Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 102980
• Name: oriT_pGR-1870
• Organism: Klebsiella pneumoniae
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NC_023905 (80687..80736 [-], 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_pGR-1870
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_HTC14_RS00685_pGR-1870

• ID: 2235
• GenBank: WP_024269743
• Name: traI_HTC14_RS00685_pGR-1870
• UniProt ID: W6AUB9
• Length: 1753 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1753 a.a.
• Molecular weight: 190506.54 Da
• Isoelectric Point: 6.3661

>WP_024269743.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGMFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRHNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGASGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQKSVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTSFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTI
QTQIRSGQLLNAPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTQAQEKAIQ
KALSEGETLPAGQPASLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILE
PRNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTL
GGD

Protein domains

Predicted by InterproScan.

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

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

• TrwC relaxase (TrwC) (10-284)

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

• AAA domain (AAA_30) (971-1157)

Protein structure

No available structure.

T4CP

traD_HTC14_RS00680_pGR-1870

• ID: 1924
• GenBank: WP_004152620
• Name: traD_HTC14_RS00680_pGR-1870
• UniProt ID: _
• Length: 770 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 770 a.a.
• Molecular weight: 85871.84 Da
• Isoelectric Point: 5.0101

>WP_004152620.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDTPEPGPADTDSHASEQPEPVSPPA
PAVMTVTPAPVKSPPTTKRPAAEPSVRATEPPVLRGTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

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: 80129..109315

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HTC14_RS00450 (D647_p45061)	75146..75496	+	351	WP_004152758	hypothetical protein	-
HTC14_RS00455	75644..75820	+	177	WP_159376550	hypothetical protein	-
HTC14_RS00460 (D647_p45062)	76132..76488	+	357	WP_004152717	hypothetical protein	-
HTC14_RS00465 (D647_p45063)	76549..76761	+	213	WP_004152718	hypothetical protein	-
HTC14_RS00470 (D647_p45064)	76772..76996	+	225	WP_004152719	hypothetical protein	-
HTC14_RS00475 (D647_p45065)	77077..77397	+	321	WP_004152720	type II toxin-antitoxin system RelE/ParE family toxin	-
HTC14_RS00480 (D647_p45066)	77387..77665	+	279	WP_004152721	helix-turn-helix transcriptional regulator	-
HTC14_RS00485 (D647_p45067)	77666..78079	+	414	WP_004152722	helix-turn-helix domain-containing protein	-
HTC14_RS00490	78432..78608	+	177	WP_159376550	hypothetical protein	-
HTC14_RS00495 (D647_p45068)	78913..79734	+	822	WP_004178064	DUF932 domain-containing protein	-
HTC14_RS00500 (D647_p45069)	79767..80096	+	330	WP_011977736	DUF5983 family protein	-
HTC14_RS00505 (D647_p45070)	80129..80614	-	486	WP_004178063	transglycosylase SLT domain-containing protein	virB1
HTC14_RS00510 (D647_p45071)	81048..81440	+	393	WP_004178062	conjugal transfer relaxosome DNA-binding protein TraM	-
HTC14_RS00515 (D647_p45072)	81654..82349	+	696	WP_004178061	transcriptional regulator TraJ family protein	-
HTC14_RS00520 (D647_p45073)	82433..82804	+	372	WP_004208838	TraY domain-containing protein	-
HTC14_RS00525 (D647_p45074)	82858..83226	+	369	WP_004178060	type IV conjugative transfer system pilin TraA	-
HTC14_RS00530 (D647_p45075)	83240..83545	+	306	WP_004178059	type IV conjugative transfer system protein TraL	traL
HTC14_RS00535 (D647_p45076)	83565..84131	+	567	WP_004152602	type IV conjugative transfer system protein TraE	traE
HTC14_RS00540 (D647_p45077)	84118..84858	+	741	WP_024269739	type-F conjugative transfer system secretin TraK	traK
HTC14_RS00545 (D647_p45078)	84858..86282	+	1425	WP_024269740	F-type conjugal transfer pilus assembly protein TraB	traB
HTC14_RS00550 (D647_p45079)	86275..86871	+	597	WP_004152599	conjugal transfer pilus-stabilizing protein TraP	-
HTC14_RS00555 (D647_p45080)	86894..87463	+	570	WP_004152598	type IV conjugative transfer system lipoprotein TraV	traV
HTC14_RS00560 (D647_p45081)	87595..88005	+	411	WP_004152597	lipase chaperone	-
HTC14_RS00565 (D647_p45082)	88010..88300	+	291	WP_004152596	hypothetical protein	-
HTC14_RS00570 (D647_p45083)	88324..88542	+	219	WP_004171484	hypothetical protein	-
HTC14_RS00575 (D647_p45084)	88543..88860	+	318	WP_004152595	hypothetical protein	-
HTC14_RS00580 (D647_p45085)	88927..89331	+	405	WP_004152594	hypothetical protein	-
HTC14_RS00585	89627..90025	+	399	WP_004153071	hypothetical protein	-
HTC14_RS00590 (D647_p45086)	90097..92736	+	2640	WP_004152592	type IV secretion system protein TraC	virb4
HTC14_RS00595 (D647_p45087)	92736..93125	+	390	WP_004152591	type-F conjugative transfer system protein TrbI	-
HTC14_RS00600 (D647_p45088)	93125..93751	+	627	WP_004152590	type-F conjugative transfer system protein TraW	traW
HTC14_RS00605 (D647_p45089)	93795..94754	+	960	WP_015065634	conjugal transfer pilus assembly protein TraU	traU
HTC14_RS00610 (D647_p45090)	94767..95405	+	639	WP_004152672	type-F conjugative transfer system pilin assembly protein TrbC	trbC
HTC14_RS00615 (D647_p45091)	95464..97419	+	1956	WP_004152673	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
HTC14_RS00620 (D647_p45092)	97451..97705	+	255	WP_004152674	conjugal transfer protein TrbE	-
HTC14_RS00625	97683..97931	+	249	WP_004152675	hypothetical protein	-
HTC14_RS00630 (D647_p45093)	97944..98270	+	327	WP_004152676	hypothetical protein	-
HTC14_RS00635 (D647_p45094)	98291..99043	+	753	WP_004152677	type-F conjugative transfer system pilin assembly protein TraF	traF
HTC14_RS00640 (D647_p45095)	99054..99293	+	240	WP_004144400	type-F conjugative transfer system pilin chaperone TraQ	-
HTC14_RS00645 (D647_p45096)	99265..99822	+	558	WP_004152678	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
HTC14_RS00650 (D647_p45097)	99868..100311	+	444	WP_004152679	F-type conjugal transfer protein TrbF	-
HTC14_RS00655 (D647_p45098)	100289..101668	+	1380	WP_004165169	conjugal transfer pilus assembly protein TraH	traH
HTC14_RS00660 (D647_p45099)	101668..104517	+	2850	WP_024269741	conjugal transfer mating-pair stabilization protein TraG	traG
HTC14_RS00665 (D647_p45100)	104530..105078	+	549	WP_004152623	conjugal transfer entry exclusion protein TraS	-
HTC14_RS00670 (D647_p45101)	105262..105993	+	732	WP_004152622	conjugal transfer complement resistance protein TraT	-
HTC14_RS00675 (D647_p45102)	106185..106874	+	690	WP_004198206	hypothetical protein	-
HTC14_RS00680 (D647_p45103)	107003..109315	+	2313	WP_004152620	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 3423
• GenBank: NC_023905
• Plasmid name: pGR-1870
• Incompatibility group: IncFII
• Plasmid size: 116047 bp
• Coordinate of oriT [Strand]: 80687..80736 [-]
• Host baterium: Klebsiella pneumoniae

Cargo genes

• Drug resistance gene: blaKPC-2, blaOXA-9, blaTEM-1A
• Virulence gene: -
• Metal resistance gene: merE, merD, merA
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: AcrIE9