Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 102098
• Name: oriT_ARPG-281|unnamed12
• Organism: Klebsiella pneumoniae strain ARPG-281
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_NBOH01000052 (19366..19415 [-], 50 nt)
• oriT length: 50 nt
• IRs (inverted repeats): 7..14, 17..24 (GCAAAATT..AATTTTGC)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 50 nt

>oriT_ARPG-281|unnamed12
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_B7C46_RS26765_ARPG-281|unnamed12

• ID: 1658
• GenBank: WP_004153029
• Name: traI_B7C46_RS26765_ARPG-281|unnamed12
• UniProt ID: A0A422WEA5
• Length: 1753 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1753 a.a.
• Molecular weight: 190808.90 Da
• Isoelectric Point: 6.2081

>WP_004153029.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANRHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRLVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGQQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKKAEQTAREMAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

Protein domains

Predicted by InterproScan.

• DNA helicase TraI (TraI_C) (1433-1555)

• single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N) (577-629)

• DNA relaxase TraI 2B/2B-like domain (TraI_2B) (635-714)

• AAA domain (AAA_30) (971-1157)

• TrwC relaxase (TrwC) (10-284)

Protein structure

No available structure.

T4CP

traD_B7C46_RS26760_ARPG-281|unnamed12

• ID: 1287
• GenBank: WP_004152630
• Name: traD_B7C46_RS26760_ARPG-281|unnamed12
• UniProt ID: _
• Length: 769 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 769 a.a.
• Molecular weight: 85951.02 Da
• Isoelectric Point: 5.0632

>WP_004152630.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKITEGFIPRRLDTRVDARLSALLEEREAEGSLARALFTPDAPASGPADTDSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAAEPSVRATEPPVLRVTTVPLIKPKAAAAAAAASTASSAGIPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

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: 18808..47226

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
B7C46_RS26515 (B7C46_26415)	13825..14175	+	351	WP_004152758	hypothetical protein	-
B7C46_RS26530 (B7C46_26430)	14811..15167	+	357	WP_004152717	hypothetical protein	-
B7C46_RS26535 (B7C46_26435)	15228..15440	+	213	WP_004152718	hypothetical protein	-
B7C46_RS26540 (B7C46_26440)	15451..15675	+	225	WP_004152719	hypothetical protein	-
B7C46_RS26545 (B7C46_26445)	15756..16076	+	321	WP_004152720	type II toxin-antitoxin system RelE/ParE family toxin	-
B7C46_RS26550 (B7C46_26450)	16066..16344	+	279	WP_004152721	helix-turn-helix transcriptional regulator	-
B7C46_RS26555 (B7C46_26455)	16345..16758	+	414	WP_004152722	helix-turn-helix domain-containing protein	-
B7C46_RS26575 (B7C46_26475)	17592..18413	+	822	WP_004178064	DUF932 domain-containing protein	-
B7C46_RS26580 (B7C46_26480)	18446..18775	+	330	WP_011977736	DUF5983 family protein	-
B7C46_RS26585 (B7C46_26485)	18808..19293	-	486	WP_004178063	transglycosylase SLT domain-containing protein	virB1
B7C46_RS26590 (B7C46_26490)	19727..20119	+	393	WP_004178062	conjugal transfer relaxosome DNA-binding protein TraM	-
B7C46_RS26595 (B7C46_26495)	20333..21028	+	696	WP_004178061	transcriptional regulator TraJ family protein	-
B7C46_RS26600 (B7C46_26500)	21112..21483	+	372	WP_004208838	TraY domain-containing protein	-
B7C46_RS26605 (B7C46_26505)	21537..21905	+	369	WP_004178060	type IV conjugative transfer system pilin TraA	-
B7C46_RS26610 (B7C46_26510)	21919..22224	+	306	WP_004178059	type IV conjugative transfer system protein TraL	traL
B7C46_RS26615 (B7C46_26515)	22244..22810	+	567	WP_004152602	type IV conjugative transfer system protein TraE	traE
B7C46_RS26620 (B7C46_26520)	22797..23537	+	741	WP_004152601	type-F conjugative transfer system secretin TraK	traK
B7C46_RS26625 (B7C46_26525)	23537..24961	+	1425	WP_004152600	F-type conjugal transfer pilus assembly protein TraB	traB
B7C46_RS26630 (B7C46_26530)	24954..25550	+	597	WP_004152599	conjugal transfer pilus-stabilizing protein TraP	-
B7C46_RS26635 (B7C46_26535)	25573..26142	+	570	WP_004152598	type IV conjugative transfer system lipoprotein TraV	traV
B7C46_RS26640 (B7C46_26540)	26274..26684	+	411	WP_004152597	lipase chaperone	-
B7C46_RS26645 (B7C46_26545)	26689..26979	+	291	WP_004152596	hypothetical protein	-
B7C46_RS26650 (B7C46_26550)	27003..27221	+	219	WP_004171484	hypothetical protein	-
B7C46_RS26655 (B7C46_26555)	27222..27539	+	318	WP_004152595	hypothetical protein	-
B7C46_RS26660 (B7C46_26560)	27606..28010	+	405	WP_004152594	hypothetical protein	-
B7C46_RS26670 (B7C46_26570)	28306..28704	+	399	WP_004153071	hypothetical protein	-
B7C46_RS26675 (B7C46_26575)	28776..31415	+	2640	WP_004152592	type IV secretion system protein TraC	virb4
B7C46_RS26680 (B7C46_26580)	31415..31804	+	390	WP_004152591	type-F conjugative transfer system protein TrbI	-
B7C46_RS26685 (B7C46_26585)	31804..32430	+	627	WP_004152590	type-F conjugative transfer system protein TraW	traW
B7C46_RS26690 (B7C46_26590)	32474..33433	+	960	WP_015065634	conjugal transfer pilus assembly protein TraU	traU
B7C46_RS26695 (B7C46_26595)	33446..34084	+	639	WP_004152682	type-F conjugative transfer system pilin assembly protein TrbC	trbC
B7C46_RS26700 (B7C46_26600)	34132..36087	+	1956	WP_004153093	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
B7C46_RS26705 (B7C46_26605)	36119..36355	+	237	WP_004152683	conjugal transfer protein TrbE	-
B7C46_RS28920 (B7C46_26610)	36352..36537	+	186	WP_004152684	hypothetical protein	-
B7C46_RS26715 (B7C46_26615)	36583..36909	+	327	WP_004152685	hypothetical protein	-
B7C46_RS26720 (B7C46_26620)	36930..37682	+	753	WP_004152686	type-F conjugative transfer system pilin assembly protein TraF	traF
B7C46_RS26725 (B7C46_26625)	37693..37932	+	240	WP_004152687	type-F conjugative transfer system pilin chaperone TraQ	-
B7C46_RS26730 (B7C46_26630)	37904..38476	+	573	WP_004152688	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
B7C46_RS26735 (B7C46_26635)	38469..38897	+	429	WP_004152689	hypothetical protein	-
B7C46_RS26740 (B7C46_26640)	38884..40254	+	1371	WP_004178055	conjugal transfer pilus assembly protein TraH	traH
B7C46_RS26745 (B7C46_26645)	40254..43103	+	2850	WP_004178054	conjugal transfer mating-pair stabilization protein TraG	traG
B7C46_RS26750 (B7C46_26650)	43109..43636	+	528	WP_004153030	hypothetical protein	-
B7C46_RS26755 (B7C46_26655)	43826..44557	+	732	WP_004152629	conjugal transfer complement resistance protein TraT	-
B7C46_RS26760 (B7C46_26660)	44917..47226	+	2310	WP_004152630	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 2542
• GenBank: NZ_NBOH01000052
• Plasmid name: ARPG-281|unnamed12
• Incompatibility group: IncFII
• Plasmid size: 70039 bp
• Coordinate of oriT [Strand]: 19366..19415 [-]
• Host baterium: Klebsiella pneumoniae strain ARPG-281

Cargo genes

• Drug resistance gene: -
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: AcrIE9