Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107381
Name   oriT_pP10164-NDM in_silico
Organism   Leclercia adecarboxylata strain P10164
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KP900016 (66327..66429 [+], 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_pP10164-NDM
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4921 GenBank   WP_016479978
Name   traI_HTF08_RS00545_pP10164-NDM 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   5110 GenBank   WP_008324134
Name   traC_HTF08_RS00465_pP10164-NDM 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   5111 GenBank   WP_172686533
Name   traD_HTF08_RS00540_pP10164-NDM 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: 82184.75 Da        Isoelectric Point: 5.1609

>WP_172686533.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 65779..90904

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTF08_RS00355 (pP10164-NDM_0075) 60876..61199 + 324 WP_008324183 hypothetical protein -
HTF08_RS00360 (pP10164-NDM_0076) 61261..61620 + 360 WP_015493069 hypothetical protein -
HTF08_RS00365 (pP10164-NDM_0077) 62247..62621 + 375 WP_008324180 hypothetical protein -
HTF08_RS00370 (pP10164-NDM_0078) 62675..62962 + 288 WP_008324178 hypothetical protein -
HTF08_RS00375 (pP10164-NDM_0079) 63009..63353 + 345 WP_008324177 hypothetical protein -
HTF08_RS00380 (pP10164-NDM_0080) 63439..63702 + 264 WP_008324174 hypothetical protein -
HTF08_RS00385 (pP10164-NDM_0081) 63745..64575 + 831 WP_008324171 N-6 DNA methylase -
HTF08_RS00390 (pP10164-NDM_0083) 65202..65732 + 531 WP_008324170 antirestriction protein -
HTF08_RS00395 (pP10164-NDM_0084) 65779..66255 - 477 WP_008324168 transglycosylase SLT domain-containing protein -
HTF08_RS00400 (pP10164-NDM_0085) 66687..67079 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
HTF08_RS00405 (pP10164-NDM_0086) 67268..67957 + 690 WP_008324166 hypothetical protein -
HTF08_RS00410 (pP10164-NDM_0087) 68044..68268 + 225 WP_008324165 TraY domain-containing protein -
HTF08_RS00415 (pP10164-NDM_0088) 68326..68676 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
HTF08_RS00420 (pP10164-NDM_0089) 68827..69132 + 306 WP_016479987 type IV conjugative transfer system protein TraL traL
HTF08_RS00425 (pP10164-NDM_0090) 69147..69713 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
HTF08_RS00430 (pP10164-NDM_0091) 69700..70443 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
HTF08_RS00435 (pP10164-NDM_0092) 70430..71823 + 1394 Protein_89 F-type conjugal transfer pilus assembly protein TraB -
HTF08_RS00440 (pP10164-NDM_0094) 71845..72384 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
HTF08_RS00445 (pP10164-NDM_0095) 72504..72728 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
HTF08_RS00450 72732..72917 + 186 WP_008324139 hypothetical protein -
HTF08_RS00455 (pP10164-NDM_0096) 72901..73302 + 402 WP_016479985 hypothetical protein -
HTF08_RS00460 (pP10164-NDM_0097) 73292..73858 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
HTF08_RS00465 (pP10164-NDM_0098) 73851..76481 + 2631 WP_008324134 type IV secretion system protein TraC virb4
HTF08_RS00470 (pP10164-NDM_0100) 76478..76825 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
HTF08_RS00475 (pP10164-NDM_0101) 76825..77472 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
HTF08_RS00480 (pP10164-NDM_0102) 77475..78461 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
HTF08_RS00485 (pP10164-NDM_0103) 78478..79107 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTF08_RS00490 (pP10164-NDM_0104) 79104..80957 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTF08_RS00495 (pP10164-NDM_0105) 80989..81177 + 189 WP_008324128 conjugal transfer protein TrbE -
HTF08_RS00500 (pP10164-NDM_0106) 81208..81957 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
HTF08_RS00505 (pP10164-NDM_0107) 81974..82222 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
HTF08_RS00510 (pP10164-NDM_0108) 82212..82766 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTF08_RS00515 (pP10164-NDM_0109) 82759..83187 + 429 WP_008324122 hypothetical protein -
HTF08_RS00520 (pP10164-NDM_0110) 83174..84543 + 1370 Protein_106 conjugal transfer pilus assembly protein TraH -
HTF08_RS00525 (pP10164-NDM_0111) 84543..87365 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
HTF08_RS00530 (pP10164-NDM_0112) 87387..87818 + 432 WP_008324118 entry exclusion protein -
HTF08_RS00590 88035..88232 + 198 WP_239693874 hypothetical protein -
HTF08_RS00595 (pP10164-NDM_0113) 88240..88569 + 330 WP_223856629 hypothetical protein -
HTF08_RS00540 (pP10164-NDM_0114) 88703..90904 + 2202 WP_172686533 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   7818 GenBank   NZ_KP900016
Plasmid name   pP10164-NDM Incompatibility group   IncFII
Plasmid size   99276 bp Coordinate of oriT [Strand]   66327..66429 [+]
Host baterium   Leclercia adecarboxylata strain P10164

Cargo genes

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