Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106857
Name   oriT_pRtrCIAT899a in_silico
Organism   Rhizobium tropici CIAT 899
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_020060 (193424..193467 [+], 44 nt)
oriT length   44 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: 44 nt

>oriT_pRtrCIAT899a
GGATCCGAAGGGCGCAATTATACGTCGCTGTCGCGACGCCCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4525 GenBank   WP_015341947
Name   traA_RTCIAT899_RS19530_pRtrCIAT899a insolico UniProt ID   A0A6P1C4N7
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122531.74 Da        Isoelectric Point: 9.5484

>WP_015341947.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVIPADAPEWLRSMIADR
SVSGASEAFWNMVEDFEKRSDAQLAKDVTIALPLELTPEQNIALVRDFVEQHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTADGFGAKKIAVTGPDGNPIRNDAGKIVYELWAGSIDDFNAFRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIDLEPTIHLGVGTKAIERKSDAASEPVELERLDLQEARRSENVRRIDRNPELVLAL
IMREKSVFDERDVAKILHRYVDDAALFQSLMVRILLCPETFRIEREGIDLASGIRVPAKYTTREMIRLEA
EMANRAVWLSQRSSHGVRDVVLAATFERHERLSDEQKTAIEHVAGPERIAAVIGRAGAGKTTMMRAAREA
WEAAGYHVVGGALAGKAAEGLEKEAGIISRTLASWELRWNQGRDQLDSKTVFVLDEAGMVSSRQMALFVE
AVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGKVGKAVDAYR
ANGRVIGSDLKADAVDNLIAAWDRDYNPAKTSLILAHLRRDVHMLNQMARIKLIERGVLDQGTMFKTADG
ERNFAVGDQIVFLKNEGSLGVKNGMLAKVMEVGAGRIIARIGDGENARQVLVEQRFYNNLDHGYATTIHK
SQGATVDQVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKNGGLIPILSRRNAKETTLDYEKSAFY
REALRFAEARGLNLANVARTLVRDRLEWVVGQKQKLAKLGVRLAAIAGKLGLVRVAAQSPTQNRTKEAKP
MVSGITTFAKSVEQAIEDKVAADPGLKKQWEEVSTRFHLVYAQPESAFKAVNVDAILKDETAQKSTLAKL
RTEPEHFGALKGKTGILASRSDREEREKAQTNAPALARNLERYLRQRAEAERKFEVEERAVRLKVSIDIP
ALSQSAKQTLERVRDAIDRNDLPAGLDYALADKMVKAELEGFAKAVSERFGERTFLSLTAKDPNGQTFNA
VTSGMTAGQKAEVQSAWNMMRTVQQLAAHERTTEALKHAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

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)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)


  Protein structure


Source ID Structure
AlphaFold DB A0A6P1C4N7


T4CP

ID   4590 GenBank   WP_015341945
Name   traG_RTCIAT899_RS19515_pRtrCIAT899a insolico UniProt ID   _
Length   657 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 657 a.a.        Molecular weight: 71402.16 Da        Isoelectric Point: 8.9869

>WP_015341945.1 Ti-type conjugative transfer system protein TraG [Rhizobium tropici]
MNRILLYVAPCALMMLTAIGMAGVEHWLSAFGKSDAAKQMLGRTGIALPYVVASLAGIVFLFASAGSARI
RSAGWGVFTGAIATLVVAILRETIRLSAFRGEVPAGKSILNYLDPATTIGAAAVLMSVLFGMRVAIAGNA
AFARSEPKRIYGKRALHGEADWMKLSQAEKLFDADGGMVIGERYRVDRDSVAAYAFRADSAETWGAGGTS
PLXCIDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVSKHRGDADRDVFVLDPK
RSEIGFNALDWIGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTPEND
QTLRQVRKNLSEPEPKLRERLQSIYDNSDSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAAL
VSGTSFTTQDLGEGKTDIFINVDLKTLETHSGLARVIIGSFLNAIYNRNGQMEGRTLFLLDEVARLGYMR
ILETARDAGRKYGITLLMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTVE
IDQVSRSSQASGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRREDMKRCVGTN
KFHQLKGRPDAHPIEPARSATSKADRA

  Protein domains


Predicted by InterproScan.

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

(161-633)

  Protein structure



No available structure.



ID   4591 GenBank   WP_015341956
Name   t4cp2_RTCIAT899_RS19610_pRtrCIAT899a 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: 91751.58 Da        Isoelectric Point: 5.9739

>WP_015341956.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMGGWYFAGPDSESATDLERNELSRQINTILSRLG
SGWMIQVEAVRIPTFDYPADDRCHFPDTVTRAIDAERRAHFAREQGHFESKHALVLTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVREIEQYLANTLSIRRMETREVVERGGERVARYDELLQFVRFCITG
ENHPIRLPDAPMYLDWIATAELEHGLTPKVESRFLGVVSIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSIDQDAMSMVAETEDAIAQASSQLVAYGYYTPVIVL
FDHDREALQEKAEAIRRLVQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDKGNSLLPLTLATGGDHYEIGGDAHEEGRALAFCPLSELASDGDRAWATEWIEMLVALQGVAITPDHRN
AISRQIGLMASAAGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLTLRAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIILDEAWLMLGHPVFRAKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSNATPKREYYVVTPEGRRLFDMALGP
VALSFVGASGKEELKRIGALTVEHGREWPIHWLQTRGVHDAASLLNVE

  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: 198588..211981

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RTCIAT899_RS19535 (RTCIAT899_PA01015) 196851..197417 + 567 WP_081598417 conjugative transfer signal peptidase TraF -
RTCIAT899_RS19540 (RTCIAT899_PA01020) 197407..198570 + 1164 WP_015341949 conjugal transfer protein TraB -
RTCIAT899_RS19545 (RTCIAT899_PA01025) 198588..199199 + 612 WP_015341950 TraH family protein virB1
RTCIAT899_RS19550 (RTCIAT899_PA01030) 199330..199746 + 417 WP_013984772 DUF6088 family protein -
RTCIAT899_RS19555 (RTCIAT899_PA01035) 199736..200647 + 912 WP_244441486 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
RTCIAT899_RS19560 (RTCIAT899_PA01040) 200713..200931 - 219 WP_015341952 helix-turn-helix transcriptional regulator -
RTCIAT899_RS19565 (RTCIAT899_PA01045) 201117..201437 + 321 WP_013984775 transcriptional repressor TraM -
RTCIAT899_RS19570 (RTCIAT899_PA01050) 201434..202147 - 714 WP_041678075 autoinducer binding domain-containing protein -
RTCIAT899_RS19575 (RTCIAT899_PA01055) 202471..203766 - 1296 WP_013984777 IncP-type conjugal transfer protein TrbI virB10
RTCIAT899_RS19580 (RTCIAT899_PA01060) 203784..204224 - 441 WP_013984778 conjugal transfer protein TrbH -
RTCIAT899_RS19585 (RTCIAT899_PA01065) 204228..205040 - 813 WP_015341954 P-type conjugative transfer protein TrbG virB9
RTCIAT899_RS19590 (RTCIAT899_PA01070) 205058..205720 - 663 WP_013984780 conjugal transfer protein TrbF virB8
RTCIAT899_RS19595 (RTCIAT899_PA01075) 205745..206923 - 1179 WP_013984781 P-type conjugative transfer protein TrbL virB6
RTCIAT899_RS19600 (RTCIAT899_PA01080) 206928..207104 - 177 WP_013984782 entry exclusion protein TrbK -
RTCIAT899_RS19605 (RTCIAT899_PA01085) 207098..207901 - 804 WP_015341955 P-type conjugative transfer protein TrbJ virB5
RTCIAT899_RS19610 (RTCIAT899_PA01090) 207873..210329 - 2457 WP_015341956 conjugal transfer protein TrbE virb4
RTCIAT899_RS19615 (RTCIAT899_PA01095) 210339..210638 - 300 WP_013984785 conjugal transfer protein TrbD virB3
RTCIAT899_RS19620 (RTCIAT899_PA01100) 210631..211014 - 384 WP_013984786 TrbC/VirB2 family protein virB2
RTCIAT899_RS19625 (RTCIAT899_PA01105) 211004..211981 - 978 WP_015341957 P-type conjugative transfer ATPase TrbB virB11
RTCIAT899_RS19630 (RTCIAT899_PA01110) 211992..212618 - 627 WP_015341958 acyl-homoserine-lactone synthase TraI -
RTCIAT899_RS19635 (RTCIAT899_PA01115) 213007..214221 + 1215 WP_013984789 plasmid partitioning protein RepA -
RTCIAT899_RS19640 (RTCIAT899_PA01120) 214218..215243 + 1026 WP_013984790 plasmid partitioning protein RepB -
RTCIAT899_RS19645 (RTCIAT899_PA01125) 215399..216610 + 1212 WP_013984791 plasmid replication protein RepC -

Host bacterium

ID   7294 GenBank   NC_020060
Plasmid name   pRtrCIAT899a Incompatibility group   -
Plasmid size   216610 bp Coordinate of oriT [Strand]   193424..193467 [+]
Host baterium   Rhizobium tropici CIAT 899

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -