Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106858
Name   oriT_pRtrCIAT899b in_silico
Organism   Rhizobium tropici CIAT 899
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_020061 (526427..526462 [+], 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_pRtrCIAT899b
ATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4526 GenBank   WP_004119830
Name   traA_RTCIAT899_RS22115_pRtrCIAT899b insolico UniProt ID   A0A6P1CE10
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122039.84 Da        Isoelectric Point: 10.0272

>WP_004119830.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVIPADAPSWLRTMIADR
SVSGASEAFWNSVEIFEKRVDAQLAKDVTVALPMELSSEQNIELVRDFIERHITSKGMIADWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKVAVTGPGGKPVRNDAGKIVYELWAGSLDDFNAFRDGWFACQNRHLARAG
LDLRVDGHSFEKQGINLTPTIHLGVGAKAIERKSAEAERAPSLERLELQEERRAENARRIQRRPELVLDL
ITREKSVFDERDVAKILHRYIDDAGLFQSLMARILQSPETLRLERERIEFSGGLRVPTKYTTRDLVRLEA
EMANRAIWLAQRSSHGVADAVREATFARHLRLADEQKTAIAHVTGGERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGILSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQMALFVE
AATKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYGELENIYRQREQWMREASLDLARGNIGRAVEAYR
AQGRVSGADLKADAVQALIADWNRDYDPQRSSLILAHLRRDVRMLNGMARAKLVERGLVADGFAFRTEDG
HRKFAAGDQIVFLKNEGSLGVKNGMLAKVVDATPGRIVAEVGDGEHRRQVTVEQRFYANLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDFGLYHGRRSFAKAGGLIPILSRRQAKETTLDYASGRFY
AQALRFADARGLHLVNVARTVVRDRIEWTVRQKSKLAALGARLAAIARRLGLSAGAAKTSQSHSMQEAKP
MVSGITTFPKSLEQVVEDLLAADAGLKKQWEEVSARFHLVYAQPEDAFKAVNVDAMLRNEAAAKSTITKI
GSEPETFGALKGKTGILAGRADKQAHERAVTNAPALARNLERYLRQRTEAEHKYDAEERAVRMKISLDIP
ALSPAAKQTLERVRDAIDRNDLPAGLENALADKMVKAELEGFARAVSERFGERTFLPLAAKDMTGQTFQS
VTSSMSAGQKAEVQSAWSTMRTVQQLSAHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

MobA/MobL family (MobA_MobL)

(17-243)

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

(860-955)

AAA domain (AAA_30)

(382-568)


  Protein structure


Source ID Structure
AlphaFold DB A0A6P1CE10


T4CP

ID   4592 GenBank   WP_004119814
Name   traG_RTCIAT899_RS22100_pRtrCIAT899b 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: 71115.08 Da        Isoelectric Point: 9.0145

>WP_004119814.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTRILLFVAPCALMMLMAIGMTGTELWLSHFGKSDAARQMLGRAGIALPYVAASVVGIIFLFASAGSARI
RTAGWGVVTGATATLVLAVLREASRLSAYLEQVPAGKTVFNYLDPATAIGAAAVLMSALFGMRVAIAGNA
TFARAEPKRIVGKRALHGEADWMKLSQAEKLFAESGGIVIGERYRVDRDSIAAPSFRADSAASWGAGGKS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVLKHRGDANRDVFVLDPK
HSEIGFNALDWIGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTTEND
QTLRQVRKNLSEPEPQLRQRLHEIYDDSNSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAAL
VSGTSFSTSDLADGKTDVFINIDLKTLETHAGLARVIIGAFLNAIYNRNGEMQGRALFLLDEVARLGYMR
ILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTVE
IDQVSRSVQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKGCVGAR
AFSKAANPAENSPDRPARSAASKADREQ

  Protein domains


Predicted by InterproScan.

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

(161-633)

  Protein structure



No available structure.



ID   4593 GenBank   WP_004119853
Name   t4cp2_RTCIAT899_RS22185_pRtrCIAT899b 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: 91767.71 Da        Isoelectric Point: 6.3780

>WP_004119853.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRAPDPSFADLVPYAGLVDNGVLLLKDGSLMAAWYFAGPDSESATALDRNELSRHINTILSRLG
SGWMIQVEAVRIPTFDYPSDNRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEVSRKKTYADTVLFIFKNAVREIEQYFANTLSIRRMETREALERGGARVARYDELLQFVRFCITG
DNHPIRLPDVPMFLDWIATAELEHGLTSKVESRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMNMVAETEEAIAQASSQLVAYGYYTPVIVL
FDHDREGLQEKAESIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDKGNSLLPLTLATGGDHYEIGGDAQEEAKALAFCPLSDLSSDSDRAWAAEWIEMLIALQGVTITPDHRN
AVSRQIGLMASAAGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEKDGLLLGSFQTFEIEELMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAASEPGTREFYERIGFNERQIEIVSNAIPKREYYVATSEGRRLFDMSLGP
VALSFVGASGKEDLKRIRTLSSKHGRDWPIHWLRTRGVQDAAALLNLE

  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: 531585..544823

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RTCIAT899_RS22120 (RTCIAT899_PB02875) 529850..530416 + 567 WP_004119831 conjugative transfer signal peptidase TraF -
RTCIAT899_RS22125 (RTCIAT899_PB02880) 530406..531569 + 1164 WP_004119833 conjugal transfer protein TraB -
RTCIAT899_RS22130 (RTCIAT899_PB02885) 531585..532193 + 609 WP_004119835 TraH family protein virB1
RTCIAT899_RS22135 (RTCIAT899_PB02890) 532457..532693 - 237 WP_004119837 helix-turn-helix transcriptional regulator -
RTCIAT899_RS22140 (RTCIAT899_PB02895) 532943..533257 + 315 WP_004119838 transcriptional repressor TraM -
RTCIAT899_RS22145 (RTCIAT899_PB02900) 533261..533929 - 669 WP_051043311 autoinducer binding domain-containing protein -
RTCIAT899_RS22150 (RTCIAT899_PB02905) 534013..535209 + 1197 WP_004110519 IS256 family transposase -
RTCIAT899_RS22155 (RTCIAT899_PB02910) 535491..536792 - 1302 WP_004119844 IncP-type conjugal transfer protein TrbI virB10
RTCIAT899_RS22160 (RTCIAT899_PB02915) 536803..537237 - 435 WP_004119847 conjugal transfer protein TrbH -
RTCIAT899_RS22165 (RTCIAT899_PB02920) 537241..538053 - 813 WP_004119849 P-type conjugative transfer protein TrbG virB9
RTCIAT899_RS22170 (RTCIAT899_PB02925) 538070..538732 - 663 WP_004119850 conjugal transfer protein TrbF virB8
RTCIAT899_RS22175 (RTCIAT899_PB02930) 538757..539935 - 1179 WP_004119851 P-type conjugative transfer protein TrbL virB6
RTCIAT899_RS22180 (RTCIAT899_PB02935) 539940..540743 - 804 WP_004119852 P-type conjugative transfer protein TrbJ virB5
RTCIAT899_RS22185 (RTCIAT899_PB02940) 540715..543171 - 2457 WP_004119853 conjugal transfer protein TrbE virb4
RTCIAT899_RS22190 (RTCIAT899_PB02945) 543181..543480 - 300 WP_004119854 conjugal transfer protein TrbD virB3
RTCIAT899_RS22195 (RTCIAT899_PB02950) 543473..543856 - 384 WP_004119857 TrbC/VirB2 family protein virB2
RTCIAT899_RS22200 (RTCIAT899_PB02955) 543846..544823 - 978 WP_004119858 P-type conjugative transfer ATPase TrbB virB11
RTCIAT899_RS22205 (RTCIAT899_PB02960) 544820..545458 - 639 WP_004119859 acyl-homoserine-lactone synthase TraI -
RTCIAT899_RS22210 (RTCIAT899_PB02965) 545837..547057 + 1221 WP_028755142 plasmid partitioning protein RepA -
RTCIAT899_RS22215 (RTCIAT899_PB02970) 547117..548091 + 975 WP_004119861 plasmid partitioning protein RepB -
RTCIAT899_RS22220 (RTCIAT899_PB02975) 548253..549467 + 1215 WP_004119862 plasmid replication protein RepC -

Host bacterium

ID   7295 GenBank   NC_020061
Plasmid name   pRtrCIAT899b Incompatibility group   -
Plasmid size   549467 bp Coordinate of oriT [Strand]   526427..526462 [+]
Host baterium   Rhizobium tropici CIAT 899

Cargo genes

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