVRLDNGRDVVISEDSYRNVDHGYAATIHKSQGATVDRTFVLATGMMDQHLTYVSMTRHRDRADL
YAAKEDFEAKPEWGRKPHVDHAAGVTGALVETGQAKFRPSDEDADDSPYADVRTDDGTIHRLWGVSLPKA
LEEGGVSEGDTVTLRKDGVERVTIKVPVVDEQTGQKRFEEREVDRNVWTAKRIETSEERQQRIEQESHRP
DLFKQLVERLSRSGAKTTTLDFESEASYRAQAQDFARRRGLDHLSLAAAAVEENLSRRWAGIAERRKQLA
KLWERAGVAFGFTIERERRVAYNEERAEPQPVEADVVGSRYLIPPATGFARSADEDALLAQLASPAWKER
EAILRPLLAKIYRDPDAALVALNALSSDTSIEPRRLADDLANAPDRLGRLRGSDLIIDGRAARDERNTAI
TALRDLLPLARAHATEFRRNGERFDLGEQRRRTHMSLPIPALSEKAMARLMEIEAVRRQGGDDAYKTAFA
LATEDRSIVQEVKAVSEALSARFGWSAFTAKADAVAERNMIERMPEDLTSISGEKLTRLFEAVKRFADEQ
HLVERRDRSKIVAAASADPQKENVPMLAAVTEFKTAVDEEARSRALATPLYRHQRAALAAVASTIWRDPA
GAVGKIEELLQKGFAGERIAAAVTNDPAAYGALRGSDRLVDRMLAAGRERKEVVQAVPEAGARLRALGSA
YVNLLDAERQATTEERRRMAVAIPGLSTAAEDVLMRLTAEAKNNGRKLSGSAASLGPDIRREFAAVSSAL
DERFGRSAIIRGEKDLSNRVPPAQHRAFEVMQEKLKVLQQTVRRESSEQIISERRQRTTNRSIDL

  Protein domains


Predicted by InterproScan.

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

(1045-1125)

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

(1307-1397)

MobA/MobL family (MobA_MobL)

(17-249)

AAA domain (AAA_30)

(391-577)


  Protein structure



No available structure.




T4CP

ID   15419 GenBank   WP_327212793
Name   traG_U8Q06_RS36035_pRlX4 insolico UniProt ID   _
Length   637 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 70453.33 Da        Isoelectric Point: 9.4055

>WP_327212793.1 Ti-type conjugative transfer system protein TraG [Rhizobium beringeri]
MALKGRLHPSLLLVFVPIAVTAITVYITGWRWTALAHGLSGKTEYWFLRAAPVPALLSGPLAGLLTVWAL
PLHRRRPIAIASFLCFLVVTGFYALREYGRLVPSVERGVVTWNQALSYLDFIAVIGALAGFMAVAVAARI
SVVVPEAVKRARGGTFGDADWLSMSAAAKLFPPEGEIVVGERYRVDKEIVHQLPFDPKDRSTWGQGGQAP
LLTYNQDFDSTHMLFFAGSGGYKTTSNVLPTALRYTGPLICLDPSTEVAPMVVEHRTRILGREVMVLDPA
NPIMGFNVLDGIEHSKRKEEDIVGIAHMLLSESLRFESSTGSYFQNQAHNLLTGLLAHVMLSPECSGRRN
LRSLRQIVSEPEPSVLAMLRDIQEHSETAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFRSSDIVTGKTDVFLNIPASILRSYPGIGRVIIGSLINAMVQADGGFSRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLLYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVQG
RSRNIGWDTKGGGTRKSERVNFQRRPLIMPHEITQSMRKDEQIIIVPGHSPIRCGRAIYFRRKDMDAQAK
ANRFVRR

  Protein domains


Predicted by InterproScan.

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

(161-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 691557..701155

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U8Q06_RS34580 (U8Q06_34580) 687640..688638 + 999 WP_327212694 ABC transporter substrate-binding protein -
U8Q06_RS34585 (U8Q06_34585) 688622..690397 + 1776 WP_327212695 adenylate/guanylate cyclase domain-containing protein -
U8Q06_RS34590 (U8Q06_34590) 690573..690926 - 354 WP_128404288 MarR family transcriptional regulator -
U8Q06_RS34595 (U8Q06_34595) 691018..691557 + 540 WP_327212696 hypothetical protein -
U8Q06_RS34600 (U8Q06_34600) 691557..692219 + 663 WP_327212697 lytic transglycosylase domain-containing protein virB1
U8Q06_RS34605 (U8Q06_34605) 692216..692515 + 300 WP_128404291 TrbC/VirB2 family protein virB2
U8Q06_RS34610 (U8Q06_34610) 692521..692859 + 339 WP_327212698 type IV secretion system protein VirB3 virB3
U8Q06_RS34615 (U8Q06_34615) 692852..695218 + 2367 WP_327212699 VirB4 family type IV secretion system protein virb4
U8Q06_RS34620 (U8Q06_34620) 695254..695916 + 663 WP_327212855 P-type DNA transfer protein VirB5 virB5
U8Q06_RS34625 (U8Q06_34625) 695913..696137 + 225 WP_128410222 EexN family lipoprotein -
U8Q06_RS34630 (U8Q06_34630) 696141..697061 + 921 WP_327212700 type IV secretion system protein virB6
U8Q06_RS34635 (U8Q06_34635) 697114..697398 + 285 WP_233943224 hypothetical protein -
U8Q06_RS34640 (U8Q06_34640) 697400..698071 + 672 WP_327212701 virB8 family protein virB8
U8Q06_RS34645 (U8Q06_34645) 698068..698925 + 858 WP_327212702 P-type conjugative transfer protein VirB9 virB9
U8Q06_RS34650 (U8Q06_34650) 698935..700107 + 1173 WP_327212703 type IV secretion system protein VirB10 virB10
U8Q06_RS34655 (U8Q06_34655) 700115..701155 + 1041 WP_327212704 P-type DNA transfer ATPase VirB11 virB11
U8Q06_RS34660 (U8Q06_34660) 701249..701704 + 456 WP_222313228 NUDIX hydrolase -
U8Q06_RS34665 (U8Q06_34665) 701701..702723 + 1023 WP_327212705 PHB depolymerase family esterase -
U8Q06_RS34670 (U8Q06_34670) 702806..702958 + 153 Protein_648 P-type DNA transfer ATPase VirB11 -
U8Q06_RS34675 (U8Q06_34675) 703177..703392 - 216 WP_130832663 DUF3072 domain-containing protein -
U8Q06_RS34680 (U8Q06_34680) 703639..704550 - 912 WP_130660240 LysR family transcriptional regulator -
U8Q06_RS34685 (U8Q06_34685) 704650..705411 + 762 WP_327212706 SDR family NAD(P)-dependent oxidoreductase -

Host bacterium

ID   21258 GenBank   NZ_CP140877
Plasmid name   pRlX4 Incompatibility group   -
Plasmid size   1103503 bp Coordinate of oriT [Strand]   995218..995246 [+]
Host baterium   Rhizobium beringeri strain TP13

Cargo genes

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