Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105286
Name   oriT_pRHBSTW-00355_3 in_silico
Organism   Citrobacter freundii strain RHBSTW-00355
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056588 (47380..47482 [+], 103 nt)
oriT length   103 nt
IRs (inverted repeats)      89..94, 96..101  (AAATAA..TTATTT)
 28..33, 40..45  (GCAAAA..TTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 103 nt

>oriT_pRHBSTW-00355_3
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3617 GenBank   WP_016247523
Name   traI_HV173_RS26740_pRHBSTW-00355_3 insolico UniProt ID   _
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189271.47 Da        Isoelectric Point: 6.0696

>WP_016247523.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKYISPGRKYPQLHVALPAFDRNGRKAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLEGEARPWN
PGAITGGRVWADGLPDATGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDRPAGGADVAV
RDVVRDMDRIKETPASPLTLPDAPEERRRDEAVSQVVRESVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

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

(631-710)

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

(573-625)

DNA helicase TraI (TraI_C)

(1430-1551)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(967-1150)


  Protein structure



No available structure.




T4CP

ID   3582 GenBank   WP_016247530
Name   traC_HV173_RS26650_pRHBSTW-00355_3 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 98887.60 Da        Isoelectric Point: 5.7673

>WP_016247530.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNPLDSVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRKRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDALYPTERELDPLKDLNYQCVDDTFDLKVKADYMTLGLRGNGRNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPCVAQEAKEWGD
LRQRLSSGQSSLVSYFLNVTLFCRDDQETALKVEQDVLNSFRKNGFELISPRFNHMRNFLVNLPFMAGGG
LFKQLRESGVLQRAESFNVANLMPVVADSPLATSGLLAPTYRNQLAFIDLFSRGMGNTNFNMAVCGTSGA
GKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLKFNPFANVTDDTIDEMAERLRDQL
SVMASPNGNLDEVHEGLLLKAVKATWLTKKNQARIDDVVDYLMMARDSEEYSGSPTIRSRLDEMVVLLTQ
YTRDGVYGSYFNSDEPSLKDEARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDEG
WRLLDFKNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSETASSAARAAWGNSSYKIILKQSAKEFAK
YNQLYPDQYSQLQRDMIKGFGSAKDNWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFLQQRRRE
GLSIHEAVWELAWKKSGPEMAALERWLHEHEGKTIS

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(470-765)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   3583 GenBank   WP_181549191
Name   traD_HV173_RS26735_pRHBSTW-00355_3 insolico UniProt ID   _
Length   766 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 766 a.a.        Molecular weight: 86103.96 Da        Isoelectric Point: 5.1629

>WP_181549191.1 type IV conjugative transfer system coupling protein TraD [Citrobacter freundii]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQMLQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDAEVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPE
LKTKAEEAEQLPPGISESGEVVDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 46832..75725

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV173_RS26540 (HV173_26545) 41929..42252 + 324 WP_008324183 hypothetical protein -
HV173_RS27650 42314..42454 + 141 WP_016247538 hypothetical protein -
HV173_RS27655 42482..42673 + 192 WP_231371985 hypothetical protein -
HV173_RS26550 (HV173_26555) 43300..43674 + 375 WP_008324180 hypothetical protein -
HV173_RS26555 (HV173_26560) 43728..44015 + 288 WP_008324178 hypothetical protein -
HV173_RS26560 (HV173_26565) 44062..44406 + 345 WP_008324177 hypothetical protein -
HV173_RS26565 (HV173_26570) 44492..44755 + 264 WP_008324174 hypothetical protein -
HV173_RS26570 (HV173_26575) 44798..45628 + 831 WP_181549190 N-6 DNA methylase -
HV173_RS26575 (HV173_26580) 46255..46785 + 531 WP_008324170 antirestriction protein -
HV173_RS26580 (HV173_26585) 46832..47308 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
HV173_RS26585 (HV173_26590) 47740..48132 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
HV173_RS26590 (HV173_26595) 48321..49010 + 690 WP_008324166 hypothetical protein -
HV173_RS26595 (HV173_26600) 49097..49321 + 225 WP_008324165 TraY domain-containing protein -
HV173_RS26600 (HV173_26605) 49379..49729 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
HV173_RS26605 (HV173_26610) 49880..50185 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
HV173_RS26610 (HV173_26615) 50200..50766 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
HV173_RS26615 (HV173_26620) 50753..51496 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
HV173_RS26620 (HV173_26625) 51483..52877 + 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
HV173_RS26625 (HV173_26630) 52899..53438 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
HV173_RS26630 (HV173_26635) 53558..53782 + 225 WP_016247532 TraR/DksA C4-type zinc finger protein -
HV173_RS26635 (HV173_26640) 53786..53923 + 138 WP_016247531 hypothetical protein -
HV173_RS26640 (HV173_26645) 53955..54356 + 402 WP_008324137 hypothetical protein -
HV173_RS26645 (HV173_26650) 54346..54912 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
HV173_RS26650 (HV173_26655) 54905..57535 + 2631 WP_016247530 type IV secretion system protein TraC virb4
HV173_RS26655 (HV173_26660) 57532..57879 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
HV173_RS26660 (HV173_26665) 57879..58526 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
HV173_RS26665 (HV173_26670) 58529..59515 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
HV173_RS26670 (HV173_26675) 59532..60161 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV173_RS26675 (HV173_26680) 60158..62011 + 1854 WP_016247529 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV173_RS26680 (HV173_26685) 62043..62231 + 189 WP_008324128 conjugal transfer protein TrbE -
HV173_RS26685 (HV173_26690) 62262..63011 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
HV173_RS26690 (HV173_26695) 63028..63276 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
HV173_RS26695 (HV173_26700) 63266..63820 + 555 WP_016247528 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV173_RS26700 (HV173_26705) 63969..64574 - 606 WP_000509966 recombinase family protein -
HV173_RS26705 (HV173_26710) 64669..67566 + 2898 WP_001553819 Tn3-like element Tn5403 family transposase -
HV173_RS26710 (HV173_26715) 67542..67910 + 369 WP_249417279 conjugal transfer protein TrbF -
HV173_RS26715 (HV173_26720) 67897..69267 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
HV173_RS26720 (HV173_26725) 69267..72089 + 2823 WP_032432555 conjugal transfer mating-pair stabilization protein TraG traG
HV173_RS26725 (HV173_26730) 72111..72542 + 432 WP_008324118 entry exclusion protein -
HV173_RS26730 (HV173_26735) 72617..73291 + 675 WP_016247525 tetratricopeptide repeat protein -
HV173_RS26735 (HV173_26740) 73425..75725 + 2301 WP_181549191 type IV conjugative transfer system coupling protein TraD prgC

Host bacterium

ID   5724 GenBank   NZ_CP056588
Plasmid name   pRHBSTW-00355_3 Incompatibility group   IncFII
Plasmid size   84673 bp Coordinate of oriT [Strand]   47380..47482 [+]
Host baterium   Citrobacter freundii strain RHBSTW-00355

Cargo genes

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