Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106068
Name   oriT_pA23BA in_silico
Organism   Hafnia alvei strain A23BA
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP050151 (53837..53914 [-], 78 nt)
oriT length   78 nt
IRs (inverted repeats)      59..64, 73..78  (AAAACA..TGTTTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 78 nt

>oriT_pA23BA
CTCACCACCAAAAAGACCACACCCCTCGCAAAACTAAAGTTTCGCTGATTTCTCTTTTAAAACATAATCTTGTGTTTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4073 GenBank   WP_166493875
Name   traI_HBA19_RS21555_pA23BA insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 190811.68 Da        Isoelectric Point: 5.9345

>WP_166493875.1 conjugative transfer relaxase/helicase TraI [Hafnia alvei]
MMSFSQVKSAGGAAGYYTDKDNYYVLGSMDDRWHGEGAKLLGLEGSIDKDTFTRALKGLLPDGSDLSRLQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIEAHNRAVDVALKQVEALASTRTMRDGVSETVLTGNLV
IARFNHDTSRDQDPQLHTHSVVLNATRNEDKWQALSSDTVGKTGFSDNVLANQIAFGKIYRQALRTDVEA
MGYEVDVVGKHGMWEMRDVPVDVFSNRRKAIEEAVGADASLKSRDVAALDTRKSKEVLEPTQKMAEWLTT
LKTTGFDMEAYRKLADTRVQDGLTPAPLAQEPADVGLAVTQAISLLSERKTQFTYADVLAKTVGQLPALD
GVIQQARGGIDDAIARQQLIPLDKEKGIFTSDVHVLDELSIDALSKEVMRQGHVQVSPNSKIDRPAPYSD
AVSVLAQDKPPMAILSGAGGALVQRDRVAELVDLAHEQGREVQILAGDTKARGYLQQDAQLAKEAVLPKR
SMLDGTAFVPNSTLIVEQGEKLTLKEAVSLLDGAVRNNVQLLVMDSQQRSGTGSALNVLRDAGVNDYRYQ
GGKQIDAVVVGEADKNQRYAQLAHDYVAHLQAGGKGVVQTSGVREQDILTDTVRAELKTQGVLSLQDITV
PTLVPVWVDSKSRTVRDHYREGMVMEKWDGETKTHERFVIERVTGKTHSLTLRNEAGESQQIKLSALNSQ
WSLYRAQQLPVAVGEKLNVLGKMPEHKLRAGDELSVVSHAEGKLAVVRNGKGGSQSLPVGNSPFSAIKVG
HAWVEGLGRSVSDEATVFVAASNRDLDKMTLNQLSRSGAQIQMFSAQSPEKTAEKLARHPAFKVVTQQIK
TVAGESVLDDALQHQKTALNTPIQQAIHLAVPSLENQKLAFSRVSLLAAAQEFSNGKLTLPAIEQEVREQ
VKSGALIAVDVAQGHGNDLLVSRASFEAEKSIIRHIAEGKEAVTPLMSDVPERLLAGLTTGQQAATRMIL
ETPDRFVAVQGYAGVGKTTQFRAVMQAINTLPEERRPRVIGLGPTHRAVGEMRGAGLDAQTLASFLYDTA
QQQRQGETLDYRNTVFVVDESSMLGNTDMAKTYALIAAGGGRAVFSGDSDQLQPIAPGQPFKLQQTRSAA
DVAIMQEIVRQTPALRPAVYRMIERDISGALATVESVAPAQVPRQPGAWVPDSSVMEFTREQENAIREAI
QEAGDGLRIDEGKPTTLYESIVADYMGRTPDARAQTLIVTHLNDDRRAVNAMIHRARENAGELGDKTSIP
ILVTANVRDGELRRLSTWEEHRGDRVLMDNTYHQIADIDKQAELITLRDNAGNTRLLSPREAASEGVTLY
QQDVITVGVGDKMRFSKSDNERGYIANSVWTVSDIAGDGVTLTDGQQQRTVQPYRDEAQSHIDLAYAVTA
HGAQGASESFAIALEGTDGGRKQMVSFESVYVALSRSKQHVQVYTDNREGWVSAMGKTQGHRNAHDVLAP
RDERTVNNAERLMRQATPLPEVAVGRALLKQSGLQEGQSLARFIAPGRKYPQPHVALPAFDQNGKSAGVW
LAPMTQGDSLDAHALSTEGRVFGSEEAQFVALQASRNGENQLATTVREGVTLAARHPESGVVVRLSGDGR
PWNPAAMTGGKLWVDKVAEVTTGTATDTAADITPADVSDSRRAEELAREALEKQAEKTAQEMLGTGKPEQ
EVTLPDEKVKALVGDVIKGLAGTRDDKSPLPELPDARVQTEAVNKVVAENQQRERLQQLDNEVVRDLQRE
KTLGGD

  Protein domains


Predicted by InterproScan.

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(574-623)

TrwC relaxase (TrwC)

(11-282)

DNA helicase TraI (TraI_C)

(1432-1550)

AAA domain (AAA_30)

(968-1151)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(632-711)


  Protein structure



No available structure.




T4CP

ID   4088 GenBank   WP_166493876
Name   traD_HBA19_RS21560_pA23BA insolico UniProt ID   _
Length   740 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 740 a.a.        Molecular weight: 82853.21 Da        Isoelectric Point: 5.3256

>WP_166493876.1 type IV conjugative transfer system coupling protein TraD [Hafnia alvei]
MSFNAKDMTQGGQIAAMRFRMFGQIANIIFYCLFLLFLTITTLTLMFRLSWQTFINGIIYWWCRTLGPMR
ELMRSQPVYQIEYYGKKFPYNAQQILNDKYTLWCGEQLWTSFVIAAVVGGIVCTVTFFVASWILGHQGKK
QSEDEITGGRKLTDDPKEVAAMLKRDGNASDIKIEKLPLIKNSEIQNFCLHGTVGSGKSEFIRRLMNHAR
KRGDMVIVYDRSCEFVKSYYDPAKDKILNPLDARCANWDLWRECLTQPDFDNVANTLIPMGSSEDPFWQG
SGRTIFAEAGFRMRKDDDRSYAKLVDTLLSIKIDKLRAYLKSTPAANLVDEKIEKTAISIRAVLTNYVKA
IRYLQGIERNGEPFTIRDWMRGVREDGNNGWLFISSNADTHASLKPVISMWLSLAIRGLLAMGENRQRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVLGFQSYAQLEDIYGAKGAATLFDVLNTRAFFRSPSKQIA
DFAAGEIGEKEQLKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDIQTLPDLTCYITLPGPYPAVKLPL
KYQTRPKVAPEFIARTIDTDAETHLSAVLAAREEEGRGIAELFTPDAETAEPASTENEPVAETATQTRTT
PPVTPLREESAPKPAPKTSPKAAAASTTAASATAAAVVAPVGGVEQELEEHEEALPPGIDSQGELVDPDA
YERWQAEHEANGQRTMQRREEVNINHGQSSHDDVEVGDTF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.



ID   4089 GenBank   WP_166493884
Name   traC_HBA19_RS21620_pA23BA insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 98813.45 Da        Isoelectric Point: 5.4440

>WP_166493884.1 type IV secretion system protein TraC [Hafnia alvei]
MSALEKITDTVNSMLSALKMPDESTAANQILANMKFPQFSRLLPYRDYDEETGLFMNATTMGFVLEAQPL
VGANVQVVESLENLLRTKMPRGIPLSIHLMSSKQVGEGIEYGLREFSWSGEQAPKFNAITRAYYMRAAET
RFSLPDGMDLPLTLRNYRLIISCCVPSKKKSRADILELENRLKIIRASLHGASIHTQPVDAQGFINIVGE
MVNHDPDQLYPQRRELDTFMDLNYQCIDDSFDLKVKAECLTIGLRSGTQQKTSRARVLNFQLARNPEIAF
LWNSADNYSNLLTPELSIACPFIITLTLMVEDQVKSHSEANLKYLDLEKKSKTSYGKFFPGVEQEAKEWG
ELRQRLGGNQSSIVSYFMNITAFCEDDNEKALAYEQYILNSYRKNGFELTSPRFNHMRNFLSSLPFMAGE
GLFKELQAAGVIRRAETFNVANLMPVVADSPLAPSGLLAPTYRNQLAFIDLFYEGMNNTNFNMAVCGTSG
AGKTGLIQPLIRSVLDTGGFAWVFDMGDGYKSLCENMGGVYLDGDTLKFNPFANIINIDLSAERVRDQLS
VMASPNGNLDEVHEALLMRAVKAAWLSKQNKARIDDVVDYLEFSKNSDEYKDSPTIRSRLDEMIVLLDQY
TVKGTYGEYFNSDEPSLSEDARMVVLELGGLESRPSLLVAVMFSLIIYIGNRMYGTNRSVKKLNVIDEGW
KLLDFKNQKVGTFIEKGYRTARRHNGSYITITQNIVDFDSPEASSAARAAWGNSSYKAILKQSAKEFAKY
NQLYPDQFKPFERDMIAKFGSAKDQWFSSFMLSVEAHSSWHRLFVDPLSRAMYSSKEEDFEFIQTKRQEG
MGIHDAVYALACRNFPQEMASLEAWVDEHDNGSIK

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraC protein (TraC_F_IV)

(37-276)

TraG P-loop domain (P-loop_TraG)

(468-850)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 29888..54467

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HBA19_RS21560 (HBA19_21560) 29888..32110 - 2223 WP_166493876 type IV conjugative transfer system coupling protein TraD virb4
HBA19_RS21565 (HBA19_21565) 32251..32784 - 534 WP_166493877 conjugal transfer protein TraS -
HBA19_RS21570 (HBA19_21570) 32781..35633 - 2853 WP_166493878 conjugal transfer mating-pair stabilization protein TraG traG
HBA19_RS21575 (HBA19_21575) 35633..37003 - 1371 WP_166493879 conjugal transfer pilus assembly protein TraH traH
HBA19_RS21580 (HBA19_21580) 36990..37550 - 561 WP_166493923 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HBA19_RS21585 (HBA19_21585) 37543..37779 - 237 WP_046360173 type-F conjugative transfer system pilin chaperone TraQ -
HBA19_RS21590 (HBA19_21590) 37791..38516 - 726 WP_234608920 type-F conjugative transfer system pilin assembly protein TraF traF
HBA19_RS21595 (HBA19_21595) 38660..40462 - 1803 WP_206023462 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HBA19_RS21600 (HBA19_21600) 40485..41153 - 669 WP_240938381 type-F conjugative transfer system pilin assembly protein TrbC trbC
HBA19_RS21605 (HBA19_21605) 41186..42178 - 993 WP_166493882 conjugal transfer pilus assembly protein TraU traU
HBA19_RS21610 (HBA19_21610) 42175..42807 - 633 WP_166493883 type-F conjugative transfer system protein TraW traW
HBA19_RS21615 (HBA19_21615) 42811..43143 - 333 WP_166493925 type-F conjugative transfer system protein TrbI -
HBA19_RS21620 (HBA19_21620) 43197..45824 - 2628 WP_166493884 type IV secretion system protein TraC virb4
HBA19_RS21625 (HBA19_21625) 45881..46342 - 462 WP_166493885 hypothetical protein -
HBA19_RS21630 (HBA19_21630) 46345..46566 - 222 WP_166493886 TraR/DksA family transcriptional regulator -
HBA19_RS21635 (HBA19_21635) 46693..47229 - 537 WP_166493926 type IV conjugative transfer system lipoprotein TraV traV
HBA19_RS21640 (HBA19_21640) 47472..47840 - 369 WP_166493887 hypothetical protein -
HBA19_RS21645 (HBA19_21645) 47830..48273 - 444 WP_166493888 conjugal transfer protein TraP -
HBA19_RS21650 (HBA19_21650) 48266..49672 - 1407 WP_166493927 F-type conjugal transfer pilus assembly protein TraB traB
HBA19_RS21655 (HBA19_21655) 49669..50376 - 708 WP_240938383 type-F conjugative transfer system secretin TraK traK
HBA19_RS21660 (HBA19_21660) 50390..50956 - 567 WP_046360187 type IV conjugative transfer system protein TraE traE
HBA19_RS21665 (HBA19_21665) 50974..51279 - 306 WP_046360188 type IV conjugative transfer system protein TraL traL
HBA19_RS21670 (HBA19_21670) 51295..51660 - 366 WP_166493890 type IV conjugative transfer system pilin TraA -
HBA19_RS22000 51728..51895 - 168 WP_240938384 TraY domain-containing protein -
HBA19_RS21680 (HBA19_21680) 52269..52997 - 729 WP_166493892 PAS domain-containing protein -
HBA19_RS21685 (HBA19_21685) 53193..53576 - 384 WP_166493893 conjugal transfer relaxosome DNA-binding protein TraM -
HBA19_RS21690 (HBA19_21690) 53991..54467 + 477 WP_046360192 transglycosylase SLT domain-containing protein virB1
HBA19_RS21695 (HBA19_21695) 54690..55517 - 828 WP_046360193 DUF932 domain-containing protein -
HBA19_RS21700 (HBA19_21700) 55570..55806 - 237 WP_046360194 hypothetical protein -
HBA19_RS21705 (HBA19_21705) 55894..56256 - 363 WP_166493894 hypothetical protein -
HBA19_RS21710 (HBA19_21710) 57045..57470 - 426 WP_166493928 IS200/IS605 family transposase -
HBA19_RS21715 (HBA19_21715) 57642..58367 - 726 WP_166493895 plasmid SOS inhibition protein A -
HBA19_RS21720 (HBA19_21720) 58364..58768 - 405 WP_166493896 conjugation system SOS inhibitor PsiB family protein -

Host bacterium

ID   6505 GenBank   NZ_CP050151
Plasmid name   pA23BA Incompatibility group   IncFII
Plasmid size   85042 bp Coordinate of oriT [Strand]   53837..53914 [-]
Host baterium   Hafnia alvei strain A23BA

Cargo genes

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