Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120825
Name   oriT_pRlX2 in_silico
Organism   Rhizobium beringeri strain TP24
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140853 (1049353..1049381 [+], 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_pRlX2
AGGGCGCAATATACGTCGCTATCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13135 GenBank   WP_327206347
Name   traA_U8P69_RS32300_pRlX2 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: 169872.50 Da        Isoelectric Point: 7.1210

>WP_327206347.1 Ti-type conjugative transfer relaxase TraA [Rhizobium beringeri]
MAIMFVRAQVISRGAGRSIVSAAAYRHRTRMMDEQAGTSFSYRGGASELVHEELALPDQMPTWLRTAIDG
RSVAGASEALWNAVDAFEKRADAQLARELIIALPEELTRAENIALVREFVRDNFTSKGMVADWVYHDRDG
NPHIHLMTTLRPLTEEGFGQKKVAVTGDDGAPLRVVTPDRPKGRIVYRLWAGDKETMKAWKIAWADTANR
HLALAGHEVRLDGRSYAEQGLDGIAQTHLGPEKAALVRKGRELHFAPADLARRQEMADRLLADPTLLLKQ
LSNERSTFDERDIAKALHRHVDDPAVFANIRGRLMASDDLIMLKPQQIDAETGKASEPAIFTTREILRSE
YDMARSAQVLSEHRGFAVSDRVVAAAISNVETRDPQKSFHLDPEQVDAVRHVTRDNGIAAVVGLAGAGKS
TLLAAARVAWESDGRRVIGAALAGKAAEGLEDSSGIRSRTLAAWELTWASGRELLERGNVLVIDEAGMVS
SQQMARVLDIAEQAEAKVVLVGDGMQLQPIQAGAAFRAITERIGFAELAGVRRQRQQWAREASRLFARGE
VEQGLDAYARHGHLVEAGTRDEVIARIVGDWSEARKLAIETSVRQGNDGRLRGDELLVLAHTNEDVKRLN
EALRSVMSQEGALSENRTFRTERGARDFAAGDRIIFLENARFIEPRAPRLGPQHVKNGMLGTVVSTGDKR
GDTLLSVRLDNGRDVVISEDSYRNVDHGYAATIHKSQGATVDRTFVLATGMMDQHLTYVSMTRHRDRADL
YAAKEDFEAKPEWGRKPHVDHAAGVTGALVETGQAKFRPSDEDADDSPYADVRTDDGTIHRLWGVSLPKA
LEEGGVSEGDTVTLRKDGVERVTIKVPVVDEQTGQKRFEEREVDRNVWTAKRIETSEERRQRIEQESHRP
DLFKQLVERLSRSGAKTTTLDFESEAGYCAQAQDFARRRGLDHLSLAAAAVEESLSRRWAGIAERRKQLA
KLWERAGVAFGFTIERERRVAYNEERAEPQPVEADVVGSRYLIPPATGFARSAEEDARLAQLASPAWKER
EALLRPLLETIYRDPDAALVALNALSSDTSIEPRRLADDLANAPERLGRLRGSDLIVDGRAARDERNTAI
TALRDLLPLARAHATEFRRNGERFDLGEQRRRTHMSLPIPALSEKAMARLMEIEAVRRQGGDDAYKTAFA
LATEDRSIVQEVKAVSEALSARFGWSAFTAKADAVAERNMIERMPEDLTSISGEKLTRLFEAVKRFADEQ
HLVERRDRSKIVAAASADPQKENVPMLAAVTEFKTAVDEEARSRALATPLYRHQRAALAAVASTIWRDPA
GAVGKIEELLQKGFAGERIAAAVTNDPAAYGALRGSDRLVDRMLAAGRERKEVVQAVPEAGARLRALGSA
YVNLLDAERQATTEERRRMAVAIPGLSTAAEDVLMRLTAEAKNNGRKLSGSAASLGPDIRREFAAVSSAL
DERFGRSAIIRGEKDLSNRVPPAQHRAFEVMQEKLKVLQQTVRRESSEQIISERRQRTTNRSIDL

  Protein domains


Predicted by InterproScan.

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

(1044-1125)

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   15415 GenBank   WP_128410164
Name   traG_U8P69_RS32285_pRlX2 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: 70390.14 Da        Isoelectric Point: 9.2899

>WP_128410164.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MALKGRLHPSLLLVFVPIAVTAITVYITGWRWTALAHGLSGKTEYWFLRAAPVPALLSGPLAGLLTVWAL
PLHRRRPIAIASFLCFLVVTGFYTLREYGRLVPSVERGVVTWNQALSYLDFIAVIGALAGFMAVAVAARI
SVVVPEAVKRARGGTFGDADWLSMAAAAKLFPRDGEIVVGERYRVDKETVHEAPFDPKDRSTWGQGGQAP
LLTYNQDFDSTHMLFFAGSGGYKTTSNVLPTALRYTGPLICLDPSTEVAPMVVEHRTRILGREVMVLDPA
NPIMGFNVLDGIEHSKRKEEDIVGIAHMLLSESLRFESSTGSYFQNQAHNLLTGLLAHVMLSPECSGRRN
LRSLRQIVSEPEPSVLAMLRDIQEHSETAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFRSSDIVTGKTDVFLNIPASILRSYPGIGRVIIGSLINAMVQADGGFSRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLLYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVQG
RSRNIGWDTKGGGTRKSESVNFQRRPLIMPHEITQSMRKDEQIIIVPGHSPIRCGRAIYFRRKDMDAQAK
ANRFVRR

  Protein domains


Predicted by InterproScan.

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

(167-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 675933..685497

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U8P69_RS30260 (U8P69_30250) 672019..673017 + 999 WP_130766748 ABC transporter substrate-binding protein -
U8P69_RS30265 (U8P69_30255) 673001..674776 + 1776 WP_327206284 adenylate/guanylate cyclase domain-containing protein -
U8P69_RS30270 (U8P69_30260) 674952..675305 - 354 WP_128404288 MarR family transcriptional regulator -
U8P69_RS30275 (U8P69_30265) 675397..675933 + 537 WP_327206285 hypothetical protein -
U8P69_RS30280 (U8P69_30270) 675933..676595 + 663 WP_327206286 type IV secretion system protein VirB1 virB1
U8P69_RS30285 (U8P69_30275) 676592..676891 + 300 WP_327206287 TrbC/VirB2 family protein virB2
U8P69_RS30290 (U8P69_30280) 676897..677235 + 339 WP_327206288 type IV secretion system protein VirB3 virB3
U8P69_RS30295 (U8P69_30285) 677228..679595 + 2368 Protein_630 VirB4 family type IV secretion system protein -
U8P69_RS30300 (U8P69_30290) 679628..680293 + 666 WP_245002731 P-type DNA transfer protein VirB5 virB5
U8P69_RS30305 (U8P69_30295) 680290..680523 + 234 WP_130666525 EexN family lipoprotein -
U8P69_RS30310 (U8P69_30300) 680527..681447 + 921 WP_130666526 type IV secretion system protein virB6
U8P69_RS30315 (U8P69_30305) 681500..681784 + 285 WP_130666527 hypothetical protein -
U8P69_RS30320 (U8P69_30310) 681786..682457 + 672 WP_130666528 virB8 family protein virB8
U8P69_RS30325 (U8P69_30315) 682454..683311 + 858 WP_327206289 P-type conjugative transfer protein VirB9 virB9
U8P69_RS30330 (U8P69_30320) 683321..684493 + 1173 WP_130766738 type IV secretion system protein VirB10 virB10
U8P69_RS30335 (U8P69_30325) 684502..685497 + 996 WP_130766737 P-type DNA transfer ATPase VirB11 virB11
U8P69_RS30340 (U8P69_30330) 686212..686427 - 216 WP_130766736 DUF3072 domain-containing protein -
U8P69_RS30345 (U8P69_30335) 686675..687007 - 333 Protein_640 LysR substrate-binding domain-containing protein -
U8P69_RS30350 (U8P69_30340) 687014..687100 + 87 Protein_641 SDR family oxidoreductase -
U8P69_RS30355 (U8P69_30345) 687320..688228 - 909 WP_327206511 nucleotidyltransferase and HEPN domain-containing protein -
U8P69_RS30360 (U8P69_30350) 688572..688988 + 417 WP_130660238 UPF0158 family protein -
U8P69_RS30365 (U8P69_30355) 689551..689772 + 222 WP_130806847 hypothetical protein -

Host bacterium

ID   21254 GenBank   NZ_CP140853
Plasmid name   pRlX2 Incompatibility group   -
Plasmid size   1157677 bp Coordinate of oriT [Strand]   1049353..1049381 [+]
Host baterium   Rhizobium beringeri strain TP24

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   bphC
Symbiosis gene   fixA, fixB
Anti-CRISPR   AcrIIA9