Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121982
Name   oriT_pKOX_NDM1 in_silico
Organism   Klebsiella michiganensis E718
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_021501 (94490..94592 [-], 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_pKOX_NDM1
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13857 GenBank   WP_016479978
Name   traI_A225_RS30620_pKOX_NDM1 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   16225 GenBank   WP_016479979
Name   traD_A225_RS30625_pKOX_NDM1 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.



ID   16226 GenBank   WP_008324134
Name   traC_A225_RS30700_pKOX_NDM1 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: 69970..95140

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
A225_RS30625 (A225_NDM1p0410) 69970..72216 - 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4
A225_RS34985 72350..72679 - 330 WP_223856629 tetratricopeptide repeat protein -
A225_RS34990 72687..73025 - 339 WP_032072912 tetratricopeptide repeat protein -
A225_RS35070 73100..73315 - 216 WP_320077096 hypothetical protein -
A225_RS35075 73261..73530 - 270 WP_320077097 hypothetical protein -
A225_RS30640 (A225_NDM1p0415) 73552..76374 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
A225_RS30645 (A225_NDM1p0420) 76374..77744 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
A225_RS30650 (A225_NDM1p0430) 77731..78159 - 429 WP_008324122 hypothetical protein -
A225_RS30655 (A225_NDM1p0435) 78152..78706 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
A225_RS30660 (A225_NDM1p0440) 78696..78944 - 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
A225_RS30665 (A225_NDM1p0445) 78961..79710 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
A225_RS30670 (A225_NDM1p0450) 79741..79929 - 189 WP_008324128 conjugal transfer protein TrbE -
A225_RS30675 (A225_NDM1p0455) 79961..81814 - 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
A225_RS30680 (A225_NDM1p0460) 81811..82440 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
A225_RS30685 (A225_NDM1p0465) 82457..83443 - 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
A225_RS30690 (A225_NDM1p0470) 83446..84093 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
A225_RS30695 (A225_NDM1p0475) 84093..84440 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
A225_RS30700 (A225_NDM1p0480) 84437..87067 - 2631 WP_008324134 type IV secretion system protein TraC virb4
A225_RS30705 (A225_NDM1p0485) 87060..87626 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
A225_RS30710 (A225_NDM1p0490) 87616..88017 - 402 WP_016479985 hypothetical protein -
A225_RS32875 (A225_NDM1p0495) 88001..88186 - 186 WP_008324139 hypothetical protein -
A225_RS30715 88190..88414 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
A225_RS30720 (A225_NDM1p0500) 88534..89073 - 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
A225_RS30725 (A225_NDM1p0505) 89095..90489 - 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
A225_RS30730 (A225_NDM1p0510) 90476..91219 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
A225_RS30735 (A225_NDM1p0515) 91206..91772 - 567 WP_016247535 type IV conjugative transfer system protein TraE traE
A225_RS30740 (A225_NDM1p0520) 91787..92092 - 306 WP_016479987 type IV conjugative transfer system protein TraL traL
A225_RS30745 (A225_NDM1p0525) 92243..92593 - 351 WP_016247536 type IV conjugative transfer system pilin TraA -
A225_RS30750 (A225_NDM1p0530) 92651..92875 - 225 WP_008324165 TraY domain-containing protein -
A225_RS30755 92962..93651 - 690 WP_008324166 hypothetical protein -
A225_RS30760 (A225_NDM1p0535) 93840..94232 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
A225_RS30765 (A225_NDM1p0160) 94664..95140 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
A225_RS30770 (A225_NDM1p0540) 95187..95717 - 531 WP_008324170 antirestriction protein -
A225_RS30775 (A225_NDM1p0545) 96344..97174 - 831 WP_008324171 N-6 DNA methylase -
A225_RS34995 (A225_NDM1p0550) 97217..97393 - 177 WP_016479991 hypothetical protein -
A225_RS30785 (A225_NDM1p0555) 97565..97909 - 345 WP_008324177 hypothetical protein -
A225_RS30790 97956..98243 - 288 WP_008324178 hypothetical protein -
A225_RS30795 (A225_NDM1p0560) 98297..98671 - 375 WP_008324180 hypothetical protein -
A225_RS30800 (A225_NDM1p0565) 99298..99657 - 360 WP_015493069 hypothetical protein -
A225_RS34560 (A225_NDM1p0570) 99719..100042 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   22409 GenBank   NC_021501
Plasmid name   pKOX_NDM1 Incompatibility group   IncFIB
Plasmid size   110781 bp Coordinate of oriT [Strand]   94490..94592 [-]
Host baterium   Klebsiella michiganensis E718

Cargo genes

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