Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107448
Name   oriT_pRCCGE525b in_silico
Organism   Rhizobium jaguaris strain CCGE525
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP032696 (528397..528432 [+], 36 nt)
oriT length   36 nt
IRs (inverted repeats)      21..26, 31..36  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 36 nt

>oriT_pRCCGE525b
ATCCGAAGGGCGCAATTATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4987 GenBank   WP_120709148
Name   traA_CCGE525_RS36755_pRCCGE525b insolico UniProt ID   _
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122071.79 Da        Isoelectric Point: 9.8490

>WP_120709148.1 Ti-type conjugative transfer relaxase TraA [Rhizobium jaguaris]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKEGLLHEEFVIPADAPQWLREMVADR
SVSGASEAFWNSVEVFEKRVDAQLAKDMTIALPMELSTEQNIELVRDFVERHITSAGMVADWVYHDAPGN
PHVHLMTTLRPLAEDGFGAKKVALTGPDGKPIRNDAGKIVYELWAGSLDDFNAFRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIGLTPTIHLGVGAKAIERKSVETDWDISLERLELQDERRAENARRIQRRPELVLDL
ITREKSVFDERDVAKILHRYIDDAGLFQGLMARILQSPDTLRLERERIEFSSGARVPAKFTTRDLIRLEA
EMANRAIWLSQRSSHGVAGPVRQATFARHLHLSDEQKTAIAYATGGARIAAVIGRAGAGKTTTMKAAREA
WETAGYRVVGGALAGKAAEGLEKEAGILSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQMALFVE
AATKAGAKLVLVGDPEQLQPIEAGAAFRAIADRVGYTELETIYRQREQWMRDASLDLARGNIGKAVEAYR
APGHVNGADFKADAVQALIADWNRDYDPAKTSLILAHLRRDVRMLNEMARSKLVERGLVAEGFVFRTEDG
HRKFAAGDQVVFLRNEGSLRVKNGMLAKVVDAAPGRIVAEVGEGEHRRQVTVEQRFYANVDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHRDDLGLYYGRRSFAKAGGLIPILSRRQAKETTLDYASGRFY
GQALRFAEARGLNLVNVARTVVRDHLEWTVRQKSKLAELGARLAALAGKLGLSAAAVRTSQSHTIKESKP
MVSGITTFPRSLEQAVEDRLAADPGLKKQWEEVSNRFHIVYAQPEAAFKAAKVDTMLKDEAAAKSTIARI
GSEPEGFGALKGKTGILASRADKQNRERAVTNAPALARNLERYLRQRTEAECKYEVEERALRLKVSLDIP
ALTPVAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFARAVSERFGERTFLSLTAKSPNGQTFNA
VTTGMTAGQKAEVGSAWSSMRTVQRLSAHERAAESLTQTETLRQSKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-567)

MobA/MobL family (MobA_MobL)

(17-243)

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

(859-955)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)


  Protein structure



No available structure.




T4CP

ID   5195 GenBank   WP_120709145
Name   traG_CCGE525_RS36740_pRCCGE525b 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: 69775.91 Da        Isoelectric Point: 9.1987

>WP_120709145.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTRILLFVVPCALMISTAIGMTGIEKWLSAFGKTDTARQILGRVGIALPYIVASFEGIVLLFASAGSVRI
RTAGWGVVAGAIATVLVAVLREAMRLSAFREQVPAGRFLFNYLDPATAIGAAVVLMSALFGMRVVIAGNA
AFAKAEPKRIYGKRALHGEADWMKLSQAEQLFPEDGGIVIGERYRVDTDSVAAQSFRADRAETWGAGGTS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALIILDPSNEVAPMASKHRGGNRDVFILDPKH
SEIGFNALDWIGRFGGTKEEDIASVASWVVSDSGARGLRDDFFRASALQLLTALIADVCLSGHTIENDQT
LRQVRKNLSEPEPKLRERLQSIYDNSESDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAALVS
GTTFTTGDLAGGKTDVFINIDLKTLEMHSGLARVIIGSFLNAMCNLNGEIQGRTLFLLDEVARLGYMRIL
ETARDAGRKYGITLTMIYQSIGQMRETYGGRDATSKWFESASWISFAAINDPETADYISRRSGMTTVEID
QVSRSFQSRGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNPALRCGRAIWFRRRDMKDCINGKSF
QWGRKSITL

  Protein domains


Predicted by InterproScan.

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

(161-628)

  Protein structure



No available structure.



ID   5196 GenBank   WP_120709159
Name   t4cp2_CCGE525_RS36825_pRCCGE525b 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: 91980.91 Da        Isoelectric Point: 5.9945

>WP_120709159.1 conjugal transfer protein TrbE [Rhizobium jaguaris]
MVALKHFRTTGPSFADLVPYAGLIDNGVLLLKDGSLMAGWYFAGPDCESATDFERNELSRQINTVLSRLG
SGWMIQVEAVRIPTFDYPSDERCHFPDAVTRAIDVERRAHFAREHGHFESKHALVLTYRPLESKKTALSK
YIYSDEESRKKTYADTVLFIFKNAVREIEQYLANTLSIRRMGTRETVERGGERVARYDELLQFVRFCITG
ENHPIRLPEAPMYLDWIATAELEHGLTPKVESRFLGVIAIDGLPAESCPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQRGSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVIVL
FDRDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLVPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYDQAQIFA
FDKGNSLLPLTLATGGDHYEIGGDVQEEGRALAFCPLADLSGDADRAWAVEWIEMLVALQSVTITPDHRN
AISRQISLMASARGRSLSDFVSGVQMREIKDALYQYTVDGPMGQLLDAEEDGLSLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNQRQIEIVSNAIPKREYYVVTPEGRRLFDMAPGP
VALSFIGASGKHDLKRIRTLSSEHGRDWPIHWLQMRGVHDAASLLNFE

  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: 533554..545882

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CCGE525_RS36760 (CCGE525_36735) 531896..532384 + 489 WP_245472478 conjugative transfer signal peptidase TraF -
CCGE525_RS36765 (CCGE525_36740) 532374..533537 + 1164 WP_120709150 conjugal transfer protein TraB -
CCGE525_RS36770 (CCGE525_36745) 533554..534162 + 609 WP_120709151 TraH family protein virB1
CCGE525_RS36780 (CCGE525_36755) 534873..535109 - 237 WP_120709152 helix-turn-helix transcriptional regulator -
CCGE525_RS36785 (CCGE525_36760) 535359..535673 + 315 WP_120709153 transcriptional repressor TraM -
CCGE525_RS36790 (CCGE525_36765) 535677..536381 - 705 WP_120709220 autoinducer binding domain-containing protein -
CCGE525_RS36795 (CCGE525_36770) 536539..537840 - 1302 WP_120709154 IncP-type conjugal transfer protein TrbI virB10
CCGE525_RS36800 (CCGE525_36775) 537853..538290 - 438 WP_120709155 conjugal transfer protein TrbH -
CCGE525_RS36805 (CCGE525_36780) 538294..539112 - 819 WP_120709156 P-type conjugative transfer protein TrbG virB9
CCGE525_RS36810 (CCGE525_36785) 539130..539792 - 663 WP_120709157 conjugal transfer protein TrbF virB8
CCGE525_RS36815 (CCGE525_36790) 539817..540995 - 1179 WP_120709158 P-type conjugative transfer protein TrbL virB6
CCGE525_RS36820 (CCGE525_36795) 541000..541802 - 803 Protein_507 P-type conjugative transfer protein TrbJ -
CCGE525_RS36825 (CCGE525_36800) 541774..544230 - 2457 WP_120709159 conjugal transfer protein TrbE virb4
CCGE525_RS36830 (CCGE525_36805) 544240..544539 - 300 WP_120709160 conjugal transfer protein TrbD virB3
CCGE525_RS36835 (CCGE525_36810) 544532..544915 - 384 WP_120709161 TrbC/VirB2 family protein virB2
CCGE525_RS36840 (CCGE525_36815) 544905..545882 - 978 WP_120709162 P-type conjugative transfer ATPase TrbB virB11
CCGE525_RS36845 (CCGE525_36820) 545879..546517 - 639 WP_120709163 acyl-homoserine-lactone synthase TraI -
CCGE525_RS36850 (CCGE525_36825) 546893..548113 + 1221 WP_120709164 plasmid partitioning protein RepA -
CCGE525_RS36855 (CCGE525_36830) 548173..549147 + 975 WP_120709165 plasmid partitioning protein RepB -
CCGE525_RS36860 (CCGE525_36835) 549307..550563 + 1257 WP_120709166 plasmid replication protein RepC -

Host bacterium

ID   7883 GenBank   NZ_CP032696
Plasmid name   pRCCGE525b Incompatibility group   -
Plasmid size   550563 bp Coordinate of oriT [Strand]   528397..528432 [+]
Host baterium   Rhizobium jaguaris strain CCGE525

Cargo genes

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