Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106438
Name   oriT_pHCG3 in_silico
Organism   Afipia carboxidovorans OM5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_015689 (110638..110673 [+], 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_pHCG3
GGACCAAGGGCGCAGTAATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4294 GenBank   WP_013913803
Name   traA_OCA5_RS17600_pHCG3 insolico UniProt ID   F8C170
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122204.40 Da        Isoelectric Point: 10.3675

>WP_013913803.1 Ti-type conjugative transfer relaxase TraA [Afipia carboxidovorans]
MAITHFTPQIISRADGRSAVLAAAYRHCAKMTYEAEARVVDYTGKRNMVHDEFVLPPDAPQWACAMMATR
SAAEVSAAFWNKLEAFEKRSDAQLSKEYIIALPIELTTAQNVALMRQFVAEHILSKGQVADWVYHDDPGN
PHVHLMTSLRPLTEDGFGPKRVHVVGEDGATLRGRTGKIVYKLWAGDKNDFLSVRQGWIDLQNHHLALAG
LDVRVDGRSYAERGIDVVPTTHIGVAAKAIERRARRQGRGPDLDRLRLFEDQRQVSAERIMRRPEIVLDI
VSREKSVFDERDVAKVLHRYVDDAGTFAMLLARILQSPDAIRLEREGIDFANGARRPARYTTRELIRVEA
DMAKRAVSLSGSSSFGVSDKIRNAVLSRHAMISGEQRSAIEHITAAGSAAAVVGRAGAGKTTMMRAAREV
WEAAGYRVVGGTLAGKAAEGLEKEAGIASRTLASWELAWSKGRSVLDNRTVFVLDEAGMVASRQMATFVE
AVSRAGAKLVLVGDPEQLQPIEAGAAFRALVDRIGYAELETIYRQKAQWMRDASLDLARGRVGKALAAYR
HYGRVMGSELKAQAVTSLIDDWSRDYDPKKSTLILAHLRRDVRALNEMARASLVSRGLVDAGHAFRTEDG
ERRFAAGDQIVFLRNEGSLGVKNGMIGHVVEAAQGRFTAEIGEGVHRRRVEVDQRFYRNVDHGYATTIHK
AQGATVDRVKVLASLSLDKHLTYVALTRHREDVALYYGRRSFGKAGGLVPLLSQRNAKETTLDYERGGLY
RDALRFAANRGLHVMRAARTLISDRLDWARRQRQRFDELAARLRAVGAHLGLLDRHHTAPLSRKKEIAPM
VPGVTTWPKSIAESVEDKIVADPACRKQWQDMSARFALVFSNPEVAFKAMNFDAVLHNPAMRKATLNRLA
KEPESFGDLRGAKGILTGQAAARERHEAETNVAALSRDIERYARLRNEATRKHDAEERALRLRVTIDVPA
LSPAATLVLERIRDAIDRNDIPNALAFALSDKMVSAEIEGFNKAVAERFGEGAFLHNRAKEPKGAAFDVA
AARLRENEKPALAAAWPLMRAGQHLAAHQKQSAEAAKRVESQRQVQSRGMAMK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(383-566)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

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

(858-954)


  Protein structure


Source ID Structure
AlphaFold DB F8C170


T4CP

ID   4315 GenBank   WP_013913800
Name   traG_OCA5_RS17585_pHCG3 insolico UniProt ID   _
Length   636 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 636 a.a.        Molecular weight: 68383.21 Da        Isoelectric Point: 9.3377

>WP_013913800.1 Ti-type conjugative transfer system protein TraG [Afipia carboxidovorans]
MSANKVALSIVPSALMIGGMVALRGHEQWLASLGKTPQAALLLGRTGIALPYLGAAAIGLVFLFASAGAR
AVRAAGWGVVAGAGAVIGFAGWTEAIRLLGFVDRVRNGSVLAYTDPAMLIGGLAVAGCGLFALRVAMSGN
AAFAAAAPRRVSGPRAIHGDAQWMTINEAGRLFPDTGGIVVGERYRVDKDVAGDHAFQVRDPESWGTGGR
APLLCFDASWGSTHGIVFAGSGGYKTTSVTIPTALKWGGALVALDPSAEVAPMVIGHRRKFGRDVFVLDP
KAPEIGFNALDWIGRFGGTKEEDIASVASWIMTDVAHTHSVRDDFFRASALQLLTALIADVCLSGRTEPK
DQHLRQVRANLSEPEPKLRERLQSIYDNSTSKFVKENVASFVNMTPETFSGVYANAVKETHWLSYENYAA
LVSGNSFATDELAAGAMDVFINLDLKTLENHPGLARLIIGSLMNAIYNRAGDVAGRTLFLLDEVARLGFM
RVLETARDAGRKYGITLLMLFQSIGQMREVYGGRDAASKWFESASWMSFSAINDPETAEYISRRCGDTTV
EVSQISRSSQAAGSSRTRSRLLSRRPLILPHEITQMRSDEQIVFTAGNPPLRCGRAIYFRRKEMTASVAA
NRYQAA

  Protein domains


Predicted by InterproScan.

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

(162-631)

  Protein structure



No available structure.



ID   4316 GenBank   WP_013913818
Name   t4cp2_OCA5_RS17680_pHCG3 insolico UniProt ID   _
Length   812 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 812 a.a.        Molecular weight: 91055.64 Da        Isoelectric Point: 5.9064

>WP_013913818.1 conjugal transfer protein TrbE [Afipia carboxidovorans]
MVALRQFRHVDPSFTDLLPYAGLVAPGIILLKDGSLMAGWYFAGPDSESSTDVERNEVSRLINAVLSRLG
SGWMIQVEAVRVPARAYPARSDCHFPDAVTRAIDDERRRRFEAESGHFESQHAMILTYRPPERRKSGLAR
YVYSDDESRSTSFADTTLAFFQTSIREVEQYLANVLSVRRMQTQEVADEGSVRRARYDELFQFIRFSITG
ENHPIRLPEIPMYLDFLVTAEFHHGLSPVVDDRYLAVVGIDGFPAESWPGILNGLDLMPLTYRWSSRFMF
LDDQEARARLERTRKKWQQKVRPFFDQLFQTQSRALDQDAMLMVAETEDAIGQASSGLVAYGYYTTVIVL
FDTDERRLRDKAEAVRRLVQAEGFGARIETLNATEAYLGSLPGNWYTNIREPLISTRNLADLIPLNAVWS
GSQTAPCPFYPPNSPPLMQVASGSTPFRMNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYAGAQLFC
FDKGRSMFPLTIAAGGDHYDVGGGEGLSFCPLAELKDDSDRAWAAEWIETLVALQGVKITPDHRNAITHQ
IALMAAARGRSISDFVSGVQFREIKDALHPYTVDGPMGHLLDAEQDGLLMSDFQTFEIETLMNMGERNLV
PVLLYLFRRIEKRLTGAPSLIILDEAWLMLGHPTFRDKIREWLKVLRKANCAVLLATQSISDAERSGIID
VLKESCPTKICLPNGAARETGTRDFYERIGFNERQIEIVATAIPKREYYVASPVGRRLFDMALGPITLSF
VGATGKDDLTRIAELRQQHGADWPARWLQARGVADADTLLSA

  Protein domains


Predicted by InterproScan.

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

(193-400)

TraG P-loop domain (P-loop_TraG)

(584-710)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 108113..132114

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OCA5_RS17565 (OCA5_pHCG300990) 104410..105339 + 930 WP_013913795 zincin-like metallopeptidase domain-containing protein -
OCA5_RS17570 (OCA5_pHCG301000) 106005..106358 + 354 WP_013913796 DUF736 domain-containing protein -
OCA5_RS19330 (OCA5_pHCG301010) 106694..106861 + 168 WP_013913797 hypothetical protein -
OCA5_RS17575 (OCA5_pHCG301020) 106969..107238 - 270 WP_340622491 WGR domain-containing protein -
OCA5_RS17580 (OCA5_pHCG301030) 107449..107979 - 531 WP_013913799 thermonuclease family protein -
OCA5_RS17585 (OCA5_pHCG301040) 108113..110023 - 1911 WP_013913800 Ti-type conjugative transfer system protein TraG virb4
OCA5_RS17590 (OCA5_pHCG301050) 110010..110225 - 216 WP_013913801 type IV conjugative transfer system coupling protein TraD -
OCA5_RS17595 (OCA5_pHCG301060) 110230..110499 - 270 WP_013913802 conjugal transfer protein TraC -
OCA5_RS17600 (OCA5_pHCG301070) 110749..114060 + 3312 WP_013913803 Ti-type conjugative transfer relaxase TraA -
OCA5_RS17605 (OCA5_pHCG301080) 114057..114587 + 531 WP_013913804 conjugative transfer signal peptidase TraF -
OCA5_RS17610 (OCA5_pHCG301090) 114589..115740 + 1152 WP_013913805 conjugal transfer protein TraB -
OCA5_RS17615 (OCA5_pHCG301100) 115751..116350 + 600 WP_013913806 TraH family protein virB1
OCA5_RS17620 (OCA5_pHCG301110) 116405..116671 - 267 WP_013913807 hypothetical protein -
OCA5_RS17625 (OCA5_pHCG301120) 116741..119737 - 2997 WP_041559704 hypothetical protein -
OCA5_RS17630 119692..119937 - 246 WP_041559705 filamentous hemagglutinin N-terminal domain-containing protein -
OCA5_RS17635 (OCA5_pHCG301150) 120994..121320 + 327 WP_013913809 transcriptional repressor TraM -
OCA5_RS17640 (OCA5_pHCG301160) 121338..122057 - 720 WP_013913810 autoinducer binding domain-containing protein -
OCA5_RS17645 (OCA5_pHCG301170) 122601..123899 - 1299 WP_013913811 IncP-type conjugal transfer protein TrbI virB10
OCA5_RS17650 (OCA5_pHCG301180) 123912..124352 - 441 WP_013913812 conjugal transfer protein TrbH -
OCA5_RS17655 (OCA5_pHCG301190) 124355..125191 - 837 WP_013913813 P-type conjugative transfer protein TrbG virB9
OCA5_RS17660 (OCA5_pHCG301200) 125215..125877 - 663 WP_013913814 conjugal transfer protein TrbF virB8
OCA5_RS17665 (OCA5_pHCG301210) 125895..127091 - 1197 WP_013913815 P-type conjugative transfer protein TrbL virB6
OCA5_RS17670 (OCA5_pHCG301220) 127098..127280 - 183 WP_013913816 entry exclusion protein TrbK -
OCA5_RS17675 (OCA5_pHCG301230) 127277..128080 - 804 WP_013913817 P-type conjugative transfer protein TrbJ virB5
OCA5_RS17680 (OCA5_pHCG301240) 128055..130493 - 2439 WP_013913818 conjugal transfer protein TrbE virb4
OCA5_RS17685 (OCA5_pHCG301250) 130502..130801 - 300 WP_013913819 conjugal transfer protein TrbD virB3
OCA5_RS17690 (OCA5_pHCG301260) 130794..131159 - 366 WP_013913820 TrbC/VirB2 family protein virB2
OCA5_RS17695 (OCA5_pHCG301270) 131149..132114 - 966 WP_041559706 P-type conjugative transfer ATPase TrbB virB11
OCA5_RS17700 (OCA5_pHCG301280) 132126..132752 - 627 WP_013913822 acyl-homoserine-lactone synthase TraI -

Host bacterium

ID   6875 GenBank   NC_015689
Plasmid name   pHCG3 Incompatibility group   -
Plasmid size   133057 bp Coordinate of oriT [Strand]   110638..110673 [+]
Host baterium   Afipia carboxidovorans OM5

Cargo genes

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