Detailed information of oriT

oriT


The information of the oriT region


oriTDB ID   105618
Name   oriT_pRetNXC12e in_silico
Organism   Rhizobium etli strain NXC12
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP020911 (284291..284319 [-], 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_pRetNXC12e
AGGGCGCAATATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase


ID   3814 GenBank   WP_086084174
Name   traA_NXC12_RS29575_pRetNXC12e insolico UniProt ID   _
Length   1543 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1543 a.a.        Molecular weight: 171228.51 Da        Isoelectric Point: 9.0655

>WP_086084174.1 Ti-type conjugative transfer relaxase TraA [Rhizobium etli]
MAIMFVRAQVISRGAGRSIVSAAAYRHRTRMMDEQAGTSFSYRGGAGELMHEELALPDEIPDWLRSAISG
QSVSNASEVFWNAVDAFETRGDAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEDGFGRKKVPVLGGDGKPLRVITPDRPNGNIVYKVWAGDKETLKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQTHLGPEKAALARKGRELHFAPADLARRQEMADRLLADPERLLTQ
LVNERSTFDERDIAKALHRYVDDPSDFANIRARLMASTELVMLKPQEIDTQTGKASEPAVFTTRDMLRIE
YEMAQSARVLSGRRDFGVSERHVSAAIESIETRDPQKRFRLDPEQVDAIRHVTGDDGIAAVVGLAGAGKS
TLLAAARLAWESQGRRVIGAALAGKAAEGLEDSSGIKSRTLASWELAWANGRDTLHRGDVVVIDEAGMVS
SPQMARVLDIVEQAEAKVVLVGDAMQLQPIQAGAAFRAISERIGFAELAGVRRQRHGWARDASRLFARGE
IDKGLDAYAGHGHLVEAETRQEIVDRIVADWREARRQAIGRSVSEGRDGSLGGDELLVLAHTNADVKRLN
EALRSVMTGEGALGESRSFRTERGAREFAAGDRVIFLENARFIEPRARRLGPQYVKNGMLGTVVSTGDAK
GEVLLSVRLDNGSKVVFGEESYRNVDHGYAATIHKSQGATVERTFVLASGMMDRHLTYVSMTRHRDRADL
YAAKEDFAAKPEWGRKPRVDHAAGVTGELVETGEAKFRPDDEDADDSPYADLRTGDGTVHRLWGVSLPKA
LEDAGILEGDTVTLRKDGIERVKVEVPVIGEKTGQKRYEEREVDRNVWTAKQIETATERQERIERESHRP
DVFKQLVERLSRSGAKTTTLDFDSEAGYRAHAQDFARRRGIEHLSLVAAEMEESLSRRWAWIAEKREQVE
KLWERASVALGFAIERERRISYNEQRAETRAEVRSLYTRYLIQPATAFARSVDEDARLAQLSSPAWKEQE
AILRPVLEKIYRDPDAALVALNALASNTSIAPRELASNLAAAPDRLGRLRGSDLIVDGRAARDERNVAMA
ALQELLPLARAHATGFRRNAERFELREQTRRAHMSLSIPALSERAMTRLMEIEAVRAQGGDDAYKMAFAL
AAQDRTVVREIKAVSEAITARFGWSAFTAKADAIADRNMVDRMPEDLTAGRREELTPLFEAVKRFAEEQH
LAERQDRSKIVAGASADLSKEPGKEKVTMPPTFAAVTEFKVLVEEEARSRALASPLYRQQRAAMADAART
IWRDPAGAVGRIEELLSKGFAADRIAAAVTNDPAAYGPLRGSSRLMDRMLASGRERKAAIEAVPETAARL
RSFGAAYANIFDAGRHAITEERRRMAVAIPALSKSAEEALTRLTAEARKDSRRLSVSAASLDPNIRREFA
AVSRALDDRFGRNAIVRGDKDLINRVPPPQRRVFEAMQERLKVLQQTVRLQSSEQIIVERRQRTSSRARG
INL

  Protein domains


Predicted by InterproScan.

(391-578)

(17-249)

(1043-1125)

(1312-1404)


  Protein structure



No available structure.




T4CP


ID   3819 GenBank   WP_086084177
Name   traG_NXC12_RS29590_pRetNXC12e insolico UniProt ID   _
Length   639 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 639 a.a.        Molecular weight: 70326.36 Da        Isoelectric Point: 9.4854

>WP_086084177.1 Ti-type conjugative transfer system protein TraG [Rhizobium etli]
MGLRGKPHPSLLLVLVPIAVTTITIYVVGWRWPELAAGMSGKIGYSFLRAAPVPPLLFGPLAGLLTVWAL
PLHRRRPVAMASLLCFLGVAAFYALREFGRLAPAVQARVVPWDRALSYVDMVAVIAAVAGFLAVAVSARI
SVVVPDEIKRARRGIFGDADWLPMAAAGKLFPPDGEIVVGERYRVDREIVHALPFDANDRSTWGQGGKAP
LLTYKQDFDSTHMLFFAGSGGYKTTSNVVPTALKYTGPLICLDPSTEVAPIVVEHRTNALRREVMVLDPT
NPTMGFNVLDGIETSSQKEEDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYAGRRN
LRSLREIVSEPEPSVLATLRDIQENSQADFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKPSDIVSGRKDVFLNIPASILRSYPGIGRVIIGSLINAMMQADGAFRRRTLFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIEGCAFASYAAIKALDTARSVSAQCGEMTVEVKG
SSRNLGWDKRAAGPRKSESISFQRRPLIMPHEITQSMRKDEQIIVVQGHSPIRCGRAIYFRRKEMDAVAK
ANRFVKSIT

  Protein domains


Predicted by InterproScan.

