Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121009
Name   oriT_pSTW0522-27-3 in_silico
Organism   Citrobacter portucalensis strain STW0522-27
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP022397 (48985..49087 [+], 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_pSTW0522-27-3
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13257 GenBank   WP_200923074
Name   traI_JLF33_RS26250_pSTW0522-27-3 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: 189130.35 Da        Isoelectric Point: 6.0525

>WP_200923074.1 conjugative transfer relaxase/helicase TraI [Citrobacter portucalensis]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKATGFDIKAYREAADLRVEQGNIPVTAPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARPG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNILVLDELSVSAMTRDLQRTGQADIFPDKSVPHSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEARSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGMLHVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPVGDSPFTAAKVGQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMNKVPDAQLAGLTDGQQNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERPDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLINRDIGSALTTIERVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTPEAQAQTIVITALNADRRQVNAMIHDARQDAGEVGEKDVTLPVL
TPANIRDGELRRMTTWEASRDSLVLLDSTYYSIEALDGEAHLVTLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKFISPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLAGEARPWN
PGAITGGRVWADGLPDGTGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDGPAGGADVAV
RDVVRDMERIKETPASPLTLPDAPEERRRDEAVSQVVRENVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

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

(573-625)

AAA domain (AAA_30)

(967-1152)

TrwC relaxase (TrwC)

(10-283)

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

(631-710)

DNA helicase TraI (TraI_C)

(1430-1551)


  Protein structure



No available structure.




T4CP

ID   15537 GenBank   WP_008324134
Name   traC_JLF33_RS26170_pSTW0522-27-3 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   15538 GenBank   WP_008324910
Name   traD_JLF33_RS26245_pSTW0522-27-3 insolico UniProt ID   _
Length   730 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 730 a.a.        Molecular weight: 81859.42 Da        Isoelectric Point: 5.1609

>WP_008324910.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENVGQPQQPQQPQQ
PQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQAEQDE
LSPQERQRREEVNINVHRAPEKDLEPGGYI

  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: 48437..73553

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JLF33_RS26060 (STW0522CIT27_P30460) 43499..43822 + 324 WP_057069613 hypothetical protein -
JLF33_RS26065 (STW0522CIT27_P30470) 43884..44258 + 375 WP_032637367 hypothetical protein -
JLF33_RS26070 (STW0522CIT27_P30480) 44905..45279 + 375 WP_008324180 hypothetical protein -
JLF33_RS26075 (STW0522CIT27_P30490) 45333..45620 + 288 WP_008324178 hypothetical protein -
JLF33_RS26080 (STW0522CIT27_P30500) 45667..46011 + 345 WP_008324177 hypothetical protein -
JLF33_RS26085 (STW0522CIT27_P30510) 46097..46360 + 264 WP_008324174 hypothetical protein -
JLF33_RS26090 (STW0522CIT27_P30520) 46403..47233 + 831 WP_008324171 N-6 DNA methylase -
JLF33_RS26095 (STW0522CIT27_P30530) 47860..48390 + 531 WP_008324170 antirestriction protein -
JLF33_RS26100 (STW0522CIT27_P30540) 48437..48913 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
JLF33_RS26105 (STW0522CIT27_P30550) 49345..49737 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
JLF33_RS26110 (STW0522CIT27_P30560) 49926..50615 + 690 WP_200923072 PAS fold family protein -
JLF33_RS26115 (STW0522CIT27_P30570) 50702..50926 + 225 WP_008324165 TraY domain-containing protein -
JLF33_RS26120 (STW0522CIT27_P30580) 50984..51334 + 351 WP_008324162 type IV conjugative transfer system pilin TraA -
JLF33_RS26125 (STW0522CIT27_P30590) 51485..51790 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
JLF33_RS26130 (STW0522CIT27_P30600) 51805..52371 + 567 WP_008324158 type IV conjugative transfer system protein TraE traE
JLF33_RS26135 (STW0522CIT27_P30610) 52358..53101 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
JLF33_RS26140 (STW0522CIT27_P30620) 53088..54482 + 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
JLF33_RS26145 (STW0522CIT27_P30630) 54504..55043 + 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
JLF33_RS26150 (STW0522CIT27_P30640) 55163..55387 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
JLF33_RS26155 (STW0522CIT27_P30650) 55391..55576 + 186 WP_008324139 hypothetical protein -
JLF33_RS26160 (STW0522CIT27_P30660) 55560..55961 + 402 WP_008324137 hypothetical protein -
JLF33_RS26165 (STW0522CIT27_P30670) 55951..56517 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
JLF33_RS26170 (STW0522CIT27_P30680) 56510..59140 + 2631 WP_008324134 type IV secretion system protein TraC virb4
JLF33_RS26175 (STW0522CIT27_P30690) 59137..59484 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
JLF33_RS26180 (STW0522CIT27_P30700) 59484..60131 + 648 WP_200923073 type-F conjugative transfer system protein TraW traW
JLF33_RS26185 (STW0522CIT27_P30710) 60134..61120 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
JLF33_RS26190 (STW0522CIT27_P30720) 61137..61766 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
JLF33_RS26195 (STW0522CIT27_P30730) 61763..63616 + 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
JLF33_RS26200 (STW0522CIT27_P30740) 63648..63836 + 189 WP_008324128 conjugal transfer protein TrbE -
JLF33_RS26205 (STW0522CIT27_P30750) 63867..64616 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
JLF33_RS26210 (STW0522CIT27_P30760) 64633..64881 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
JLF33_RS26215 (STW0522CIT27_P30770) 64871..65425 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
JLF33_RS26220 (STW0522CIT27_P30780) 65418..65846 + 429 WP_008324122 hypothetical protein -
JLF33_RS26225 (STW0522CIT27_P30790) 65833..67203 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
JLF33_RS26230 (STW0522CIT27_P30800) 67203..70025 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
JLF33_RS26235 (STW0522CIT27_P30810) 70047..70478 + 432 WP_008324118 entry exclusion protein -
JLF33_RS26240 (STW0522CIT27_P30820) 70553..71227 + 675 WP_008324909 tetratricopeptide repeat protein -
JLF33_RS26245 (STW0522CIT27_P30830) 71361..73553 + 2193 WP_008324910 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21438 GenBank   NZ_AP022397
Plasmid name   pSTW0522-27-3 Incompatibility group   -
Plasmid size   82401 bp Coordinate of oriT [Strand]   48985..49087 [+]
Host baterium   Citrobacter portucalensis strain STW0522-27

Cargo genes

Drug resistance gene   -
Virulence gene   wzm, wbbM, glf, wbbN, wbbO
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -