Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 105245
• Name: oriT_RHBSTW-00472|unnamed
• Organism: Klebsiella pneumoniae strain RHBSTW-00472
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP055510 (186716..186765 [-], 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_RHBSTW-00472|unnamed
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_HV207_RS28165_RHBSTW-00472|unnamed

• ID: 3602
• GenBank: WP_181247939
• Name: traI_HV207_RS28165_RHBSTW-00472|unnamed
• UniProt ID: _
• Length: 1753 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1753 a.a.
• Molecular weight: 190495.71 Da
• Isoelectric Point: 6.4832

>WP_181247939.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRAMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELACAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRHNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTI
QTQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTRVLEGKGAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALITIEQVTPEQVPRKEGVWAPGSSVVEFTPKQEKAIE
KALSEGKTLPAGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRTLNGMIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSDGKERYISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASERYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRIWADPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTL
GGD

Protein domains

Predicted by InterproScan.

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

• AAA domain (AAA_30) (971-1154)

• TrwC relaxase (TrwC) (10-284)

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

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

Protein structure

No available structure.

T4CP

traD_HV207_RS28160_RHBSTW-00472|unnamed

• ID: 3562
• GenBank: WP_228725929
• Name: traD_HV207_RS28160_RHBSTW-00472|unnamed
• UniProt ID: _
• Length: 769 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 769 a.a.
• Molecular weight: 85850.90 Da
• Isoelectric Point: 5.1769

>WP_228725929.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTVWCGEQLWTSIVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSKIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEAREAEGSLARTLFMPDAPASGPADTNSHAGEQPEPISQPA
PADMTVSPAPVKAPPTTKSPAAEPSVRATEPPVLRVTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

Protein domains

Predicted by InterproScan.

• Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind) (172-560)

• F sex factor protein N terminal (TraD_N) (32-128)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 186158..216538

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HV207_RS27935 (HV207_27945)	181175..181525	+	351	WP_015065620	hypothetical protein	-
HV207_RS27940 (HV207_27950)	182161..182517	+	357	WP_013023814	hypothetical protein	-
HV207_RS27945 (HV207_27955)	182578..182790	+	213	WP_021313197	hypothetical protein	-
HV207_RS27950 (HV207_27960)	182801..183025	+	225	WP_004152719	hypothetical protein	-
HV207_RS27955 (HV207_27965)	183106..183426	+	321	WP_004152720	type II toxin-antitoxin system RelE/ParE family toxin	-
HV207_RS27960 (HV207_27970)	183416..183694	+	279	WP_004152721	helix-turn-helix transcriptional regulator	-
HV207_RS27965 (HV207_27975)	183695..184108	+	414	WP_004182074	helix-turn-helix domain-containing protein	-
HV207_RS27970 (HV207_27980)	184942..185763	+	822	WP_015065622	DUF932 domain-containing protein	-
HV207_RS27975 (HV207_27985)	185811..186125	+	315	WP_001568110	DUF5983 family protein	-
HV207_RS27980 (HV207_27990)	186158..186643	-	486	WP_001568108	transglycosylase SLT domain-containing protein	virB1
HV207_RS27985 (HV207_27995)	187078..187470	+	393	WP_004206766	conjugal transfer relaxosome DNA-binding protein TraM	-
HV207_RS27990 (HV207_28000)	187677..188372	+	696	WP_015065624	transcriptional regulator TraJ family protein	-
HV207_RS27995 (HV207_28005)	188456..188827	+	372	WP_004208838	TraY domain-containing protein	-
HV207_RS28000 (HV207_28010)	188881..189249	+	369	WP_004178060	type IV conjugative transfer system pilin TraA	-
HV207_RS28005 (HV207_28015)	189263..189568	+	306	WP_015065625	type IV conjugative transfer system protein TraL	traL
HV207_RS28010 (HV207_28020)	189588..190154	+	567	WP_004152602	type IV conjugative transfer system protein TraE	traE
HV207_RS28015 (HV207_28025)	190141..190881	+	741	WP_004152497	type-F conjugative transfer system secretin TraK	traK
HV207_RS28020 (HV207_28030)	190881..192305	+	1425	WP_040228261	F-type conjugal transfer pilus assembly protein TraB	traB
HV207_RS28025 (HV207_28035)	192298..192717	+	420	Protein_215	conjugal transfer pilus-stabilizing protein TraP	-
HV207_RS28030 (HV207_28040)	192850..193818	+	969	WP_072210033	IS5-like element IS903B family transposase	-
HV207_RS28035 (HV207_28045)	193989..194558	+	570	WP_015065628	type IV conjugative transfer system lipoprotein TraV	traV
HV207_RS30470	194714..195112	+	399	WP_227648814	hypothetical protein	-
HV207_RS28045 (HV207_28055)	195252..196220	+	969	WP_072269220	IS5 family transposase	-
HV207_RS28050 (HV207_28060)	196282..196497	+	216	Protein_220	hypothetical protein	-
HV207_RS28055 (HV207_28065)	196521..196739	+	219	WP_004171484	hypothetical protein	-
HV207_RS28060 (HV207_28070)	196740..197057	+	318	WP_015065629	hypothetical protein	-
HV207_RS28065 (HV207_28075)	197124..197528	+	405	WP_023320104	hypothetical protein	-
HV207_RS28070 (HV207_28080)	197553..197951	+	399	WP_015065631	hypothetical protein	-
HV207_RS28075 (HV207_28085)	198023..200662	+	2640	WP_064185323	type IV secretion system protein TraC	virb4
HV207_RS28080 (HV207_28090)	200662..201051	+	390	WP_021312677	type-F conjugative transfer system protein TrbI	-
HV207_RS28085 (HV207_28095)	201051..201677	+	627	WP_015065633	type-F conjugative transfer system protein TraW	traW
HV207_RS28090 (HV207_28100)	201721..202680	+	960	WP_015065634	conjugal transfer pilus assembly protein TraU	traU
HV207_RS28095 (HV207_28105)	202693..203331	+	639	WP_015065635	type-F conjugative transfer system pilin assembly protein TrbC	trbC
HV207_RS28100 (HV207_28110)	203390..205345	+	1956	WP_015065636	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
HV207_RS28105 (HV207_28115)	205377..205613	+	237	WP_023307536	conjugal transfer protein TrbE	-
HV207_RS30730	205610..205795	+	186	WP_023307535	hypothetical protein	-
HV207_RS28110 (HV207_28120)	205841..206167	+	327	WP_004152685	hypothetical protein	-
HV207_RS28115 (HV207_28125)	206188..206940	+	753	WP_015065637	type-F conjugative transfer system pilin assembly protein TraF	traF
HV207_RS28120 (HV207_28130)	206951..207190	+	240	WP_004144400	type-F conjugative transfer system pilin chaperone TraQ	-
HV207_RS28125 (HV207_28135)	207162..207719	+	558	WP_004152678	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
HV207_RS28130 (HV207_28140)	207764..208207	+	444	WP_015065638	F-type conjugal transfer protein TrbF	-
HV207_RS28135 (HV207_28145)	208185..209564	+	1380	WP_011977731	conjugal transfer pilus assembly protein TraH	traH
HV207_RS28140 (HV207_28150)	209564..212413	+	2850	WP_135717020	conjugal transfer mating-pair stabilization protein TraG	traG
HV207_RS28145 (HV207_28155)	212419..212946	+	528	WP_064185327	hypothetical protein	-
HV207_RS28155 (HV207_28165)	213136..213867	+	732	Protein_241	conjugal transfer complement resistance protein TraT	-
HV207_RS28160 (HV207_28170)	214229..216538	+	2310	WP_228725929	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 5683
• GenBank: NZ_CP055510
• Plasmid name: RHBSTW-00472|unnamed
• Incompatibility group: IncFIB
• Plasmid size: 333723 bp
• Coordinate of oriT [Strand]: 186716..186765 [-]
• Host baterium: Klebsiella pneumoniae strain RHBSTW-00472

Cargo genes

• Drug resistance gene: -
• Virulence gene: mrkJ, mrkF, mrkD, mrkC, mrkB, mrkA
• Metal resistance gene: fecE, fecD, pcoE, pcoS, pcoR, pcoD, pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE, merR, merT, merP, merC, merA, merD, merE
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: AcrIE9