Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 120809
• Name: oriT_FDAARGOS_1439|unnamed2
• Organism: Hafnia alvei strain FDAARGOS_1439
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_JAHWJA010000003 (40702..40813 [+], 112 nt)
• oriT length: 112 nt
• IRs (inverted repeats): 59..64, 73..78 (AAAACA..TGTTTT) 28..35, 38..45 (GCAAAACT..AGTTTTGC)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 112 nt

>oriT_FDAARGOS_1439|unnamed2
CTCACCACCAAAAAGACCACACACCACGCAAAACTAAAGTTTTGCTGATTTCTCTTTTAAAACATAATCTTGTGTTTTTTAAATTGTGTTTCGTTATATTTTACAATGTTAA

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_I6L69_RS22885_FDAARGOS_1439|unnamed2

• ID: 13122
• GenBank: WP_046360166
• Name: traI_I6L69_RS22885_FDAARGOS_1439|unnamed2
• UniProt ID: _
• Length: 1756 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1756 a.a.
• Molecular weight: 190955.94 Da
• Isoelectric Point: 6.0674

>WP_046360166.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Hafnia]
MMSFSQVKSAGGAAGYYTDKDNYYVLGSMDDRWHGEGAKLLGLAGSIDKDTFTRALKGLLPDGSDLSRLQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIEAHNRAVDVALKQVEALASTRVMRDGVSETVLTGNLV
IARFNHDTSRDQDPQLHTHSVVLNATRNEDKWQALSSDTVGKTGFSENVLANQIALGKIYNLSLRREVEA
MGYEVDVVGKHGLWEMRDVPVAPFSSRRNTIVETVGADASRRSRDVAALDTRKSKEVLEPAQKMAEWLTT
LKTTGFDMEAYRKLADTRVQDGLTPAPLAQEPADVGLAVTQAISLLSERKTQFTYADVLAKTVGQLPALD
GVIQQAREGIDEAIARQQLIPLDKEKGIFTSDVHVLDELSIDALSKEVMRQGHVHVSPNSKIDRPAPYSD
AVSVLAQDKPPMAILSGAGGALVQRGRVAELVHLAHEQGREVQILAGDTKARAYLQQDEQLTKEAVLPKR
SMLDGTAFVPNSTLIVEQGEKLTLKEAVSLLDGAVRNNVQLLVMDSQQRSGTGSALNVLRDAGVNDYRYQ
GGKQIDAVVVGEADKNQRYAQLAHDYVAHLQAGGKGVVQTSGVREQDILTDTVRAELKTQGVLSQQDITV
PTLVPVWVDSKSRTVRDHYREGMVMEKWDGETKTHERFVIERVTGKTHSLTLRNEAGESQQIKLSALNSQ
WSLYRSEQLPVAVGEKLNVLGKMPEHKLRAGDELNVVSHAEGKIAVVRNGKGASQSLPVGDSPFSAIKVG
HAWVEGLGRSVSDEATVFVAASNRDLDKMTLNQLSRSGAQIQMYSAQSPEKTAEKLTRHPAFKVVTQQIK
TVAGESVLDAALLHQKTALNTPVQQAIHLAIPSLENQKLAFSRVSLLAAAQEFSNGKLTQPEIEQEVRQQ
VKEGALIAVDVAQGHGNDLLVSRASFEAEKSIIRHIAEGKEAVTPLMSDVPESLVAGLTTGQQAATRMIL
ETPDRFVAVQGYAGVGKTTQFRAVMQAINTLPEERRPKVVGLGPTHRAVGEMRSAGLDAQTLASFLYDTA
QQQRQGETPDYRNTVFVVDESSMLGNTDMAKTYALIAAGGGRAVFSGDHDQLQPIAPGQPFKLQQRRSAA
DVAIMQEIVRQTPALRPAVYRMIERDISGALATVESVAPIQVPRQPGAWVPDSSVMEFTRKQEDAIREAS
QEAGDGLRIDEGKPTTLYESIVADYMGRTPDARAQTLIVTHLNDDRRAVNAMIHSARENAGELGGNTSIP
ILVTANVRDGELRRLSTWEEHRGDRVLMDNTYHQIADIDKQAELITLRDNAGNTRLLSPREAASEGVTLY
KQDVITVGVGDKMRFSKSDNERGYIANSVWTVSDVAGDSVTLTDGQQQRTVKPYRDEAQSHIDLAYAVTA
HGAQGASESFAIALEGTDGGRKQMVSFESVYVALSRSKQHVQVYTDNREGWVNAMGKTQARSTAHDVLAP
RDERTVNNAERLMRQATPLPEVAVGRALLKQSGLQEGQSLARFIAPGRKYPQPHVALPAFDQNGKSAGVW
LAPMTQGESLDVNALSTEGRVFGSEEAQFVALQASRNGENQLATTMREGVTLAARHPDSGVVVRLSGDGR
PWNPAAMTGGKLWVDKVAEVTAGTATDTAVDITPADVGDSRRAEEIAREALEKQAEKIAQEMLGADKPEQ
DVTLPDEKVKALVGDVIKGLAGTRDDKSPLPELPDARVQTEAVNKVVAENQQRERLQQLDNEVVRDLQRE
KTLGGD

Protein domains

Predicted by InterproScan.

• TrwC relaxase (TrwC) (11-282)

• AAA domain (AAA_30) (968-1153)

• DNA helicase TraI (TraI_C) (1432-1549)

• DNA relaxase TraI 2B/2B-like domain (TraI_2B) (632-711)

• single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N) (574-626)

Protein structure

No available structure.

Auxiliary protein

WP_046360191_FDAARGOS_1439|unnamed2

• ID: 7319
• GenBank: WP_046360191
• Name: WP_046360191_FDAARGOS_1439|unnamed2
• UniProt ID: _
• Length: 127 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 127 a.a.
• Molecular weight: 14410.54 Da
• Isoelectric Point: 4.8151

>WP_046360191.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Hafnia]
MARIQVYVSDEVSEKINAITLKRRAEGAKEKDISNSSIASMLLELGLRVYEAQMERKESGFNQMEFNKVL
LENVVKTQLSMAKVLGISSLSPHVASLEKFKYSTMVENIMDDAKTIIDNFFQVNEEE

Protein domains

Predicted by InterproScan.

• TraM protein, DNA-binding (Tra_M) (1-126)

Protein structure

No available structure.

T4CP

traC_I6L69_RS22795_FDAARGOS_1439|unnamed2

• ID: 15401
• GenBank: WP_080939130
• Name: traC_I6L69_RS22795_FDAARGOS_1439|unnamed2
• UniProt ID: _
• Length: 875 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 875 a.a.
• Molecular weight: 98895.42 Da
• Isoelectric Point: 5.1660

>WP_080939130.1 MULTISPECIES: type IV secretion system protein TraC [Hafnia]
MSALEKITDTVNSMLSALKMPDESTAANQILANMKFPQFSRLLPYRDYDEETGLFMNATTMGFVLEAQPL
VGANVQVVESLENLLRTKMPRGIPLSIHLMSSKQVGEGIEYGLREFSWSGEQAPKFNAITRAYYMRAAET
RFSLPDGMDLPLTLRNYRLIISCCVPSKKKSRADILELENRYKIIRASLHGASIHTQPVDAQGFINIVGE
MVNHDPDQLYPQRRELDTYMDLNYQCIDDSFDLKVKAECLTIGLRSGTQQETSRARVLNFQLARNPEIAF
LWNSADNYSNLLTPELSIACPFIITLTLMVEDQVKSHSEANLKYLDLEKKSKTSYGKFFPGVEQEAKEWG
DLRQRLAGNQSSIVSYFMNITAFCEDDNEKALEYEQDIVNSYRKNGFELTSPRFNHMRNFLSSLPFMAGE
GLFKELQAAGVIRRAETFNVANLMPVVADSPLAPSGLLAPTYRNQLAFIDLFYEGMNNTNFNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAWVFDMGGGYKSLCENMGGVYLDGDTLKFNPFANIIDIDLSAERVRDQLS
VMASPNGNLDEVHEALLMRAVKAAWLSKQNKARIDDVVDYLEFSKNSDEYKDSPTIRSRLDEMIVLLDQY
TVKGTYGEYFNSDEPSLSEDARMVVLELGGLESRQSLLVAVMFSLIIYIENRMYDTPRTVKKLNVIDEGW
KLLDFKNQKVGTFIEKGYRTARRHNGSYITITQNIVDFDSPEASSAARAAWGNSSYKAILKQSAKEFAKY
NQLYPDQFKPFERDMIAKFGSAKKQWFSSFMLSVEAQSSWHRLFVDPLSRAMYSSKGEDFEFIQTKRQEG
MGIHDAVYALACRNFPQEMASLEAWVDEHDNGSIK

Protein domains

Predicted by InterproScan.

• TraC protein (TraC_F_IV) (37-276)

• TraG P-loop domain (P-loop_TraG) (468-772)

• Family of unknown function (DUF5934) (DUF5934) (290-447)

Protein structure

No available structure.

traD_I6L69_RS22880_FDAARGOS_1439|unnamed2

• ID: 15402
• GenBank: WP_046360167
• Name: traD_I6L69_RS22880_FDAARGOS_1439|unnamed2
• UniProt ID: _
• Length: 740 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 740 a.a.
• Molecular weight: 82793.16 Da
• Isoelectric Point: 5.2446

>WP_046360167.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Hafnia]
MSFNAKDMTQGGQIAAMRFRMFGQIANIIFYCLFLLFLTITTLTLMFRLSWQTFINGIIYWWCRTLGPMR
ELMRSQPVYQIEYYGKKFPYNAQQILNDKYTLWCGEQLWTSFVIAAVVGGIVCTVTFFVASWILGHQGKK
QSEDEITGGRKLTDDPKEVAAMLKRDGNASDIKIEKLPLIKNSEIQNFCLHGTVGSGKSEFIRRLMNHAR
KRGDMVIVYDRSCEFVKSYYDPAKDKILNPLDARCANWDLWRECLTQPDFDNVANTLIPMGSSEDPFWQG
SGRTIFAEAGFRMRKDDDRSYAKLVDTLLSIKIDKLRAYLKSTPAANLVDEKIEKTAISIRAVLTNYVKA
IRYLQGIERNGEPFTIRDWMRGVREDGNNGWLFISSNADTHASLKPVISMWLSLAIRGLLAMGENRQRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVLGFQSYAQLEDIYGAKGAATLFDVLNTRAFFRSPSKQIA
DFAAGEIGEKEQLKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDIQTLPDLTCYITLPGPYPAVKLPL
KYQVRPKVAPEFIARSIDTDAETHLSAVLAAREEEGRGIAELFTPDAETAEPAATENEPVAETATQTQTT
PPVTPLREESAPKPAPKTSPKAAAASTTAASATAAAVVAPVGGVEQELEEHEEALPPGIDSQGELVDPDA
YERWQAEHEANGQRTMQRREEVNINHGQSSHDDVEVGDTF

Protein domains

Predicted by InterproScan.

• Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind) (173-560)

