Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 121304
• Name: oriT_pPS00262_4A.4
• Organism: Klebsiella variicola strain PS00262.4
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP127500 (27760..27808 [-], 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: GGTGTGGTGA
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 49 nt

>oriT_pPS00262_4A.4
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_QQ383_RS31725_pPS00262_4A.4

• ID: 13444
• GenBank: WP_110219713
• Name: traI_QQ383_RS31725_pPS00262_4A.4
• UniProt ID: _
• Length: 1753 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1753 a.a.
• Molecular weight: 190646.70 Da
• Isoelectric Point: 6.2582

>WP_110219713.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSADKAADYYTNKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGRLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQLHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRTQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGVRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGLLTVQRPGQKTTQTLTVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVPMADIDTTI
QAQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAVGGGRAVPSGDTDQLPPIASGQPFRLTQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
NALSEGKTLPAGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSDGKERYISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASERYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWADPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTL
GGD

Protein domains

Predicted by InterproScan.

• AAA domain (AAA_30) (971-1157)

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

• TrwC relaxase (TrwC) (11-284)

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

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

Protein structure

No available structure.

Auxiliary protein

WP_020805752_pPS00262_4A.4

• ID: 7417
• GenBank: WP_020805752
• Name: WP_020805752_pPS00262_4A.4
• 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_QQ383_RS31720_pPS00262_4A.4

• ID: 15743
• GenBank: WP_110219714
• Name: traD_QQ383_RS31720_pPS00262_4A.4
• UniProt ID: _
• Length: 766 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 766 a.a.
• Molecular weight: 85407.28 Da
• Isoelectric Point: 5.0101

>WP_110219714.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQHTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPDDAGSHAGERPELASQPA
PAEVTVSPAPVKAPATTTMPAAEPSARTAEPPVLRVTTVPLIKPKAAAAASTASSAGNPAAAAGGTEQEL
AQQSVEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINRSHRHDEQDDVEIGGNF

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: 30187..55809

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
QQ383_RS31535 (QQ383_31505)	26640..27170	+	531	WP_065954381	antirestriction protein	-
QQ383_RS31540 (QQ383_31510)	27208..27645	-	438	WP_065954401	transglycosylase SLT domain-containing protein	-
QQ383_RS31545 (QQ383_31515)	28119..28511	+	393	WP_020805752	conjugal transfer relaxosome DNA-binding protein TraM	-
QQ383_RS31550 (QQ383_31520)	28749..29450	+	702	WP_224324939	hypothetical protein	-
QQ383_RS31555 (QQ383_31525)	29536..29736	+	201	WP_048289787	TraY domain-containing protein	-
QQ383_RS31560 (QQ383_31530)	29805..30173	+	369	WP_020316649	type IV conjugative transfer system pilin TraA	-
QQ383_RS31565 (QQ383_31535)	30187..30492	+	306	WP_004178059	type IV conjugative transfer system protein TraL	traL
QQ383_RS31570 (QQ383_31540)	30512..31078	+	567	WP_020316627	type IV conjugative transfer system protein TraE	traE
QQ383_RS31575 (QQ383_31545)	31065..31805	+	741	WP_020804840	type-F conjugative transfer system secretin TraK	traK
QQ383_RS31580 (QQ383_31550)	31805..33229	+	1425	WP_023316397	F-type conjugal transfer pilus assembly protein TraB	traB
QQ383_RS31585 (QQ383_31555)	33222..33818	+	597	WP_023316398	conjugal transfer pilus-stabilizing protein TraP	-
QQ383_RS31590 (QQ383_31560)	33841..34410	+	570	WP_086893255	type IV conjugative transfer system lipoprotein TraV	traV
QQ383_RS31595 (QQ383_31565)	34542..34952	+	411	WP_020805613	hypothetical protein	-
QQ383_RS31600 (QQ383_31570)	34957..35241	+	285	WP_119173789	hypothetical protein	-
QQ383_RS31605 (QQ383_31575)	35265..35483	+	219	WP_124038229	hypothetical protein	-
QQ383_RS31610 (QQ383_31580)	35484..35795	+	312	WP_124038230	hypothetical protein	-
QQ383_RS31615 (QQ383_31585)	35862..36266	+	405	WP_023316404	hypothetical protein	-
QQ383_RS31620 (QQ383_31590)	36263..36553	+	291	WP_020323516	hypothetical protein	-
QQ383_RS31625 (QQ383_31595)	36561..36959	+	399	WP_072156904	hypothetical protein	-
QQ383_RS31630 (QQ383_31600)	37031..39670	+	2640	WP_042946320	type IV secretion system protein TraC	virb4
QQ383_RS31635 (QQ383_31605)	39670..40059	+	390	WP_086893260	type-F conjugative transfer system protein TrbI	-
QQ383_RS31640 (QQ383_31610)	40059..40685	+	627	WP_020314628	type-F conjugative transfer system protein TraW	traW
QQ383_RS31645 (QQ383_31615)	40729..41688	+	960	WP_168712236	conjugal transfer pilus assembly protein TraU	traU
QQ383_RS31650 (QQ383_31620)	41701..42339	+	639	WP_040107937	type-F conjugative transfer system pilin assembly protein TrbC	trbC
QQ383_RS31655 (QQ383_31625)	42398..44353	+	1956	WP_110219676	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
QQ383_RS31660 (QQ383_31630)	44386..44667	+	282	WP_022644736	hypothetical protein	-
QQ383_RS31665 (QQ383_31635)	44657..44884	+	228	WP_012540032	conjugal transfer protein TrbE	-
QQ383_RS31670 (QQ383_31640)	44895..45221	+	327	WP_020323521	hypothetical protein	-
QQ383_RS31675 (QQ383_31645)	45242..45994	+	753	WP_004152677	type-F conjugative transfer system pilin assembly protein TraF	traF
QQ383_RS31680 (QQ383_31650)	46005..46244	+	240	WP_023340931	type-F conjugative transfer system pilin chaperone TraQ	-
QQ383_RS31685 (QQ383_31655)	46216..46773	+	558	WP_086893263	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
QQ383_RS31690 (QQ383_31660)	46819..47262	+	444	WP_049248035	F-type conjugal transfer protein TrbF	-
QQ383_RS31695 (QQ383_31665)	47240..48619	+	1380	WP_072198238	conjugal transfer pilus assembly protein TraH	traH
QQ383_RS31700 (QQ383_31670)	48619..51462	+	2844	WP_110219715	conjugal transfer mating-pair stabilization protein TraG	traG
QQ383_RS31705 (QQ383_31675)	51473..52006	+	534	WP_224324940	hypothetical protein	-
QQ383_RS31710 (QQ383_31680)	52417..53148	+	732	WP_004152629	conjugal transfer complement resistance protein TraT	-
QQ383_RS31715 (QQ383_31685)	53339..53431	+	93	Protein_75	hypothetical protein	-
QQ383_RS31720 (QQ383_31690)	53509..55809	+	2301	WP_110219714	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 21732
• GenBank: NZ_CP127500
• Plasmid name: pPS00262_4A.4
• Incompatibility group: IncFIA
• Plasmid size: 134238 bp
• Coordinate of oriT [Strand]: 27760..27808 [-]
• Host baterium: Klebsiella variicola strain PS00262.4

Cargo genes

• Drug resistance gene: -
• Virulence gene: -
• Metal resistance gene: merE, merD, merA, merF, merP, merT, merR2, arsC, arsB
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: AcrIE9