(171-635)

  Protein structure



No available structure.




T4SS


T4SS were predicted by using oriTfinder2.

Region 1: 292877..307414

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NXC12_RS33705 (NXC12_PE00263) 288556..288723 - 168 WP_016735266 hypothetical protein -
NXC12_RS29620 (NXC12_PE00264) 289038..289361 - 324 WP_008530485 DUF736 family protein -
NXC12_RS29625 (NXC12_PE00265) 289824..290156 + 333 WP_198388454 WGR domain-containing protein -
NXC12_RS29630 (NXC12_PE00266) 290291..290692 - 402 WP_086084182 type II toxin-antitoxin system VapC family toxin -
NXC12_RS29635 (NXC12_PE00267) 290692..290928 - 237 WP_086084183 type II toxin-antitoxin system VapB family antitoxin -
NXC12_RS29640 (NXC12_PE00268) 291516..292724 + 1209 WP_086084184 DUF1173 domain-containing protein -
NXC12_RS29645 (NXC12_PE00269) 292877..293908 - 1032 WP_086084185 P-type DNA transfer ATPase VirB11 virB11
NXC12_RS29650 (NXC12_PE00270) 293917..295092 - 1176 WP_086084186 type IV secretion system protein VirB10 virB10
NXC12_RS29655 (NXC12_PE00271) 295101..295958 - 858 WP_086084187 P-type conjugative transfer protein VirB9 virB9
NXC12_RS29660 (NXC12_PE00272) 295955..296626 - 672 WP_086084188 virB8 family protein virB8
NXC12_RS34310 (NXC12_PE00273) 296628..296912 - 285 WP_086084189 hypothetical protein -
NXC12_RS29670 (NXC12_PE00274) 296947..297879 - 933 WP_198388457 type IV secretion system protein virB6
NXC12_RS29675 (NXC12_PE00275) 297882..298115 - 234 WP_086084190 EexN family lipoprotein -
NXC12_RS29680 (NXC12_PE00276) 298112..298813 - 702 WP_157700475 P-type DNA transfer protein VirB5 virB5
NXC12_RS29685 (NXC12_PE00277) 298810..301176 - 2367 WP_086084191 VirB4 family type IV secretion system protein virb4
NXC12_RS29690 (NXC12_PE00278) 301169..301507 - 339 WP_086084192 type IV secretion system protein VirB3 virB3
NXC12_RS29695 (NXC12_PE00279) 301513..301812 - 300 WP_086084193 TrbC/VirB2 family protein virB2
NXC12_RS29700 (NXC12_PE00280) 301809..302468 - 660 WP_086084194 lytic transglycosylase domain-containing protein virB1
NXC12_RS29705 (NXC12_PE00281) 302472..303008 - 537 WP_086084195 hypothetical protein -
NXC12_RS29710 (NXC12_PE00282) 303107..303472 + 366 WP_020919765 MarR family transcriptional regulator -
NXC12_RS29715 303825..304107 + 283 Protein_290 HU family DNA-binding protein -
NXC12_RS34315 (NXC12_PE00284) 304162..304326 - 165 WP_244920145 hypothetical protein -
NXC12_RS33350 304736..305134 + 399 WP_157700476 hypothetical protein -
NXC12_RS29730 (NXC12_PE00286) 305131..306066 - 936 WP_086084517 DUF2493 domain-containing protein -
NXC12_RS29735 (NXC12_PE00287) 306380..307414 - 1035 WP_020919760 toprim domain-containing protein traP
NXC12_RS34655 (NXC12_PE00288) 307427..308200 - 774 WP_020919759 DUF6117 family protein -
NXC12_RS29745 (NXC12_PE00289) 308289..309479 - 1191 WP_020919758 hypothetical protein -
NXC12_RS29750 (NXC12_PE00290) 309556..310212 - 657 WP_020919757 hypothetical protein -
NXC12_RS29755 (NXC12_PE00291) 310285..312402 - 2118 WP_020919756 ParB/RepB/Spo0J family partition protein -


Host bacterium


ID   6056 GenBank   NZ_CP020911
Plasmid name   pRetNXC12e Incompatibility group   -
Plasmid size   978479 bp Coordinate of oriT [Strand]   284291..284319 [-]
Host baterium   Rhizobium etli strain NXC12

Cargo genes


Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   bphB, LinG, dxnH, bphC
Symbiosis gene   fixB, fixA, fixG, fixQ, fixO, fixN
Anti-CRISPR   AcrIIA9