oriTDB

Detailed information of oriT

oriT
Relaxase
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	101401
Name	oriT_pKP33.8_NDM-1
Organism	Klebsiella pneumoniae strain Kp33
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_VXIW01000008 (77440..77542 [-], 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_pKP33.8_NDM-1
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_F3Y18_RS27695_pKP33.8_NDM-1

ID	1283	GenBank	WP_016479978
Name	traI_F3Y18_RS27695_pKP33.8_NDM-1	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.

ID	894	GenBank	WP_073568742
Name	traD_F3Y18_RS27700_pKP33.8_NDM-1	UniProt ID	_
Length	757 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 757 a.a. Molecular weight: 85011.77 Da Isoelectric Point: 5.1609

                        >WP_073568742.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]

MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR

DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ

QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR

QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA

IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV

WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA

EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL

KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ

PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAE

QLPPGISESGEVVDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

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	895	GenBank	WP_008324134
Name	traC_F3Y18_RS27775_pKP33.8_NDM-1	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: 52892..78090

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
F3Y18_RS27700 (F3Y18_27705)	52892..55165	-	2274	WP_073568742	type IV conjugative transfer system coupling protein TraD	virb4
F3Y18_RS29240	55299..55628	-	330	WP_223856629	hypothetical protein	-
F3Y18_RS29245	55636..55974	-	339	WP_032072912	tetratricopeptide repeat protein	-
F3Y18_RS27710 (F3Y18_27715)	56049..56480	-	432	WP_008324118	entry exclusion protein	-
F3Y18_RS27715 (F3Y18_27720)	56502..59324	-	2823	WP_008324119	conjugal transfer mating-pair stabilization protein TraG	traG
F3Y18_RS27720 (F3Y18_27725)	59324..60694	-	1371	WP_016247527	conjugal transfer pilus assembly protein TraH	traH
F3Y18_RS27725 (F3Y18_27730)	60681..61109	-	429	WP_008324122	hypothetical protein	-
F3Y18_RS27730 (F3Y18_27735)	61102..61656	-	555	WP_008324125	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
F3Y18_RS27735 (F3Y18_27740)	61646..61894	-	249	WP_016479982	type-F conjugative transfer system pilin chaperone TraQ	-
F3Y18_RS27740 (F3Y18_27745)	61911..62660	-	750	WP_008324127	type-F conjugative transfer system pilin assembly protein TraF	traF
F3Y18_RS27745 (F3Y18_27750)	62691..62879	-	189	WP_008324128	conjugal transfer protein TrbE	-
F3Y18_RS27750 (F3Y18_27755)	62911..64764	-	1854	WP_016479983	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
F3Y18_RS27755 (F3Y18_27760)	64761..65390	-	630	WP_008324130	type-F conjugative transfer system pilin assembly protein TrbC	trbC
F3Y18_RS27760 (F3Y18_27765)	65407..66393	-	987	WP_042934586	conjugal transfer pilus assembly protein TraU	traU
F3Y18_RS27765 (F3Y18_27770)	66396..67043	-	648	WP_008324132	type-F conjugative transfer system protein TraW	traW
F3Y18_RS27770 (F3Y18_27775)	67043..67390	-	348	WP_008324133	type-F conjugative transfer system protein TrbI	-
F3Y18_RS27775 (F3Y18_27780)	67387..70017	-	2631	WP_008324134	type IV secretion system protein TraC	virb4
F3Y18_RS27780 (F3Y18_27785)	70010..70576	-	567	WP_008324135	conjugal transfer pilus-stabilizing protein TraP	-
F3Y18_RS29250	70566..70733	-	168	WP_223274120	Clp protease	-
F3Y18_RS27790 (F3Y18_27795)	70951..71136	-	186	WP_008324139	hypothetical protein	-
F3Y18_RS27795 (F3Y18_27800)	71140..71364	-	225	WP_008324141	TraR/DksA C4-type zinc finger protein	-
F3Y18_RS27800 (F3Y18_27805)	71484..72023	-	540	WP_016247533	type IV conjugative transfer system lipoprotein TraV	traV
F3Y18_RS27805 (F3Y18_27810)	72045..73439	-	1395	WP_016479986	F-type conjugal transfer pilus assembly protein TraB	traB
F3Y18_RS27810 (F3Y18_27815)	73426..74169	-	744	WP_008324157	type-F conjugative transfer system secretin TraK	traK
F3Y18_RS27815 (F3Y18_27820)	74156..74722	-	567	WP_016247535	type IV conjugative transfer system protein TraE	traE
F3Y18_RS27820 (F3Y18_27825)	74737..75042	-	306	WP_008324160	type IV conjugative transfer system protein TraL	traL
F3Y18_RS27825 (F3Y18_27830)	75193..75543	-	351	WP_016247536	type IV conjugative transfer system pilin TraA	-
F3Y18_RS27830 (F3Y18_27835)	75601..75825	-	225	WP_008324165	TraY domain-containing protein	-
F3Y18_RS27835 (F3Y18_27840)	75912..76601	-	690	WP_008324166	hypothetical protein	-
F3Y18_RS27840 (F3Y18_27845)	76790..77182	-	393	WP_008324167	conjugal transfer relaxosome DNA-binding protein TraM	-
F3Y18_RS27845 (F3Y18_27850)	77614..78090	+	477	WP_008324168	transglycosylase SLT domain-containing protein	virB1
F3Y18_RS27850 (F3Y18_27855)	78137..78667	-	531	WP_008324170	antirestriction protein	-
F3Y18_RS27855 (F3Y18_27860)	79294..80124	-	831	WP_008324171	N-6 DNA methylase	-
F3Y18_RS27860 (F3Y18_27865)	80167..80430	-	264	WP_008324174	hypothetical protein	-
F3Y18_RS27865 (F3Y18_27870)	80516..80860	-	345	WP_008324177	hypothetical protein	-
F3Y18_RS27870 (F3Y18_27875)	80907..81194	-	288	WP_008324178	hypothetical protein	-
F3Y18_RS27875 (F3Y18_27880)	81248..81622	-	375	WP_008324180	hypothetical protein	-
F3Y18_RS27880 (F3Y18_27885)	82249..82608	-	360	WP_015493069	hypothetical protein	-
F3Y18_RS28985 (F3Y18_27890)	82670..82993	-	324	WP_008324183	hypothetical protein	-

Host bacterium

ID	1845	GenBank	NZ_VXIW01000008
Plasmid name	pKP33.8_NDM-1	Incompatibility group	IncFIB
Plasmid size	101574 bp	Coordinate of oriT [Strand]	77440..77542 [-]
Host baterium	Klebsiella pneumoniae strain Kp33

Cargo genes

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