Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121119
Name   oriT_pF2021-NDM in_silico
Organism   Citrobacter freundii strain F2021
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP137197 (33889..33991 [+], 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_pF2021-NDM
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13335 GenBank   WP_016479978
Name   traI_R4T18_RS24895_pF2021-NDM insolico UniProt ID   A0A0G3B767
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189285.41 Da        Isoelectric Point: 6.0099

>WP_016479978.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWAAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKYISPGRKYPQPHVALPAFDRNGRKAGVWLS
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)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)

AAA domain (AAA_30)

(967-1150)


  Protein structure



No available structure.




T4CP

ID   15623 GenBank   WP_008324134
Name   traC_R4T18_RS24810_pF2021-NDM 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: 98841.51 Da        Isoelectric Point: 5.7676

>WP_008324134.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacterales]
MSNPLDSVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRKRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDALYPTERELDPLKDLNYQCVDDTFDLKVKADYMTLGLRGNGRNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPGVAQEAKEWGD
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   15624 GenBank   WP_016479979
Name   traD_R4T18_RS24890_pF2021-NDM insolico UniProt ID   _
Length   748 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 748 a.a.        Molecular weight: 83951.64 Da        Isoelectric Point: 5.1609

>WP_016479979.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISES
GEVVDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 33341..58512

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R4T18_RS24700 (R4T18_24695) 28438..28761 + 324 WP_008324183 hypothetical protein -
R4T18_RS24705 (R4T18_24700) 28823..29182 + 360 WP_015493069 hypothetical protein -
R4T18_RS24710 (R4T18_24705) 29809..30183 + 375 WP_008324180 hypothetical protein -
R4T18_RS24715 (R4T18_24710) 30237..30524 + 288 WP_008324178 hypothetical protein -
R4T18_RS24720 (R4T18_24715) 30571..30915 + 345 WP_008324177 hypothetical protein -
R4T18_RS24725 (R4T18_24720) 31001..31264 + 264 WP_008324174 hypothetical protein -
R4T18_RS24730 (R4T18_24725) 31307..32137 + 831 WP_008324171 N-6 DNA methylase -
R4T18_RS24735 (R4T18_24730) 32764..33294 + 531 WP_008324170 antirestriction protein -
R4T18_RS24740 (R4T18_24735) 33341..33817 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
R4T18_RS24745 (R4T18_24740) 34249..34641 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
R4T18_RS24750 (R4T18_24745) 34830..35519 + 690 WP_008324166 hypothetical protein -
R4T18_RS24755 (R4T18_24750) 35606..35830 + 225 WP_008324165 TraY domain-containing protein -
R4T18_RS24760 (R4T18_24755) 35888..36238 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
R4T18_RS24765 (R4T18_24760) 36389..36694 + 306 WP_016479987 type IV conjugative transfer system protein TraL traL
R4T18_RS24770 (R4T18_24765) 36709..37275 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
R4T18_RS24775 (R4T18_24770) 37262..38005 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
R4T18_RS24780 (R4T18_24775) 37992..39386 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
R4T18_RS24785 (R4T18_24780) 39408..39947 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
R4T18_RS24790 (R4T18_24785) 40067..40291 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
R4T18_RS24795 (R4T18_24790) 40295..40480 + 186 WP_008324139 hypothetical protein -
R4T18_RS24800 (R4T18_24795) 40464..40865 + 402 WP_016479985 hypothetical protein -
R4T18_RS24805 (R4T18_24800) 40855..41421 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
R4T18_RS24810 (R4T18_24805) 41414..44044 + 2631 WP_008324134 type IV secretion system protein TraC virb4
R4T18_RS24815 (R4T18_24810) 44041..44388 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
R4T18_RS24820 (R4T18_24815) 44388..45035 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
R4T18_RS24825 (R4T18_24820) 45038..46024 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
R4T18_RS24830 (R4T18_24825) 46041..46670 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
R4T18_RS24835 (R4T18_24830) 46667..48520 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
R4T18_RS24840 (R4T18_24835) 48552..48740 + 189 WP_008324128 conjugal transfer protein TrbE -
R4T18_RS24845 (R4T18_24840) 48771..49520 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
R4T18_RS24850 (R4T18_24845) 49537..49785 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
R4T18_RS24855 (R4T18_24850) 49775..50329 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
R4T18_RS24860 (R4T18_24855) 50322..50750 + 429 WP_008324122 hypothetical protein -
R4T18_RS24865 (R4T18_24860) 50737..52107 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
R4T18_RS24870 (R4T18_24865) 52107..54929 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
R4T18_RS24875 (R4T18_24870) 54951..55382 + 432 WP_008324118 entry exclusion protein -
R4T18_RS24880 (R4T18_24875) 55457..55795 + 339 WP_032072912 tetratricopeptide repeat protein -
R4T18_RS24885 (R4T18_24880) 55803..56132 + 330 WP_223856629 tetratricopeptide repeat protein -
R4T18_RS24890 (R4T18_24885) 56266..58512 + 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21547 GenBank   NZ_CP137197
Plasmid name   pF2021-NDM Incompatibility group   IncFIB
Plasmid size   98831 bp Coordinate of oriT [Strand]   33889..33991 [+]
Host baterium   Citrobacter freundii strain F2021

Cargo genes

Drug resistance gene   sul1, rmtC, blaNDM-1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -