Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 105428
• Name: oriT_p20762-2
• Organism: Salmonella enterica subsp. enterica serovar Typhimurium strain CVM 20762
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP051406 (9725..9994 [+], 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_p20762-2
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_HFQ58_RS24015_p20762-2

• ID: 3701
• GenBank: WP_000986921
• Name: traI_HFQ58_RS24015_p20762-2
• 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_p20762-2

• ID: 1673
• GenBank: WP_001151546
• Name: WP_001151546_p20762-2
• 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_p20762-2

• ID: 1674
• GenBank: WP_001676655
• Name: WP_001676655_p20762-2
• 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_HFQ58_RS23920_p20762-2

• ID: 3688
• GenBank: WP_000793310
• Name: traC_HFQ58_RS23920_p20762-2
• 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_HFQ58_RS24000_p20762-2

• ID: 3689
• GenBank: WP_000009318
• Name: traD_HFQ58_RS24000_p20762-2
• UniProt ID: _
• Length: 720 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 720 a.a.
• Molecular weight: 81447.01 Da
• Isoelectric Point: 5.1045

>WP_000009318.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Salmonella]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQPTVV
SDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREE
VNINVHRGHGKDEPEPGDDF

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) (173-560)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 9184..35540

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HFQ58_RS23820 (HFQ58_23850)	4340..6337	+	1998	WP_000117513	ParB/RepB/Spo0J family partition protein	-
HFQ58_RS23825 (HFQ58_23855)	6377..6811	+	435	WP_010999943	conjugation system SOS inhibitor PsiB	-
HFQ58_RS23830 (HFQ58_23860)	6808..7545	+	738	WP_000581933	plasmid SOS inhibition protein A	-
HFQ58_RS24620	7580..7708	+	129	WP_000372429	hypothetical protein	-
HFQ58_RS23835 (HFQ58_23865)	7794..7952	+	159	WP_001704449	hypothetical protein	-
HFQ58_RS23840 (HFQ58_23870)	8055..8873	+	819	Protein_11	DUF932 domain-containing protein	-
HFQ58_RS23845 (HFQ58_23875)	9184..9654	-	471	WP_001526856	transglycosylase SLT domain-containing protein	virB1
HFQ58_RS23850 (HFQ58_23880)	10069..10449	+	381	WP_001151546	conjugal transfer relaxosome DNA-binding protein TraM	-
HFQ58_RS23855 (HFQ58_23885)	10642..11328	+	687	WP_000336297	PAS domain-containing protein	-
HFQ58_RS23860 (HFQ58_23890)	11422..11649	+	228	WP_001676655	conjugal transfer relaxosome protein TraY	-
HFQ58_RS23865 (HFQ58_23895)	11691..12053	+	363	WP_001274201	type IV conjugative transfer system pilin TraA	-
HFQ58_RS23870 (HFQ58_23900)	12068..12379	+	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
HFQ58_RS23875 (HFQ58_23905)	12401..12967	+	567	WP_000399768	type IV conjugative transfer system protein TraE	traE
HFQ58_RS23880 (HFQ58_23910)	12954..13694	+	741	WP_001230719	type-F conjugative transfer system secretin TraK	traK
HFQ58_RS23885 (HFQ58_23915)	13694..15115	+	1422	WP_000146700	F-type conjugal transfer pilus assembly protein TraB	traB
HFQ58_RS23890 (HFQ58_23920)	15105..15701	+	597	WP_000527896	conjugal transfer pilus-stabilizing protein TraP	-
HFQ58_RS23895 (HFQ58_23925)	15679..15924	+	246	WP_010999944	DUF2689 domain-containing protein	virb4
HFQ58_RS23900 (HFQ58_23930)	15921..16436	+	516	WP_001079995	type IV conjugative transfer system lipoprotein TraV	traV
HFQ58_RS23905 (HFQ58_23935)	16571..16792	+	222	WP_001278699	conjugal transfer protein TraR	-
HFQ58_RS23910 (HFQ58_23940)	16785..17252	+	468	WP_000549562	hypothetical protein	-
HFQ58_RS23915 (HFQ58_23945)	17369..17632	+	264	WP_001239255	hypothetical protein	-
HFQ58_RS23920 (HFQ58_23950)	17648..20296	+	2649	WP_000793310	type IV secretion system protein TraC	virb4
HFQ58_RS23925 (HFQ58_23955)	20271..20657	+	387	WP_000105164	type-F conjugative transfer system protein TrbI	-
HFQ58_RS23930 (HFQ58_23960)	20654..21286	+	633	WP_000871995	type-F conjugative transfer system protein TraW	traW
HFQ58_RS23935 (HFQ58_23965)	21283..22275	+	993	WP_000833320	conjugal transfer pilus assembly protein TraU	traU
HFQ58_RS23940 (HFQ58_23970)	22294..22602	+	309	WP_010999945	hypothetical protein	-
HFQ58_RS23945 (HFQ58_23975)	22587..23225	+	639	WP_000554823	type-F conjugative transfer system pilin assembly protein TrbC	trbC
HFQ58_RS23950 (HFQ58_23980)	23262..23681	+	420	WP_001229397	HNH endonuclease signature motif containing protein	-
HFQ58_RS23955 (HFQ58_23985)	23678..25504	+	1827	WP_000827528	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
HFQ58_RS23960 (HFQ58_23990)	25515..25730	+	216	WP_000700023	conjugal transfer protein TrbE	-
HFQ58_RS23965 (HFQ58_23995)	25742..26491	+	750	WP_001226854	type-F conjugative transfer system pilin assembly protein TraF	traF
HFQ58_RS23970 (HFQ58_24000)	26705..26998	+	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
HFQ58_RS23975 (HFQ58_24005)	26985..27533	+	549	WP_000055840	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
HFQ58_RS23980 (HFQ58_24010)	27523..28905	+	1383	WP_001161719	conjugal transfer pilus assembly protein TraH	traH
HFQ58_RS23985 (HFQ58_24015)	28902..31724	+	2823	WP_001007086	conjugal transfer mating-pair stabilization protein TraG	traG
HFQ58_RS23990 (HFQ58_24020)	31740..32234	+	495	WP_010999946	entry exclusion protein	-
HFQ58_RS23995 (HFQ58_24025)	32270..33001	+	732	WP_000782438	conjugal transfer complement resistance protein TraT	-
HFQ58_RS24000 (HFQ58_24030)	33378..35540	+	2163	WP_000009318	type IV conjugative transfer system coupling protein TraD	virb4
HFQ58_RS24005 (HFQ58_24035)	35549..35947	-	399	WP_000911322	type II toxin-antitoxin system VapC family toxin	-
HFQ58_RS24010 (HFQ58_24040)	35947..36174	-	228	WP_000450265	toxin-antitoxin system antitoxin VapB	-

Host bacterium

• ID: 5866
• GenBank: NZ_CP051406
• Plasmid name: p20762-2
• Incompatibility group: IncFII
• Plasmid size: 95919 bp
• Coordinate of oriT [Strand]: 9725..9994 [+]
• Host baterium: Salmonella enterica subsp. enterica serovar Typhimurium strain CVM 20762

Cargo genes

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