Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 102916
• Name: oriT_FDAARGOS_94|unnamed
• Organism: Salmonella enterica strain FDAARGOS_94
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP014050 (3142..3411 [+], 270 nt)
• oriT length: 270 nt
• IRs (inverted repeats): 245..253, 262..270 (CACCCCTGG..CCAGGGGTG) 92..98, 111..117 (ATTTAAT..ATTAAAT) 103..108, 111..116 (TTTAAT..ATTAAA) 33..38, 41..46 (AAAATT..AATTTT)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 270 nt

>oriT_FDAARGOS_94|unnamed
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_AL463_RS00195_FDAARGOS_94|unnamed

• ID: 2188
• GenBank: WP_000986921
• Name: traI_AL463_RS00195_FDAARGOS_94|unnamed
• UniProt ID: Q93GL4
• Length: 1752 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1752 a.a.
• Molecular weight: 191683.72 Da
• Isoelectric Point: 5.9311

>WP_000986921.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Salmonella]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVVNVTQHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYRESADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIVADRRSQTNLKQDERLSGELITGRR
QLQEGMLFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGMREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKMPVADGERLMVTGKIPGLRVSVGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNSLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPESERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHS
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS
EREMMNAERLFSTARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIVGDGRPW
NPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPEEKT
AQAVREIAGQEQDRMTPPEREPPLPESVLREPQRERETIREVARENRGRERLQQMEQEMVRDLQKEKTPG
GD

Protein domains

Predicted by InterproScan.

• AAA domain (AAA_30) (967-1158)

• TrwC relaxase (TrwC) (11-282)

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

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

• DNA helicase TraI (TraI_C) (1430-1553)

Protein structure

• AlphaFold DB: Q93GL4

Auxiliary protein

WP_001151546_FDAARGOS_94|unnamed

• ID: 891
• GenBank: WP_001151546
• Name: WP_001151546_FDAARGOS_94|unnamed
• UniProt ID: Q93GP1
• Length: 126 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 126 a.a.
• Molecular weight: 14366.30 Da
• Isoelectric Point: 5.7236

>WP_001151546.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Salmonella]
MAKVNVYISNEVHNKITAIVEKRRQEGARDKDISFSGTSSMLLELGLRVYEAQMERKESPFNQTEFNKVL
LENVLKTQSSVAKILGIGSLSPHVAGNPKFEYANMVEDIKEKVSSEMERFFHENEE

Protein domains

Predicted by InterproScan.

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

Protein structure

• AlphaFold DB: Q93GP1

WP_001676655_FDAARGOS_94|unnamed

• ID: 892
• GenBank: WP_001676655
• Name: WP_001676655_FDAARGOS_94|unnamed
• UniProt ID: H3JT82
• Length: 75 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 75 a.a.
• Molecular weight: 9147.26 Da
• Isoelectric Point: 9.6183

>WP_001676655.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Salmonella]
MRRRNAREGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRYPDFYNEEIFREVIEETES
TFKEI

Protein domains

Predicted by InterproScan.

• TraY domain (TraY) (14-61)

Protein structure

• AlphaFold DB: H3JT82

T4CP

traC_AL463_RS00100_FDAARGOS_94|unnamed

• ID: 1859
• GenBank: WP_000793310
• Name: traC_AL463_RS00100_FDAARGOS_94|unnamed
• UniProt ID: _
• Length: 882 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 882 a.a.
• Molecular weight: 100382.20 Da
• Isoelectric Point: 6.9316

>WP_000793310.1 MULTISPECIES: type IV secretion system protein TraC [Salmonella]
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLRKFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQTVDAKAFINIVG
EMINHNPESIHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDNGKNSTARIMSFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVTNLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITNIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRGTYEYKAETD

Protein domains

Predicted by InterproScan.

• Family of unknown function (DUF5934) (DUF5934) (289-446)

• TraG P-loop domain (P-loop_TraG) (468-763)

• TraC protein (TraC_F_IV) (38-276)

Protein structure

No available structure.

traD_AL463_RS00180_FDAARGOS_94|unnamed

• ID: 1860
• GenBank: WP_000009320
• Name: traD_AL463_RS00180_FDAARGOS_94|unnamed
• UniProt ID: _
• Length: 747 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 747 a.a.
• Molecular weight: 84627.41 Da
• Isoelectric Point: 5.1045

>WP_000009320.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQPTVVSDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGE
VVDMAAYERWRQEQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

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: 2601..29038

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
AL463_RS00010 (AL463_00010)	225..962	+	738	WP_000581933	plasmid SOS inhibition protein A	-
AL463_RS26010	997..1125	+	129	WP_000372429	hypothetical protein	-
AL463_RS25575	1211..1369	+	159	WP_001704449	hypothetical protein	-
AL463_RS25580 (AL463_24045)	1472..2290	+	819	Protein_4	DUF932 domain-containing protein	-
AL463_RS00020 (AL463_00025)	2601..3071	-	471	WP_001526856	transglycosylase SLT domain-containing protein	virB1
AL463_RS00030 (AL463_00030)	3486..3866	+	381	WP_001151546	conjugal transfer relaxosome DNA-binding protein TraM	-
AL463_RS00035 (AL463_00035)	4059..4745	+	687	WP_000336297	PAS domain-containing protein	-
AL463_RS00040 (AL463_24055)	4839..5066	+	228	WP_001676655	conjugal transfer relaxosome protein TraY	-
AL463_RS00045 (AL463_00040)	5108..5470	+	363	WP_001274201	type IV conjugative transfer system pilin TraA	-
AL463_RS00050 (AL463_00045)	5485..5796	+	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
AL463_RS00055 (AL463_00050)	5818..6384	+	567	WP_000399769	type IV conjugative transfer system protein TraE	traE
AL463_RS00060 (AL463_00055)	6371..7111	+	741	WP_001230719	type-F conjugative transfer system secretin TraK	traK
AL463_RS00065 (AL463_00060)	7111..8532	+	1422	WP_000146700	F-type conjugal transfer pilus assembly protein TraB	traB
AL463_RS00070 (AL463_00065)	8522..9118	+	597	WP_000527896	conjugal transfer pilus-stabilizing protein TraP	-
AL463_RS00075 (AL463_00070)	9096..9341	+	246	WP_010999944	DUF2689 domain-containing protein	virb4
AL463_RS00080 (AL463_00075)	9338..9853	+	516	WP_001079995	type IV conjugative transfer system lipoprotein TraV	traV
AL463_RS00085 (AL463_00080)	9988..10209	+	222	WP_001278699	conjugal transfer protein TraR	-
AL463_RS00090 (AL463_00085)	10202..10669	+	468	WP_000549562	hypothetical protein	-
AL463_RS00095 (AL463_00090)	10786..11049	+	264	WP_001239256	hypothetical protein	-
AL463_RS00100 (AL463_00095)	11065..13713	+	2649	WP_000793310	type IV secretion system protein TraC	virb4
AL463_RS00105 (AL463_00100)	13688..14074	+	387	WP_000105164	type-F conjugative transfer system protein TrbI	-
AL463_RS00110 (AL463_00105)	14071..14703	+	633	WP_000871995	type-F conjugative transfer system protein TraW	traW
AL463_RS00115 (AL463_00110)	14700..15692	+	993	WP_000833320	conjugal transfer pilus assembly protein TraU	traU
AL463_RS00120 (AL463_00115)	15711..16019	+	309	WP_010999945	hypothetical protein	-
AL463_RS00125 (AL463_00120)	16004..16642	+	639	WP_000554823	type-F conjugative transfer system pilin assembly protein TrbC	trbC
AL463_RS00130 (AL463_00125)	16679..17098	+	420	WP_001229397	HNH endonuclease signature motif containing protein	-
AL463_RS00135 (AL463_00130)	17095..18921	+	1827	WP_000827528	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
AL463_RS00140 (AL463_00135)	18932..19147	+	216	WP_000700023	conjugal transfer protein TrbE	-
AL463_RS00145 (AL463_00140)	19159..19908	+	750	WP_001226854	type-F conjugative transfer system pilin assembly protein TraF	traF
AL463_RS00150 (AL463_00145)	20122..20415	+	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
AL463_RS00155 (AL463_00150)	20402..20950	+	549	WP_000055840	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
AL463_RS00160 (AL463_00155)	20940..22322	+	1383	WP_001161719	conjugal transfer pilus assembly protein TraH	traH
AL463_RS00165 (AL463_00160)	22319..25141	+	2823	WP_001007086	conjugal transfer mating-pair stabilization protein TraG	traG
AL463_RS00170 (AL463_00165)	25157..25651	+	495	WP_010999946	entry exclusion protein	-
AL463_RS00175 (AL463_00170)	25687..26418	+	732	WP_000782438	conjugal transfer complement resistance protein TraT	-
AL463_RS00180 (AL463_00175)	26795..29038	+	2244	WP_000009320	type IV conjugative transfer system coupling protein TraD	prgC
AL463_RS00185 (AL463_00180)	29047..29445	-	399	WP_000911322	type II toxin-antitoxin system VapC family toxin	-
AL463_RS00190 (AL463_00185)	29445..29672	-	228	WP_000450265	toxin-antitoxin system antitoxin VapB	-

Host bacterium

• ID: 3359
• GenBank: NZ_CP014050
• Plasmid name: FDAARGOS_94|unnamed
• Incompatibility group: IncFII
• Plasmid size: 93933 bp
• Coordinate of oriT [Strand]: 3142..3411 [+]
• Host baterium: Salmonella enterica strain FDAARGOS_94

Cargo genes

• Drug resistance gene: -
• Virulence gene: rck, pefD, pefC, pefA, pefB, spvC, spvB
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -