Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108771
Name   oriT_pHCG3B in_silico
Organism   Afipia carboxidovorans OM4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_017536 (110636..110671 [+], 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_pHCG3B
GGACCAAGGGCGCAGTAATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5881 GenBank   WP_013913803
Name   traA_OCA4_RS17370_pHCG3B 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   6319 GenBank   WP_013913800
Name   traG_OCA4_RS17355_pHCG3B 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   6320 GenBank   WP_013913818
Name   t4cp2_OCA4_RS17450_pHCG3B 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: 108111..132112

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OCA4_RS17340 (OCA4_pHCG3B00990) 104408..105337 + 930 WP_013913795 zincin-like metallopeptidase domain-containing protein -
OCA4_RS17345 (OCA4_pHCG3B01000) 106003..106356 + 354 WP_013913796 DUF736 domain-containing protein -
OCA4_RS19220 106692..106859 + 168 WP_013913797 hypothetical protein -
OCA4_RS18780 (OCA4_pHCG3B01010) 106967..107212 - 246 WP_013913798 WGR domain-containing protein -
OCA4_RS17350 (OCA4_pHCG3B01020) 107447..107977 - 531 WP_013913799 thermonuclease family protein -
OCA4_RS17355 (OCA4_pHCG3B01030) 108111..110021 - 1911 WP_013913800 Ti-type conjugative transfer system protein TraG virb4
OCA4_RS17360 (OCA4_pHCG3B01040) 110008..110223 - 216 WP_013913801 type IV conjugative transfer system coupling protein TraD -
OCA4_RS17365 (OCA4_pHCG3B01050) 110228..110497 - 270 WP_013913802 conjugal transfer protein TraC -
OCA4_RS17370 (OCA4_pHCG3B01060) 110747..114058 + 3312 WP_013913803 Ti-type conjugative transfer relaxase TraA -
OCA4_RS17375 (OCA4_pHCG3B01070) 114055..114585 + 531 WP_013913804 conjugative transfer signal peptidase TraF -
OCA4_RS17380 (OCA4_pHCG3B01080) 114587..115738 + 1152 WP_013913805 conjugal transfer protein TraB -
OCA4_RS17385 (OCA4_pHCG3B01090) 115749..116348 + 600 WP_013913806 TraH family protein virB1
OCA4_RS17390 (OCA4_pHCG3B01100) 116403..116669 - 267 WP_013913807 hypothetical protein -
OCA4_RS17395 (OCA4_pHCG3B01110) 116739..119735 - 2997 WP_041559704 hypothetical protein -
OCA4_RS17400 119690..119935 - 246 WP_041559705 filamentous hemagglutinin N-terminal domain-containing protein -
OCA4_RS17405 (OCA4_pHCG3B01140) 120992..121318 + 327 WP_013913809 transcriptional repressor TraM -
OCA4_RS17410 (OCA4_pHCG3B01150) 121336..122055 - 720 WP_013913810 autoinducer binding domain-containing protein -
OCA4_RS17415 (OCA4_pHCG3B01160) 122599..123897 - 1299 WP_013913811 IncP-type conjugal transfer protein TrbI virB10
OCA4_RS17420 (OCA4_pHCG3B01170) 123910..124350 - 441 WP_013913812 conjugal transfer protein TrbH -
OCA4_RS17425 (OCA4_pHCG3B01180) 124353..125189 - 837 WP_013913813 P-type conjugative transfer protein TrbG virB9
OCA4_RS17430 (OCA4_pHCG3B01190) 125213..125875 - 663 WP_013913814 conjugal transfer protein TrbF virB8
OCA4_RS17435 (OCA4_pHCG3B01200) 125893..127089 - 1197 WP_013913815 P-type conjugative transfer protein TrbL virB6
OCA4_RS17440 (OCA4_pHCG3B01210) 127096..127278 - 183 WP_013913816 entry exclusion protein TrbK -
OCA4_RS17445 (OCA4_pHCG3B01220) 127275..128078 - 804 WP_013913817 P-type conjugative transfer protein TrbJ virB5
OCA4_RS17450 (OCA4_pHCG3B01230) 128053..130491 - 2439 WP_013913818 conjugal transfer protein TrbE virb4
OCA4_RS17455 (OCA4_pHCG3B01240) 130500..130799 - 300 WP_013913819 conjugal transfer protein TrbD virB3
OCA4_RS17460 (OCA4_pHCG3B01250) 130792..131157 - 366 WP_013913820 TrbC/VirB2 family protein virB2
OCA4_RS17465 (OCA4_pHCG3B01260) 131147..132112 - 966 WP_041559706 P-type conjugative transfer ATPase TrbB virB11
OCA4_RS17470 (OCA4_pHCG3B01270) 132124..132750 - 627 WP_013913822 acyl-homoserine-lactone synthase TraI -

Host bacterium

ID   9206 GenBank   NC_017536
Plasmid name   pHCG3B Incompatibility group   -
Plasmid size   133055 bp Coordinate of oriT [Strand]   110636..110671 [+]
Host baterium   Afipia carboxidovorans OM4

Cargo genes

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