Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102585
Name   oriT_pA12a in_silico
Organism   Rhizobium tropici strain A12
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAADZA010000008 (116967..117010 [-], 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_pA12a
GGATCCGAAGGGCGCAATTATACGTCGCTGTCGCGACGCCCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1933 GenBank   WP_015341947
Name   traA_GXW80_RS10330_pA12a 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   1562 GenBank   WP_015341956
Name   t4cp2_GXW80_RS10250_pA12a 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.



ID   1563 GenBank   WP_028003106
Name   traG_GXW80_RS10345_pA12a 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: 71430.45 Da        Isoelectric Point: 8.9869

>WP_028003106.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobiaceae]
MNRILLYVAPCALMMLTAIGMAGVEHWLSAFGKSDAAKQMLGRTGIALPYVVASLAGIVFLFASAGSARI
RSAGWGVFTGAIATLVVAILRETIRLSAFRGEVPAGKSILNYLDPATTIGAAAVLMSVLFGMRVAIAGNA
AFARSEPKRIYGKRALHGEADWMKLSQAEKLFDADGGMVIGERYRVDRDSVAAYAFRADSAETWGAGGTS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVSKHRGDADRDVFVLDPK
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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 98453..111846

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GXW80_RS10215 (GXW80_10215) 93824..95035 - 1212 WP_013984791 plasmid replication protein RepC -
GXW80_RS10220 (GXW80_10220) 95191..96216 - 1026 WP_013984790 plasmid partitioning protein RepB -
GXW80_RS10225 (GXW80_10225) 96213..97427 - 1215 WP_013984789 plasmid partitioning protein RepA -
GXW80_RS10230 (GXW80_10230) 97816..98442 + 627 WP_015341958 acyl-homoserine-lactone synthase TraI -
GXW80_RS10235 (GXW80_10235) 98453..99430 + 978 WP_015341957 P-type conjugative transfer ATPase TrbB virB11
GXW80_RS10240 (GXW80_10240) 99420..99803 + 384 WP_013984786 TrbC/VirB2 family protein virB2
GXW80_RS10245 (GXW80_10245) 99796..100095 + 300 WP_013984785 conjugal transfer protein TrbD virB3
GXW80_RS10250 (GXW80_10250) 100105..102561 + 2457 WP_015341956 conjugal transfer protein TrbE virb4
GXW80_RS10255 (GXW80_10255) 102533..103336 + 804 WP_015341955 P-type conjugative transfer protein TrbJ virB5
GXW80_RS10260 (GXW80_10260) 103330..103506 + 177 WP_013984782 entry exclusion protein TrbK -
GXW80_RS10265 (GXW80_10265) 103511..104689 + 1179 WP_013984781 P-type conjugative transfer protein TrbL virB6
GXW80_RS10270 (GXW80_10270) 104714..105376 + 663 WP_013984780 conjugal transfer protein TrbF virB8
GXW80_RS10275 (GXW80_10275) 105394..106206 + 813 WP_015341954 P-type conjugative transfer protein TrbG virB9
GXW80_RS10280 (GXW80_10280) 106210..106650 + 441 WP_013984778 conjugal transfer protein TrbH -
GXW80_RS10285 (GXW80_10285) 106668..107963 + 1296 WP_013984777 IncP-type conjugal transfer protein TrbI virB10
GXW80_RS10290 (GXW80_10290) 108287..109000 + 714 WP_041678075 autoinducer binding domain-containing protein -
GXW80_RS10295 (GXW80_10295) 108997..109317 - 321 WP_013984775 transcriptional repressor TraM -
GXW80_RS10300 (GXW80_10300) 109503..109721 + 219 WP_015341952 helix-turn-helix transcriptional regulator -
GXW80_RS10305 (GXW80_10305) 109787..110698 - 912 WP_244441486 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
GXW80_RS10310 (GXW80_10310) 110688..111104 - 417 WP_013984772 DUF6088 family protein -
GXW80_RS10315 (GXW80_10315) 111235..111846 - 612 WP_015341950 TraH family protein virB1
GXW80_RS10320 (GXW80_10320) 111864..113027 - 1164 WP_015341949 conjugal transfer protein TraB -
GXW80_RS10325 (GXW80_10325) 113017..113583 - 567 WP_081598417 conjugative transfer signal peptidase TraF -

Host bacterium

ID   3029 GenBank   NZ_JAADZA010000008
Plasmid name   pA12a Incompatibility group   -
Plasmid size   194114 bp Coordinate of oriT [Strand]   116967..117010 [-]
Host baterium   Rhizobium tropici strain A12

Cargo genes

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