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

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 40149..67295

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
I6L69_RS22695 (I6L69_22690)	36460..36864	+	405	WP_052739773	conjugation system SOS inhibitor PsiB family protein	-
I6L69_RS22700 (I6L69_22695)	36861..37586	+	726	WP_052739772	plasmid SOS inhibition protein A	-
I6L69_RS22705 (I6L69_22700)	38360..38722	+	363	WP_046360195	hypothetical protein	-
I6L69_RS22710 (I6L69_22705)	38810..39046	+	237	WP_046360194	hypothetical protein	-
I6L69_RS22715 (I6L69_22710)	39099..39926	+	828	WP_046360193	DUF932 domain-containing protein	-
I6L69_RS22720 (I6L69_22715)	40149..40625	-	477	WP_046360192	transglycosylase SLT domain-containing protein	virB1
I6L69_RS22725 (I6L69_22720)	41062..41445	+	384	WP_046360191	conjugal transfer relaxosome DNA-binding protein TraM	-
I6L69_RS22730 (I6L69_22725)	41641..42369	+	729	WP_046360190	PAS domain-containing protein	-
I6L69_RS23570	42741..42908	+	168	WP_230676555	TraY domain-containing protein	-
I6L69_RS22740 (I6L69_22735)	42976..43341	+	366	WP_046360189	type IV conjugative transfer system pilin TraA	-
I6L69_RS22745 (I6L69_22740)	43357..43662	+	306	WP_046360188	type IV conjugative transfer system protein TraL	traL
I6L69_RS22750 (I6L69_22745)	43680..44246	+	567	WP_046360187	type IV conjugative transfer system protein TraE	traE
I6L69_RS22755 (I6L69_22750)	44233..44967	+	735	WP_046360186	type-F conjugative transfer system secretin TraK	traK
I6L69_RS22760 (I6L69_22755)	44964..46358	+	1395	WP_046360185	F-type conjugal transfer pilus assembly protein TraB	traB
I6L69_RS22765 (I6L69_22760)	46348..46716	+	369	WP_046360184	hypothetical protein	-
I6L69_RS22770 (I6L69_22765)	46718..46930	+	213	WP_046360183	hypothetical protein	-
I6L69_RS22775 (I6L69_22770)	46965..47501	+	537	WP_046360182	type IV conjugative transfer system lipoprotein TraV	traV
I6L69_RS22780 (I6L69_22775)	47632..47853	+	222	WP_230676554	TraR/DksA family transcriptional regulator	-
I6L69_RS22785 (I6L69_22780)	47876..48304	+	429	WP_155397564	hypothetical protein	-
I6L69_RS22790 (I6L69_22785)	48342..48803	+	462	WP_046360181	hypothetical protein	-
I6L69_RS22795 (I6L69_22790)	48860..51487	+	2628	WP_080939130	type IV secretion system protein TraC	virb4
I6L69_RS22800 (I6L69_22795)	51487..51873	+	387	WP_046360179	type-F conjugative transfer system protein TrbI	-
I6L69_RS22805 (I6L69_22800)	51877..52509	+	633	WP_046360178	type-F conjugative transfer system protein TraW	traW
I6L69_RS22810 (I6L69_22805)	52506..53498	+	993	WP_046360177	conjugal transfer pilus assembly protein TraU	traU
I6L69_RS22815 (I6L69_22810)	53512..54096	+	585	WP_046360176	hypothetical protein	-
I6L69_RS22820 (I6L69_22815)	54165..54758	+	594	WP_046360175	hypothetical protein	-
I6L69_RS22825 (I6L69_22820)	54814..55005	+	192	WP_155397563	hypothetical protein	-
I6L69_RS22830 (I6L69_22825)	55095..55763	+	669	WP_052739771	type-F conjugative transfer system pilin assembly protein TrbC	trbC
I6L69_RS22835 (I6L69_22830)	55756..57588	+	1833	WP_230676553	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
I6L69_RS22840 (I6L69_22835)	57732..58457	+	726	WP_046360202	type-F conjugative transfer system pilin assembly protein TraF	traF
I6L69_RS22845 (I6L69_22840)	58469..58705	+	237	WP_046360173	type-F conjugative transfer system pilin chaperone TraQ	-
I6L69_RS22850 (I6L69_22845)	58698..59252	+	555	WP_046360172	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
I6L69_RS22855 (I6L69_22850)	59264..59854	+	591	WP_046360201	DUF2726 domain-containing protein	-
I6L69_RS22860 (I6L69_22855)	59851..60180	+	330	WP_046360171	hypothetical protein	-
I6L69_RS22865 (I6L69_22860)	60167..61537	+	1371	WP_046360170	conjugal transfer pilus assembly protein TraH	traH
I6L69_RS22870 (I6L69_22865)	61537..64389	+	2853	WP_046360169	conjugal transfer mating-pair stabilization protein TraG	traG
I6L69_RS22875 (I6L69_22870)	64386..64931	+	546	WP_046360168	hypothetical protein	-
I6L69_RS22880 (I6L69_22875)	65073..67295	+	2223	WP_046360167	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 21238
• GenBank: NZ_JAHWJA010000003
• Plasmid name: FDAARGOS_1439|unnamed2
• Incompatibility group: IncFII
• Plasmid size: 98780 bp
• Coordinate of oriT [Strand]: 40702..40813 [+]
• Host baterium: Hafnia alvei strain FDAARGOS_1439

Cargo genes

• Drug resistance gene: -
• Virulence gene: mrkF, mrkC
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -