Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115814
Name   oriT_54A:C|unnamed2 in_silico
Organism   Enterobacter ludwigii strain 54A:C
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP134656 (73065..73151 [-], 87 nt)
oriT length   87 nt
IRs (inverted repeats)      28..35, 38..45  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 87 nt

>oriT_54A:C|unnamed2
CTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTGCTGATTGGCTCTTTAAATCATGCAGTTAGTTAAAAAGTAATGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10133 GenBank   WP_311382035
Name   traI_RIK68_RS24890_54A:C|unnamed2 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: 189200.57 Da        Isoelectric Point: 6.2072

>WP_311382035.1 conjugative transfer relaxase/helicase TraI [Enterobacter ludwigii]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYDTETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKATGFDIKAYREAADLRVEQGNIPVTAPEAIDINSSVGQSIAMLSDRRARFTYSELLATTLGQLPARPG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRAGKADIFPEKGVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVHIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMTFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGLSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGMLHVAEGDRLAVLGQAQGTRLKGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVGQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGALLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERPDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLINRDIGSALTTIERVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTPEAQAQTIVITALNADRRQVNAMIHDARQDAGEVGEKEVTLPVL
TPANIRDGELRRMTTWEASRDSLVLLDSTYYSIEALDGEAHLVTLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGLAALSQIGLQPEGSMAKFISPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLGGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLVGEARPWN
PGAITGGRVWADSLPDSTGTQPGETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDGPAGGADVAV
RDVVRDMKRIKETPVSPLTLPDAPEERRRDEAVSQVVRENVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(967-1152)

DNA helicase TraI (TraI_C)

(1430-1551)

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

(573-625)

TrwC relaxase (TrwC)

(10-283)

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

(631-710)


  Protein structure



No available structure.




T4CP

ID   11838 GenBank   WP_311382034
Name   traD_RIK68_RS24895_54A:C|unnamed2 insolico UniProt ID   _
Length   734 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 734 a.a.        Molecular weight: 82090.63 Da        Isoelectric Point: 5.1609

>WP_311382034.1 type IV conjugative transfer system coupling protein TraD [Enterobacter ludwigii]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGVIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVIAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQLAPAPRAADTASASASAAGAGGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQA
EQDELSPLERQRREEVNINVHRAPEKDLEPGGYI

  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.



ID   11839 GenBank   WP_063925869
Name   traC_RIK68_RS24970_54A:C|unnamed2 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: 98769.44 Da        Isoelectric Point: 5.7676

>WP_063925869.1 type IV secretion system protein TraC [Enterobacter ludwigii]
MSNPLDTVTRTVNALVTALKMPDESAKANDVLGQMSFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRKRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDALYPTERELDPLKDLNYQCVDDSFDLKVKADYMTLGLRGNGRNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPGVAQEAKEWGD
LRQRLSSGQSSLVSYFLNVTLFCRDDQETALKVEQDVLNSFRKNGFELISPRFNHMRNFLVNLPFMAGGG
LFKQLRESGVVQRAESFNVANLMPVVADSPLATSGLLAPTYRNQLAFIDLFSRGMGNTNFNMAVCGTSGA
GKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLKFNPFANVTDDTIDEMAERLRDQL
SVMASPNGNLDEVHEGLLLKAVKATWLTKKNQARIDDVVDYLMMARDSEEYSGSPTIRSRLDEMVVLLTQ
YTRDGVYGSYFNSDEPSLKDEARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDEG
WRLLDFKNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSETASSAARAAWGNSSYKIILKQSAKEFAK
YNQLYPDQYSQLQRDMIKGFGSAKDNWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFLQQRRRE
GLSIHEAVWELAWKKSGPEMAALERWLHEHEGKTIS

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(38-276)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(470-765)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 48636..73699

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RIK68_RS24895 (RIK68_24895) 48636..50840 - 2205 WP_311382034 type IV conjugative transfer system coupling protein TraD virb4
RIK68_RS24900 (RIK68_24900) 51015..51746 - 732 WP_063925860 conjugal transfer complement resistance protein TraT -
RIK68_RS24905 (RIK68_24905) 51840..52151 + 312 WP_063925861 heavy metal-binding domain-containing protein -
RIK68_RS24910 (RIK68_24910) 52153..55011 - 2859 WP_063925862 conjugal transfer mating-pair stabilization protein TraG traG
RIK68_RS24915 (RIK68_24915) 55011..56381 - 1371 WP_059514056 conjugal transfer pilus assembly protein TraH traH
RIK68_RS24920 (RIK68_24920) 56368..56796 - 429 WP_063925863 hypothetical protein -
RIK68_RS24925 (RIK68_24925) 56789..57343 - 555 WP_063925864 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
RIK68_RS24930 (RIK68_24930) 57333..57581 - 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
RIK68_RS24935 (RIK68_24935) 57598..58347 - 750 WP_063925865 type-F conjugative transfer system pilin assembly protein TraF traF
RIK68_RS24940 (RIK68_24940) 58378..58566 - 189 WP_016674191 hypothetical protein -
RIK68_RS24945 (RIK68_24945) 58598..60478 - 1881 WP_063925866 type-F conjugative transfer system mating-pair stabilization protein TraN traN
RIK68_RS24950 (RIK68_24950) 60475..61104 - 630 WP_063925867 type-F conjugative transfer system pilin assembly protein TrbC trbC
RIK68_RS24955 (RIK68_24955) 61121..62107 - 987 WP_063925890 conjugal transfer pilus assembly protein TraU traU
RIK68_RS24960 (RIK68_24960) 62110..62757 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
RIK68_RS24965 (RIK68_24965) 62757..63104 - 348 WP_063925868 type-F conjugative transfer system protein TrbI -
RIK68_RS24970 (RIK68_24970) 63101..65731 - 2631 WP_063925869 type IV secretion system protein TraC virb4
RIK68_RS24975 (RIK68_24975) 65724..66290 - 567 WP_063925870 conjugal transfer protein TraP -
RIK68_RS24980 (RIK68_24980) 66280..66576 - 297 WP_063925891 hypothetical protein -
RIK68_RS24985 (RIK68_24985) 66749..66973 - 225 WP_016674195 TraR/DksA C4-type zinc finger protein -
RIK68_RS24990 (RIK68_24990) 67093..67632 - 540 WP_063925871 type IV conjugative transfer system lipoprotein TraV traV
RIK68_RS24995 (RIK68_24995) 67654..69048 - 1395 WP_063925872 F-type conjugal transfer pilus assembly protein TraB traB
RIK68_RS25000 (RIK68_25000) 69035..69778 - 744 WP_063925873 type-F conjugative transfer system secretin TraK traK
RIK68_RS25005 (RIK68_25005) 69765..70331 - 567 WP_025759824 type IV conjugative transfer system protein TraE traE
RIK68_RS25010 (RIK68_25010) 70346..70651 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
RIK68_RS25015 (RIK68_25015) 70802..71152 - 351 WP_058610053 type IV conjugative transfer system pilin TraA -
RIK68_RS25020 (RIK68_25020) 71210..71434 - 225 WP_008324165 TraY domain-containing protein -
RIK68_RS25025 (RIK68_25025) 71521..72210 - 690 WP_063925874 hypothetical protein -
RIK68_RS25030 (RIK68_25030) 72399..72791 - 393 WP_063925875 conjugal transfer relaxosome DNA-binding protein TraM -
RIK68_RS25035 (RIK68_25035) 73223..73699 + 477 WP_063925876 transglycosylase SLT domain-containing protein virB1
RIK68_RS25040 (RIK68_25040) 73746..74276 - 531 WP_311382033 antirestriction protein -
RIK68_RS25045 (RIK68_25045) 74903..75733 - 831 WP_063925878 N-6 DNA methylase -
RIK68_RS25050 (RIK68_25050) 75776..76039 - 264 WP_063925879 hypothetical protein -
RIK68_RS25055 (RIK68_25055) 76125..76469 - 345 WP_047359689 hypothetical protein -
RIK68_RS25060 (RIK68_25060) 76516..76806 - 291 WP_240474975 hypothetical protein -
RIK68_RS25065 (RIK68_25065) 76857..77231 - 375 WP_032637252 hypothetical protein -
RIK68_RS25070 (RIK68_25070) 77877..78251 - 375 WP_063925880 hypothetical protein -
RIK68_RS25075 (RIK68_25075) 78313..78636 - 324 WP_063925881 hypothetical protein -

Host bacterium

ID   16247 GenBank   NZ_CP134656
Plasmid name   54A:C|unnamed2 Incompatibility group   IncFII
Plasmid size   163991 bp Coordinate of oriT [Strand]   73065..73151 [-]
Host baterium   Enterobacter ludwigii strain 54A:C

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA7