Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119558
Name   oriT_2023CK-01304|unnamed2 in_silico
Organism   Citrobacter amalonaticus strain 2023CK-01304
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140491 (31467..31569 [+], 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_2023CK-01304|unnamed2
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12358 GenBank   WP_032432552
Name   traI_U4W25_RS00370_2023CK-01304|unnamed2 insolico UniProt ID   A0A0N8IRM5
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189145.31 Da        Isoelectric Point: 6.0696

>WP_032432552.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERSNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRSATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKYISPGRKYPQLHVALPAFDRNGRKAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLEGEARPWN
PGAITGGRVWADGLPDATGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDRPAGGADVAV
RDVVRDMDRIKETPASPLTLPDAPEERRRDEAVSQVVRESVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

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

(573-625)

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

(631-710)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(967-1150)

DNA helicase TraI (TraI_C)

(1430-1551)


  Protein structure



No available structure.




T4CP

ID   14506 GenBank   WP_323848174
Name   traC_U4W25_RS00290_2023CK-01304|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: 98899.55 Da        Isoelectric Point: 5.6505

>WP_323848174.1 type IV secretion system protein TraC [Citrobacter amalonaticus]
MSNPLDSVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDEETGLFMNEKTMGFMLEAQP
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   14507 GenBank   WP_016247524
Name   traD_U4W25_RS00365_2023CK-01304|unnamed2 insolico UniProt ID   _
Length   739 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 739 a.a.        Molecular weight: 82905.53 Da        Isoelectric Point: 5.1629

>WP_016247524.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDAEVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAW
EAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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: 30919..56062

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U4W25_RS00180 (U4W25_25765) 26017..26340 + 324 WP_008324183 hypothetical protein -
U4W25_RS00185 (U4W25_25770) 26402..26761 + 360 WP_015493069 hypothetical protein -
U4W25_RS00190 (U4W25_25775) 27387..27761 + 375 WP_008324180 hypothetical protein -
U4W25_RS00195 (U4W25_25780) 27815..28102 + 288 WP_008324178 hypothetical protein -
U4W25_RS00200 (U4W25_25785) 28149..28493 + 345 WP_008324177 hypothetical protein -
U4W25_RS00205 (U4W25_25790) 28579..28842 + 264 WP_008324174 hypothetical protein -
U4W25_RS00210 (U4W25_25795) 28885..29715 + 831 WP_008324171 N-6 DNA methylase -
U4W25_RS00215 (U4W25_25800) 30342..30872 + 531 WP_008324170 antirestriction protein -
U4W25_RS00220 (U4W25_25805) 30919..31395 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
U4W25_RS00225 (U4W25_25810) 31827..32219 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
U4W25_RS00230 (U4W25_25815) 32408..33097 + 690 WP_008324166 hypothetical protein -
U4W25_RS00235 (U4W25_25820) 33184..33408 + 225 WP_008324165 TraY domain-containing protein -
U4W25_RS00240 (U4W25_25825) 33466..33816 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
U4W25_RS00245 (U4W25_25830) 33967..34272 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
U4W25_RS00250 (U4W25_25835) 34287..34853 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
U4W25_RS00255 (U4W25_25840) 34840..35583 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
U4W25_RS00260 (U4W25_25845) 35570..36964 + 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
U4W25_RS00265 (U4W25_25850) 36986..37525 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
U4W25_RS00270 (U4W25_25855) 37645..37869 + 225 WP_016247532 TraR/DksA C4-type zinc finger protein -
U4W25_RS00275 (U4W25_25860) 37873..38058 + 186 WP_008324139 hypothetical protein -
U4W25_RS00280 (U4W25_25865) 38042..38443 + 402 WP_008324137 hypothetical protein -
U4W25_RS00285 (U4W25_25870) 38433..38999 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
U4W25_RS00290 (U4W25_25875) 38992..41622 + 2631 WP_323848174 type IV secretion system protein TraC virb4
U4W25_RS00295 (U4W25_25880) 41619..41966 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
U4W25_RS00300 (U4W25_25885) 41966..42613 + 648 WP_057064466 type-F conjugative transfer system protein TraW traW
U4W25_RS00305 (U4W25_25890) 42616..43602 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
U4W25_RS00310 (U4W25_25895) 43619..44248 + 630 WP_045890663 type-F conjugative transfer system pilin assembly protein TrbC trbC
U4W25_RS00315 (U4W25_25900) 44245..46098 + 1854 WP_016247529 type-F conjugative transfer system mating-pair stabilization protein TraN traN
U4W25_RS00320 (U4W25_25905) 46130..46318 + 189 WP_008324128 conjugal transfer protein TrbE -
U4W25_RS00325 (U4W25_25910) 46349..47098 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
U4W25_RS00330 (U4W25_25915) 47115..47363 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
U4W25_RS00335 (U4W25_25920) 47353..47907 + 555 WP_016247528 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
U4W25_RS00340 (U4W25_25925) 47900..48328 + 429 WP_008324122 hypothetical protein -
U4W25_RS00345 (U4W25_25930) 48315..49685 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
U4W25_RS00350 (U4W25_25935) 49685..52507 + 2823 WP_101724137 conjugal transfer mating-pair stabilization protein TraG traG
U4W25_RS00355 (U4W25_25940) 52553..52960 + 408 WP_323848175 entry exclusion protein -
U4W25_RS00360 (U4W25_25945) 53053..53709 + 657 WP_323848176 tetratricopeptide repeat protein -
U4W25_RS00365 (U4W25_25950) 53843..56062 + 2220 WP_016247524 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   19988 GenBank   NZ_CP140491
Plasmid name   2023CK-01304|unnamed2 Incompatibility group   IncFII
Plasmid size   65010 bp Coordinate of oriT [Strand]   31467..31569 [+]
Host baterium   Citrobacter amalonaticus strain 2023CK-01304

Cargo genes

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