Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105617
Name   oriT_pRetNXC12d in_silico
Organism   Rhizobium etli strain NXC12
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP020910 (520262..520303 [+], 42 nt)
oriT length   42 nt
IRs (inverted repeats)      23..28, 33..38  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 42 nt

>oriT_pRetNXC12d
GGATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACGCCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3813 GenBank   WP_086083973
Name   traA_NXC12_RS28120_pRetNXC12d insolico UniProt ID   _
Length   1102 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1102 a.a.        Molecular weight: 122143.35 Da        Isoelectric Point: 9.8828

>WP_086083973.1 Ti-type conjugative transfer relaxase TraA [Rhizobium etli]
MPAPHFSVSVVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFVVPTDAPEWLRSMIANR
SVSGASGAFWNRVEDFEKRSDAQLAKDVTIALPIELTAEQNIALVRDFVEQHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTADGFGAKKIAVTGPDGNPIRNDAGKIVYELWAGSIDDFNAFRDAWFACQNRHLALAG
LDIHVDGRSFKKQGIDFEPTIHLGVGTKAIERKADGASKPLELERLEFQDARRHENVRRIDRNPELVLAM
ILREKSVFDERDVAKILHRYVDDAALFQSLMIRILLCRETFRIEREQIVLASGIRVPAKYTTRGMIRLEA
EMANRAVWLSQRSSHGVRDAVLAATFARHEHLSEEQKIAIEHVASGERIAAVIGRAGAGKTTMMNAAREA
WEAAGYRVVGAALAGKAAEGLEKEAGIISRTLASWELRWNQGRDQLDGKTVFVLDEAGMVSSRQMALFVE
AVTKAGAKLVLIGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGKVGKAVDAYR
ANGKIIGSDLKADAVDNLIAAWDRDYDPAQTSLILAHLRRDVHMLNQMARIKLIERGVLDQGTMFKTADG
ERNFAVGDQIVFLKNEASLGVKNGMLAKVVEVGAGRITARIGDGENARLVLVEQRFYNNLDHGYATTIHK
SQGATVDQVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRPFAKNGGLIPILSRRNAKETTLDYEKSAFY
RQALRFAEARGLHIVNVARTVVRDRLEWIVNQKQKLANLGARLVAVAGRLGMVRGVAQSPTQNSAKEAKP
MVSGITTFAKSVDRAIEDKVAADPGLKKQWEEVSTRFHLVYAQPVSAFKAVNVDAMLKDETVAKSTLAKI
GSEPERFGALRGKTGILASRADREEREKAQTNAPALARNLERYLRQRAEAERKFEVEERADRLKVSIDIP
ALSPNAKQKLERVRDAIDRNDLPAGLEYALADKMVKAELEGFARAVSERFGERTFLSLAAKDANGQTFNA
VTSGMTAGQKAEVQAAWNSMRTVQQLAAHERTTEALKQAETLRQTKSQGLSP

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

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

(859-955)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-567)


  Protein structure



No available structure.




T4CP

ID   3817 GenBank   WP_157700458
Name   traG_NXC12_RS28105_pRetNXC12d insolico UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 71223.47 Da        Isoelectric Point: 8.8933

>WP_157700458.1 Ti-type conjugative transfer system protein TraG [Rhizobium etli]
MNRIVLLIAPVALMFLVTIGLTGIEHWLSGFGKTEAARQMLGRAGIALPYVAAALIGIVFLFATAGSIRI
KTAGWGVVAGDVATISVAIVREVIRLAALAEQIPAGKSILCYLDPATLIGTAAAAMSACFALRVALVGNA
AFASAEPKRIRGKRALHGEADWMKLADAEKLLADAGGIVVGERYRVDKDSTAARSFRADDPDTWGAGGKS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLIVLDPSNEVAPMVSAHRTRANRDLFVVDPK
NPETGFNALDWIGQFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTAIIADVCLSGHTEKEN
QTLRQVRANLSEPEPKLRQRLQEIYDNSDSDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYQNYAAL
VSGKTFSTGDLAVGSTDVFINIDLRTLETHAGLARVIIGSFLNAIYNRGGSMKRRALFLLDEVARLGYMR
ILETARDAGRKYGITLIMIYQSIGQMRETFGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTVE
IDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVGTN
GFHRLEETPGTYPIEPARSAASKTDREK

  Protein domains


Predicted by InterproScan.

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

(161-630)

  Protein structure



No available structure.



