Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 104239
• Name: oriT_pKp1050-2
• Organism: Klebsiella pneumoniae strain 1050
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP023418 (99843..99891 [-], 49 nt)
• oriT length: 49 nt
• IRs (inverted repeats): 6..13, 16..23 (GCAAAATT..AATTTTGC)
• Location of nic site: 32..33
• Conserved sequence flanking the nic site: TGTGTGGTGA
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 49 nt

>oriT_pKp1050-2
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_CN260_RS29415_pKp1050-2

• ID: 3115
• GenBank: WP_110522030
• Name: traI_CN260_RS29415_pKp1050-2
• UniProt ID: _
• Length: 1752 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1752 a.a.
• Molecular weight: 189752.39 Da
• Isoelectric Point: 5.9228

>WP_110522030.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSQVKSAGSAGNYYTEKDNYYVTGSMEERWQGKGAETLELEGKVDKQVFTALLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALEQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKETIDPAEKMVEWMNT
LKETGFDIRGYREAADARAKELASAPAAPVKTDGPDIGDVVTNAIAGLSDRKVQFTYADLLARTVGQLEA
KPGVFERARGGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVTVTPDATVVRLAPF
SDAVSVLAQDRPAMGIVSGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQNGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGRQTTADIISEPDKGARYNRLAQEFAVSVREGQESVAQISGTREQGVLNGIIRDTLKNEGALGTKEM
AITALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLRDKEGERLDLKVSAVD
SQWSLFRADKLPVANGERLSVLGKIPETRLKGGESITVLNAEAGQLTVQRPGQKTTQALSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDATRTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIATQKAGLHTPAEQVIHLSIPLLESEALTFTRPQLLATALETGGGKVPMTEIDATIQ
AQIKAGSLLNVPVAPGQGNDLLISRQTWDAEKSILTKVLEGKDAVPPLMDSVPGSLMADLTSGQRAATRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQAPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPAQEKAIQK
ALSEGEILPVGQPATLYEALVKDYADRTPEAQLQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKAVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAITA
HGAQGASEPYAIALEGVTGGRKQMASFESAYVGLSRMKLHVQVYTDSREGWVNAIQASPSKATAHDILAP
RNERAVKTADLLFGRAQPLNETAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKNAGIW
LSPLTDKDGRLEAIGGDGRVMGNEEARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMGRQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLSREKTLG
GD

Protein domains

Predicted by InterproScan.

• single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N) (576-628)

• DNA helicase TraI (TraI_C) (1432-1554)

• DNA relaxase TraI 2B/2B-like domain (TraI_2B) (634-713)

• AAA domain (AAA_30) (970-1156)

• TrwC relaxase (TrwC) (10-283)

Protein structure

No available structure.

Auxiliary protein

WP_020805752_pKp1050-2

• ID: 1360
• GenBank: WP_020805752
• Name: WP_020805752_pKp1050-2
• UniProt ID: A0A377TIM3
• Length: 130 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 130 a.a.
• Molecular weight: 14772.81 Da
• Isoelectric Point: 4.5715

>WP_020805752.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE

Protein domains

Predicted by InterproScan.

• TraM protein, DNA-binding (Tra_M) (1-125)

Protein structure

• AlphaFold DB: A0A377TIM3

T4CP

traD_CN260_RS29410_pKp1050-2

• ID: 3019
• GenBank: WP_080848157
• Name: traD_CN260_RS29410_pKp1050-2
• UniProt ID: _
• Length: 764 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 764 a.a.
• Molecular weight: 85403.54 Da
• Isoelectric Point: 4.9713

>WP_080848157.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella/Raoultella group]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTISYYGKSLEYNAEQILADKYTIWCGEQLWTAFVFAAIVSLTVCVVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKITEGFIQRRLDARVDGRLSALLEAREAEGSLARALFTPDEPVSESAEEKAGVQPEQTKPAEDS
VLPVPVKTSSKAAEGAGKTPDVPLSGAPVTRVKTVPLIRPEPAASVTGTAAAASTAAVIATAGGTAQELA
QQPVEADQNMLPAGMNEDGVIEDMQAYDEWLAGEQTQRDMQRREEVNINHSRSEQDDIEIGGNF

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: 99276..127258

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
CN260_RS29195 (CN260_29050)	94466..95341	+	876	WP_060415463	DUF4942 domain-containing protein	-
CN260_RS29210 (CN260_29065)	96121..96459	+	339	WP_020804855	hypothetical protein	-
CN260_RS29215 (CN260_29070)	96516..96863	+	348	WP_064182675	hypothetical protein	-
CN260_RS29220 (CN260_29075)	96952..97182	+	231	WP_060415465	hypothetical protein	-
CN260_RS29225 (CN260_29080)	97229..98062	+	834	WP_060415466	N-6 DNA methylase	-
CN260_RS30925	98348..98716	-	369	WP_080848162	hypothetical protein	-
CN260_RS29230 (CN260_29085)	98711..99253	+	543	WP_060415467	antirestriction protein	-
CN260_RS29235 (CN260_29090)	99276..99698	-	423	WP_073972322	transglycosylase SLT domain-containing protein	virB1
CN260_RS29240 (CN260_29095)	100202..100594	+	393	WP_020805752	conjugal transfer relaxosome DNA-binding protein TraM	-
CN260_RS31940	100832..101533	+	702	WP_223174962	hypothetical protein	-
CN260_RS29250 (CN260_29105)	101619..101819	+	201	WP_048289787	TraY domain-containing protein	-
CN260_RS29255 (CN260_29110)	101888..102256	+	369	WP_064343525	type IV conjugative transfer system pilin TraA	-
CN260_RS29260 (CN260_29115)	102270..102575	+	306	WP_064343526	type IV conjugative transfer system protein TraL	traL
CN260_RS29265 (CN260_29120)	102591..103157	+	567	WP_064359954	type IV conjugative transfer system protein TraE	traE
CN260_RS29270 (CN260_29125)	103144..103878	+	735	WP_064343528	type-F conjugative transfer system secretin TraK	traK
CN260_RS29275 (CN260_29130)	103878..105299	+	1422	WP_053390199	F-type conjugal transfer pilus assembly protein TraB	traB
CN260_RS29280 (CN260_29135)	105292..105726	+	435	WP_020322358	conjugal transfer protein TraP	-
CN260_RS29285 (CN260_29140)	105760..106344	+	585	WP_064343530	type IV conjugative transfer system lipoprotein TraV	traV
CN260_RS29300 (CN260_29155)	106957..107145	+	189	WP_053390286	hypothetical protein	-
CN260_RS31945	107229..107630	+	402	WP_064343532	hypothetical protein	-
CN260_RS29310 (CN260_29165)	107627..107926	+	300	WP_053390308	hypothetical protein	-
CN260_RS29315 (CN260_29170)	108014..108397	+	384	WP_042946290	hypothetical protein	-
CN260_RS29320 (CN260_29175)	108490..111129	+	2640	WP_064343533	type IV secretion system protein TraC	virb4
CN260_RS29325 (CN260_29180)	111129..111521	+	393	WP_117977340	type-F conjugative transfer system protein TrbI	-
CN260_RS29330 (CN260_29185)	111518..112144	+	627	WP_064343535	type-F conjugative transfer system protein TraW	traW
CN260_RS29335 (CN260_29190)	112188..113147	+	960	WP_229295972	conjugal transfer pilus assembly protein TraU	traU
CN260_RS29340 (CN260_29195)	113160..113807	+	648	WP_064343536	type-F conjugative transfer system pilin assembly protein TrbC	trbC
CN260_RS29345 (CN260_29200)	113804..114187	+	384	WP_053390297	hypothetical protein	-
CN260_RS29350 (CN260_29205)	114184..116139	+	1956	WP_082226156	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
CN260_RS29355 (CN260_29210)	116171..116431	+	261	WP_053390216	hypothetical protein	-
CN260_RS29360 (CN260_29215)	116424..117035	+	612	WP_117977341	hypothetical protein	-
CN260_RS29365 (CN260_29220)	117025..117267	+	243	WP_082226157	conjugal transfer protein TrbE	-
CN260_RS29370 (CN260_29225)	117313..117639	+	327	WP_053390219	hypothetical protein	-
CN260_RS29375 (CN260_29230)	117660..118412	+	753	WP_053390220	type-F conjugative transfer system pilin assembly protein TraF	traF
CN260_RS29380 (CN260_29235)	118423..118659	+	237	WP_053390221	type-F conjugative transfer system pilin chaperone TraQ	-
CN260_RS29385 (CN260_29240)	118634..119194	+	561	WP_039698500	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
CN260_RS29390 (CN260_29245)	119181..120551	+	1371	WP_049078362	conjugal transfer pilus assembly protein TraH	traH
CN260_RS29395 (CN260_29250)	120551..123394	+	2844	WP_049078361	conjugal transfer mating-pair stabilization protein TraG	traG
CN260_RS29400 (CN260_29255)	123400..123915	+	516	WP_049078360	conjugal transfer protein TraS	-
CN260_RS29405 (CN260_29260)	123978..124724	+	747	WP_049078359	hypothetical protein	-
CN260_RS29410 (CN260_29265)	124964..127258	+	2295	WP_080848157	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 4678
• GenBank: NZ_CP023418
• Plasmid name: pKp1050-2
• Incompatibility group: IncFII
• Plasmid size: 138885 bp
• Coordinate of oriT [Strand]: 99843..99891 [-]
• Host baterium: Klebsiella pneumoniae strain 1050

Cargo genes

• Drug resistance gene: -
• Virulence gene: -
• Metal resistance gene: merR, merT, merP, merC, merA, merD, merE
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -