Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101484
Name   oriT_MRSN 11938|unnamed in_silico
Organism   Citrobacter freundii strain MRSN 11938
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JYFY02000008 (35450..35552 [-], 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_MRSN 11938|unnamed
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTTCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1327 GenBank   WP_022652257
Name   traI_TN42_RS27360_MRSN 11938|unnamed 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   946 GenBank   WP_023307203
Name   traD_TN42_RS27365_MRSN 11938|unnamed insolico UniProt ID   _
Length   733 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 733 a.a.        Molecular weight: 82212.80 Da        Isoelectric Point: 5.1609

>WP_023307203.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENVGQPQQPQQPQQ
PQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQAE
QDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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   947 GenBank   WP_008324134
Name   traC_TN42_RS27440_MRSN 11938|unnamed 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: 10974..36100

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
TN42_RS27365 (TN42_23490) 10974..13175 - 2202 WP_023307203 type IV conjugative transfer system coupling protein TraD virb4
TN42_RS31740 13309..13638 - 330 WP_223856629 hypothetical protein -
TN42_RS31745 13646..13984 - 339 WP_032072912 tetratricopeptide repeat protein -
TN42_RS27375 (TN42_23500) 14059..14490 - 432 WP_008324118 entry exclusion protein -
TN42_RS27380 (TN42_23505) 14512..17334 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
TN42_RS27385 (TN42_23510) 17334..18704 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
TN42_RS27390 (TN42_23515) 18691..19119 - 429 WP_008324122 hypothetical protein -
TN42_RS27395 (TN42_23520) 19112..19666 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
TN42_RS27400 (TN42_23525) 19656..19904 - 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
TN42_RS27405 (TN42_23530) 19921..20670 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
TN42_RS27410 (TN42_23535) 20701..20889 - 189 WP_008324128 conjugal transfer protein TrbE -
TN42_RS27415 (TN42_23540) 20921..22774 - 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
TN42_RS27420 (TN42_23545) 22771..23400 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
TN42_RS27425 (TN42_23550) 23417..24403 - 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
TN42_RS27430 (TN42_23555) 24406..25053 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
TN42_RS27435 (TN42_23560) 25053..25400 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
TN42_RS27440 (TN42_23565) 25397..28027 - 2631 WP_008324134 type IV secretion system protein TraC virb4
TN42_RS27445 (TN42_23570) 28020..28586 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
TN42_RS27450 (TN42_23575) 28576..28977 - 402 WP_008324137 hypothetical protein -
TN42_RS27455 (TN42_23580) 28961..29146 - 186 WP_022652254 hypothetical protein -
TN42_RS27460 (TN42_23585) 29150..29374 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
TN42_RS27465 (TN42_23590) 29494..30033 - 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
TN42_RS27470 (TN42_23595) 30055..31449 - 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
TN42_RS27475 (TN42_23600) 31436..32179 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
TN42_RS27480 (TN42_23605) 32166..32732 - 567 WP_008324158 type IV conjugative transfer system protein TraE traE
TN42_RS27485 (TN42_23610) 32747..33052 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
TN42_RS27490 (TN42_23615) 33203..33553 - 351 WP_008324162 type IV conjugative transfer system pilin TraA -
TN42_RS27495 (TN42_23620) 33611..33835 - 225 WP_008324165 TraY domain-containing protein -
TN42_RS27500 (TN42_23625) 33922..34611 - 690 WP_008324166 hypothetical protein -
TN42_RS27505 (TN42_23630) 34800..35192 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
TN42_RS27510 (TN42_23635) 35624..36100 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
TN42_RS27515 (TN42_23640) 36147..36677 - 531 WP_008324170 antirestriction protein -
TN42_RS27520 (TN42_23645) 37304..38134 - 831 WP_022652253 N-6 DNA methylase -
TN42_RS27525 (TN42_23650) 38177..38440 - 264 WP_008324174 hypothetical protein -
TN42_RS27530 (TN42_23655) 38526..38870 - 345 WP_022652252 hypothetical protein -
TN42_RS27535 (TN42_23660) 38917..39204 - 288 WP_008324178 hypothetical protein -
TN42_RS27540 (TN42_23665) 39258..39632 - 375 WP_008324180 hypothetical protein -
TN42_RS27545 (TN42_29070) 40353..40619 - 267 WP_022652251 hypothetical protein -
TN42_RS27550 (TN42_23675) 40681..41004 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   1928 GenBank   NZ_JYFY02000008
Plasmid name   MRSN 11938|unnamed Incompatibility group   IncFII
Plasmid size   51002 bp Coordinate of oriT [Strand]   35450..35552 [-]
Host baterium   Citrobacter freundii strain MRSN 11938

Cargo genes

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