ID   3818 GenBank   WP_086083985
Name   t4cp2_NXC12_RS28200_pRetNXC12d insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91660.49 Da        Isoelectric Point: 6.2754

>WP_086083985.1 conjugal transfer protein TrbE [Rhizobium etli]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINTILSRLG
SGWMIQVEAVRIPTFDYPSDDHCHFPDAVTRAIDAERRAHFGREQGHFESKHALILTYRPLESKKTALSK
YIYSDDESRKKTYADTVLFIFKNAVREIEQYFANALSIRRMETREAVERGGERVARYDELLQFVRFSITG
ENHPIRLPGAPMYLDWLATAELEHGLTPKVESRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFLF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVIVL
FDNDREALQEKAEAIRRLIQAEGFGARIETLNATEAFLGSLPGNWYCNIREPLINTSNLADLVPLNSVWS
GNPTAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEHAQIFA
FDKGSALLPLTLAVGGEHYEIGGDHNGAERALAFCPLSELSNDADRAWATEWIEMLVALQGVAITPDHRN
AISRQIGLMASAAGRSLSDFVSGVQMRVIKDALHHYTVDGPMGQLLDAEQDGLSLVAVQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATHSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYQRIGFNERQIEIVSNAIPKREYYVVTPDGRRLFDIALGP
VALSFVGASGKEDLKRIRALRSEHGRDWPIHWLQLRGVHDAASLLNFE

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(191-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 525421..538461

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NXC12_RS28125 (NXC12_PD00495) 523688..524254 + 567 WP_086083974 conjugative transfer signal peptidase TraF -
NXC12_RS28130 (NXC12_PD00496) 524244..525404 + 1161 WP_086083975 conjugal transfer protein TraB -
NXC12_RS28135 (NXC12_PD00497) 525421..526032 + 612 WP_086083976 TraH family protein virB1
NXC12_RS28140 (NXC12_PD00498) 526049..526426 - 378 WP_086083977 DUF5615 family PIN-like protein -
NXC12_RS28145 (NXC12_PD00499) 526423..527055 - 633 WP_086083978 DUF433 domain-containing protein -
NXC12_RS28150 (NXC12_PD00500) 527235..527447 - 213 WP_085780566 helix-turn-helix transcriptional regulator -
NXC12_RS28155 (NXC12_PD00501) 527645..527962 + 318 WP_086083979 transcriptional repressor TraM -
NXC12_RS28160 (NXC12_PD00502) 527966..528670 - 705 WP_198388425 autoinducer binding domain-containing protein -
NXC12_RS28165 (NXC12_PD00504) 528977..530278 - 1302 WP_086083981 IncP-type conjugal transfer protein TrbI virB10
NXC12_RS28170 (NXC12_PD00505) 530290..530724 - 435 WP_086083982 conjugal transfer protein TrbH -
NXC12_RS28175 (NXC12_PD00506) 530728..531540 - 813 WP_086083983 P-type conjugative transfer protein TrbG virB9
NXC12_RS28180 (NXC12_PD00507) 531558..532220 - 663 WP_085780571 conjugal transfer protein TrbF virB8
NXC12_RS28185 (NXC12_PD00508) 532245..533423 - 1179 WP_086083984 P-type conjugative transfer protein TrbL virB6
NXC12_RS28195 (NXC12_PD00509) 533596..534399 - 804 WP_085780573 P-type conjugative transfer protein TrbJ virB5
NXC12_RS28200 (NXC12_PD00510) 534371..536827 - 2457 WP_086083985 conjugal transfer protein TrbE virb4
NXC12_RS28205 (NXC12_PD00511) 536837..537136 - 300 WP_085780575 conjugal transfer protein TrbD virB3
NXC12_RS28210 (NXC12_PD00512) 537129..537494 - 366 WP_085780576 TrbC/VirB2 family protein virB2
NXC12_RS28215 (NXC12_PD00513) 537484..538461 - 978 WP_086083986 P-type conjugative transfer ATPase TrbB virB11
NXC12_RS28220 (NXC12_PD00514) 538481..539098 - 618 WP_086083987 acyl-homoserine-lactone synthase TraI -
NXC12_RS28225 (NXC12_PD00515) 539488..540702 + 1215 WP_086083988 plasmid partitioning protein RepA -
NXC12_RS28230 (NXC12_PD00516) 540699..541724 + 1026 WP_086083989 plasmid partitioning protein RepB -
NXC12_RS28235 (NXC12_PD00518) 541881..543095 + 1215 WP_086083990 plasmid replication protein RepC -

Host bacterium

ID   6055 GenBank   NZ_CP020910
Plasmid name   pRetNXC12d Incompatibility group   -
Plasmid size   543095 bp Coordinate of oriT [Strand]   520262..520303 [+]
Host baterium   Rhizobium etli strain NXC12

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   linJ, dxnH
Symbiosis gene   nodA, nodB, nodM, nifX, nifN, nifE, nifK, nifD, nifH, nifS, nifW, fixA, fixB, fixC, fixX, nifA, nifB, nifZ, nifT, nodH, nodJ, nodI, nodU, nodS, nodC, nodD, mLTONO_5203
Anti-CRISPR   AcrIIA7