Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120619
Name   oriT_pAUSMDU8141-2 in_silico
Organism   Citrobacter farmeri strain AUSMDU00008141
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP022697 (111399..111501 [-], 103 nt)
oriT length   103 nt
IRs (inverted repeats)      89..94, 96..101  (AAATAA..TTATTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 103 nt

>oriT_pAUSMDU8141-2
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTTCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12988 GenBank   WP_022652257
Name   traI_CI104_RS27650_pAUSMDU8141-2 insolico UniProt ID   A0A3S5I3M3
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189292.49 Da        Isoelectric Point: 6.1121

>WP_022652257.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMHT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVVPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
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)

AAA domain (AAA_30)

(967-1148)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)


  Protein structure



No available structure.




T4CP

ID   15250 GenBank   WP_022652256
Name   traD_CI104_RS27655_pAUSMDU8141-2 insolico UniProt ID   _
Length   736 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 736 a.a.        Molecular weight: 82566.18 Da        Isoelectric Point: 5.1609

>WP_022652256.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENVGQPQQPQQPQQ
PQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAW
QAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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   15251 GenBank   WP_008324134
Name   traC_CI104_RS27735_pAUSMDU8141-2 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 85760..112049

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CI104_RS27655 (CI104_27655) 85760..87970 - 2211 WP_022652256 type IV conjugative transfer system coupling protein TraD virb4
CI104_RS27660 (CI104_27660) 88104..88685 - 582 WP_240528006 tetratricopeptide repeat protein -
CI104_RS27665 (CI104_27665) 88666..89697 - 1032 WP_001395480 IS630-like element ISEc33 family transposase -
CI104_RS27670 (CI104_27670) 90008..90439 - 432 WP_008324118 entry exclusion protein -
CI104_RS27675 (CI104_27675) 90461..93283 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
CI104_RS27680 (CI104_27680) 93283..94653 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
CI104_RS27685 (CI104_27685) 94640..95068 - 429 WP_008324122 hypothetical protein -
CI104_RS27690 (CI104_27690) 95061..95615 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CI104_RS27695 (CI104_27695) 95605..95853 - 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
CI104_RS27700 (CI104_27700) 95870..96619 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
CI104_RS27705 (CI104_27705) 96650..96838 - 189 WP_008324128 conjugal transfer protein TrbE -
CI104_RS27710 (CI104_27710) 96870..98723 - 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CI104_RS27715 (CI104_27715) 98720..99349 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
CI104_RS27720 (CI104_27720) 99366..100352 - 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
CI104_RS27725 (CI104_27725) 100355..101002 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
CI104_RS27730 (CI104_27730) 101002..101349 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
CI104_RS27735 (CI104_27735) 101346..103976 - 2631 WP_008324134 type IV secretion system protein TraC virb4
CI104_RS27740 (CI104_27740) 103969..104535 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
CI104_RS27745 (CI104_27745) 104525..104926 - 402 WP_008324137 hypothetical protein -
CI104_RS27750 (CI104_27750) 104910..105095 - 186 WP_022652254 hypothetical protein -
CI104_RS27755 (CI104_27755) 105099..105323 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
CI104_RS27760 (CI104_27760) 105443..105982 - 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
CI104_RS27765 (CI104_27765) 106004..107398 - 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
CI104_RS27770 (CI104_27770) 107385..108128 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
CI104_RS27775 (CI104_27775) 108115..108681 - 567 WP_008324158 type IV conjugative transfer system protein TraE traE
CI104_RS27780 (CI104_27780) 108696..109001 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
CI104_RS27785 (CI104_27785) 109152..109502 - 351 WP_008324162 type IV conjugative transfer system pilin TraA -
CI104_RS27790 (CI104_27790) 109560..109784 - 225 WP_008324165 TraY domain-containing protein -
CI104_RS27795 (CI104_27795) 109871..110560 - 690 WP_008324166 hypothetical protein -
CI104_RS27800 (CI104_27800) 110749..111141 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
CI104_RS27805 (CI104_27805) 111573..112049 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
CI104_RS27810 (CI104_27810) 112096..112626 - 531 WP_008324170 antirestriction protein -
CI104_RS27815 (CI104_27815) 113253..114083 - 831 WP_022652253 N-6 DNA methylase -
CI104_RS27820 (CI104_27820) 114126..114389 - 264 WP_008324174 hypothetical protein -
CI104_RS27825 (CI104_27825) 114475..114819 - 345 WP_022652252 hypothetical protein -
CI104_RS27830 (CI104_27830) 114866..115153 - 288 WP_008324178 hypothetical protein -
CI104_RS27835 (CI104_27835) 115207..115581 - 375 WP_008324180 hypothetical protein -
CI104_RS27840 (CI104_27840) 116302..116568 - 267 WP_022652251 hypothetical protein -
CI104_RS27845 (CI104_27845) 116630..116953 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   21048 GenBank   NZ_CP022697
Plasmid name   pAUSMDU8141-2 Incompatibility group   IncFIB
Plasmid size   149207 bp Coordinate of oriT [Strand]   111399..111501 [-]
Host baterium   Citrobacter farmeri strain AUSMDU00008141

Cargo genes

Drug resistance gene   sul2, catA2, tet(D), blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -