Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114535
Name   oriT_pDR25-2 in_silico
Organism   Enterobacter sp. JH25
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP091321 (58787..58889 [+], 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_pDR25-2
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9312 GenBank   WP_016479978
Name   traI_L2Y28_RS24480_pDR25-2 insolico UniProt ID   A0A0G3B767
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189285.41 Da        Isoelectric Point: 6.0099

>WP_016479978.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWAAAMEKSQAKSTAHDILEPRG
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)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)

AAA domain (AAA_30)

(967-1150)


  Protein structure



No available structure.




T4CP

ID   10807 GenBank   WP_008324134
Name   traC_L2Y28_RS24395_pDR25-2 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.



ID   10808 GenBank   WP_016479979
Name   traD_L2Y28_RS24475_pDR25-2 insolico UniProt ID   _
Length   748 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 748 a.a.        Molecular weight: 83951.64 Da        Isoelectric Point: 5.1609

>WP_016479979.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISES
GEVVDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 58239..83410

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L2Y28_RS24285 53336..53659 + 324 WP_008324183 hypothetical protein -
L2Y28_RS24290 53721..54080 + 360 WP_015493069 hypothetical protein -
L2Y28_RS24295 54707..55081 + 375 WP_008324180 hypothetical protein -
L2Y28_RS24300 55135..55422 + 288 WP_008324178 hypothetical protein -
L2Y28_RS24305 55469..55813 + 345 WP_008324177 hypothetical protein -
L2Y28_RS24310 55899..56162 + 264 WP_008324174 hypothetical protein -
L2Y28_RS24315 56205..57035 + 831 WP_008324171 N-6 DNA methylase -
L2Y28_RS24320 57662..58192 + 531 WP_008324170 antirestriction protein -
L2Y28_RS24325 58239..58715 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
L2Y28_RS24330 59147..59539 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
L2Y28_RS24335 59728..60417 + 690 WP_008324166 hypothetical protein -
L2Y28_RS24340 60504..60728 + 225 WP_008324165 TraY domain-containing protein -
L2Y28_RS24345 60786..61136 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
L2Y28_RS24350 61287..61592 + 306 WP_016479987 type IV conjugative transfer system protein TraL traL
L2Y28_RS24355 61607..62173 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
L2Y28_RS24360 62160..62903 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
L2Y28_RS24365 62890..64284 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
L2Y28_RS24370 64306..64845 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
L2Y28_RS24375 64965..65189 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
L2Y28_RS24380 65193..65378 + 186 WP_008324139 hypothetical protein -
L2Y28_RS24385 65362..65763 + 402 WP_016479985 hypothetical protein -
L2Y28_RS24390 65753..66319 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
L2Y28_RS24395 66312..68942 + 2631 WP_008324134 type IV secretion system protein TraC virb4
L2Y28_RS24400 68939..69286 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
L2Y28_RS24405 69286..69933 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
L2Y28_RS24410 69936..70922 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
L2Y28_RS24415 70939..71568 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
L2Y28_RS24420 71565..73418 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
L2Y28_RS24425 73450..73638 + 189 WP_008324128 conjugal transfer protein TrbE -
L2Y28_RS24430 73669..74418 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
L2Y28_RS24435 74435..74683 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
L2Y28_RS24440 74673..75227 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
L2Y28_RS24445 75220..75648 + 429 WP_008324122 hypothetical protein -
L2Y28_RS24450 75635..77005 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
L2Y28_RS24455 77005..79827 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
L2Y28_RS24460 79849..80280 + 432 WP_008324118 entry exclusion protein -
L2Y28_RS24465 80355..80693 + 339 WP_032072912 tetratricopeptide repeat protein -
L2Y28_RS24470 80701..81030 + 330 WP_223856629 tetratricopeptide repeat protein -
L2Y28_RS24475 81164..83410 + 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   14970 GenBank   NZ_CP091321
Plasmid name   pDR25-2 Incompatibility group   IncFIB
Plasmid size   123729 bp Coordinate of oriT [Strand]   58787..58889 [+]
Host baterium   Enterobacter sp. JH25

Cargo genes

Drug resistance gene   sul1, rmtC, blaNDM-1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -