Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 118795
• Name: oriT_pC3001-4-KPC
• Organism: Klebsiella quasipneumoniae strain C3001
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP039794 (100728..100776 [-], 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_pC3001-4-KPC
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_FA956_RS29645_pC3001-4-KPC

• ID: 11921
• GenBank: WP_082226159
• Name: traI_FA956_RS29645_pC3001-4-KPC
• UniProt ID: _
• Length: 1752 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1752 a.a.
• Molecular weight: 190416.67 Da
• Isoelectric Point: 5.5084

>WP_082226159.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTNNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADTRAKELASAPAAPVKTDVPDISDVVTKAIAGLSDRKVQFTYADLLARTVSQLEA
KPGVFEQTRTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDTAVVRQSPF
SDAVSVLAQDRPTMGIVSGQGGAAGQRERVAELTLMAREQGRDVHIIAADNRSREFLSADARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKMSLKETLSMLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGKQATADIISEPEKGARYSRLAQEFAASVREGQESVAQISGSREQGILNGLIRETLKSEGVLGEKDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRQHDRFVIDRVTASSNMLTLRDKEGERLDMKVSAVD
SQWTLFRADKLTVAEGERLAVLGKIPDTRLKGGESVTVLKAEEGQLTVQRPGQKTTQSLSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQGTARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIASQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
SQIQAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDNVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQVTPEQVPRKDGAWVPENSVVEFTPAQEEAIQK
ALNKGESVPAGQPTTLYEALVKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKSTRTLNPKADQAQQHIDLAYAITA
HGAQGASEPFAIALEGVAGGRERMASFESAYVGLSRMKQHVQVYTDNREGWIKAINNSPEKATAHDILEP
RNDRAVKTAGQLFSRARALDEAAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDNDGRLQVIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMERQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLNREKTLG
GD

Protein domains

Predicted by InterproScan.

• DNA helicase TraI (TraI_C) (1432-1552)

• single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N) (577-628)

• TrwC relaxase (TrwC) (11-283)

• AAA domain (AAA_30) (970-1157)

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

Protein structure

No available structure.

Auxiliary protein

WP_020805752_pC3001-4-KPC

• ID: 6814
• GenBank: WP_020805752
• Name: WP_020805752_pC3001-4-KPC
• 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_FA956_RS29640_pC3001-4-KPC

• ID: 13949
• GenBank: WP_064386203
• Name: traD_FA956_RS29640_pC3001-4-KPC
• UniProt ID: _
• Length: 772 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 772 a.a.
• Molecular weight: 86585.38 Da
• Isoelectric Point: 5.0283

>WP_064386203.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella/Raoultella group]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFIIFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTINYYGKSLEYNSEQILADKYTIWCGEQLWTSFVFAAIVSLTVCIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKHSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDIWRECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFSEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLKNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLGMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDVQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRNLDTRVDARLNALLEAREAEGSLARTLFTPDAPAPELAEKDEKVGNPPEQSQPAE
SSGTSATVKVPSTAKTPEADESGQSPEVSNPAALLTKVVTVPLTRPRPAAATGTAAVASATDVPATPAGG
TEQALETQPAEQGQDMLPPGVNEYGEIDDMHAWDEWQSGEQTQRDMQRREEVNINHSHRRDEQDDIEIGG
NF

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: 103155..130683

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
FA956_RS29455 (FA956_30170)	99596..100138	+	543	WP_053390246	antirestriction protein	-
FA956_RS29460 (FA956_30175)	100161..100583	-	423	WP_077268549	transglycosylase SLT domain-containing protein	-
FA956_RS29465 (FA956_30180)	101087..101479	+	393	WP_020805752	conjugal transfer relaxosome DNA-binding protein TraM	-
FA956_RS30010	101717..102418	+	702	WP_223174962	hypothetical protein	-
FA956_RS29475 (FA956_30190)	102504..102704	+	201	WP_048289787	TraY domain-containing protein	-
FA956_RS29480 (FA956_30195)	102773..103141	+	369	WP_064343525	type IV conjugative transfer system pilin TraA	-
FA956_RS29485 (FA956_30200)	103155..103460	+	306	WP_064343526	type IV conjugative transfer system protein TraL	traL
FA956_RS29490 (FA956_30205)	103476..104042	+	567	WP_064359954	type IV conjugative transfer system protein TraE	traE
FA956_RS29495 (FA956_30210)	104029..104763	+	735	WP_064343528	type-F conjugative transfer system secretin TraK	traK
FA956_RS29500 (FA956_30215)	104763..106184	+	1422	WP_053390199	F-type conjugal transfer pilus assembly protein TraB	traB
FA956_RS29505 (FA956_30220)	106177..106611	+	435	WP_020322358	conjugal transfer protein TraP	-
FA956_RS29510 (FA956_30225)	106645..107229	+	585	WP_205847351	type IV conjugative transfer system lipoprotein TraV	traV
FA956_RS29515 (FA956_30230)	107842..108030	+	189	WP_053390286	hypothetical protein	-
FA956_RS30015	108114..108515	+	402	WP_064343532	hypothetical protein	-
FA956_RS29525 (FA956_30240)	108512..108811	+	300	WP_053390308	hypothetical protein	-
FA956_RS29530 (FA956_30245)	108899..109282	+	384	WP_042946290	hypothetical protein	-
FA956_RS29535 (FA956_30250)	109375..112014	+	2640	WP_064343533	type IV secretion system protein TraC	virb4
FA956_RS29540 (FA956_30255)	112014..112406	+	393	WP_064343534	type-F conjugative transfer system protein TrbI	-
FA956_RS29545 (FA956_30260)	112403..113029	+	627	WP_064343535	type-F conjugative transfer system protein TraW	traW
FA956_RS29550 (FA956_30265)	113073..114032	+	960	WP_229295972	conjugal transfer pilus assembly protein TraU	traU
FA956_RS29555 (FA956_30270)	114045..114692	+	648	WP_064343536	type-F conjugative transfer system pilin assembly protein TrbC	trbC
FA956_RS29560 (FA956_30275)	114689..115072	+	384	WP_053390297	hypothetical protein	-
FA956_RS29565 (FA956_30280)	115069..117024	+	1956	WP_080848160	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
FA956_RS29570 (FA956_30285)	117056..117316	+	261	WP_053390216	hypothetical protein	-
FA956_RS29575 (FA956_30290)	117309..117920	+	612	WP_053390217	hypothetical protein	-
FA956_RS29580 (FA956_30295)	117910..118152	+	243	WP_053390218	conjugal transfer protein TrbE	-
FA956_RS29585 (FA956_30300)	118198..118524	+	327	WP_053390219	hypothetical protein	-
FA956_RS29590 (FA956_30305)	118545..119297	+	753	WP_064386181	type-F conjugative transfer system pilin assembly protein TraF	traF
FA956_RS29595	119711..120070	-	360	WP_064386183	hypothetical protein	-
FA956_RS29600 (FA956_30315)	120159..120395	+	237	WP_064386186	type-F conjugative transfer system pilin chaperone TraQ	-
FA956_RS29605 (FA956_30320)	120370..120936	+	567	WP_100663597	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
FA956_RS29610 (FA956_30325)	120929..121357	+	429	WP_100663598	conjugal transfer protein TrbF	-
FA956_RS29615 (FA956_30330)	121344..122714	+	1371	WP_064386191	conjugal transfer pilus assembly protein TraH	traH
FA956_RS29620 (FA956_30335)	122714..125593	+	2880	WP_064386194	conjugal transfer mating-pair stabilization protein TraG	traG
FA956_RS29625 (FA956_30340)	125610..126278	+	669	WP_128317877	hypothetical protein	-
FA956_RS29630 (FA956_30345)	126631..127362	+	732	WP_064386198	conjugal transfer complement resistance protein TraT	-
FA956_RS30020	127554..128246	+	693	WP_202395549	hypothetical protein	-
FA956_RS29640 (FA956_30355)	128365..130683	+	2319	WP_064386203	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 19227
• GenBank: NZ_CP039794
• Plasmid name: pC3001-4-KPC
• Incompatibility group: IncFII
• Plasmid size: 141814 bp
• Coordinate of oriT [Strand]: 100728..100776 [-]
• Host baterium: Klebsiella quasipneumoniae strain C3001

Cargo genes

• Drug resistance gene: blaKPC-2
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -