Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 113635
• Name: oriT_pSH11G993-2
• Organism: Salmonella enterica subsp. enterica serovar Typhimurium
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_OP905632 (17191..17460 [+], 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_pSH11G993-2
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCACCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_QZJ82_RS00275_pSH11G993-2

• ID: 8733
• GenBank: WP_000986921
• Name: traI_QZJ82_RS00275_pSH11G993-2
• 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_pSH11G993-2

• ID: 5114
• GenBank: WP_001151546
• Name: WP_001151546_pSH11G993-2
• 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_pSH11G993-2

• ID: 5115
• GenBank: WP_001676655
• Name: WP_001676655_pSH11G993-2
• 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_QZJ82_RS00180_pSH11G993-2

• ID: 10111
• GenBank: WP_000793310
• Name: traC_QZJ82_RS00180_pSH11G993-2
• 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_QZJ82_RS00260_pSH11G993-2

• ID: 10112
• GenBank: WP_053299623
• Name: traD_QZJ82_RS00260_pSH11G993-2
• UniProt ID: _
• Length: 735 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 735 a.a.
• Molecular weight: 83213.90 Da
• Isoelectric Point: 5.1045

>WP_053299623.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQPTVVSDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQ
EQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

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: 16650..43051

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
QZJ82_RS00075 (OEDFHHLC_00013)	11806..13803	+	1998	WP_000117513	ParB/RepB/Spo0J family partition protein	-
QZJ82_RS00080 (OEDFHHLC_00014)	13843..14277	+	435	WP_010999943	conjugation system SOS inhibitor PsiB	-
QZJ82_RS00085 (OEDFHHLC_00015)	14274..15011	+	738	WP_000581933	plasmid SOS inhibition protein A	-
QZJ82_RS00090	15046..15174	+	129	WP_000372429	hypothetical protein	-
QZJ82_RS00095	15248..15418	+	171	WP_000229547	hypothetical protein	-
QZJ82_RS00100	15521..16339	+	819	Protein_19	DUF932 domain-containing protein	-
QZJ82_RS00105 (OEDFHHLC_00018)	16650..17120	-	471	WP_001526856	transglycosylase SLT domain-containing protein	virB1
QZJ82_RS00110	17535..17915	+	381	WP_001151546	conjugal transfer relaxosome DNA-binding protein TraM	-
QZJ82_RS00115 (OEDFHHLC_00019)	18108..18794	+	687	WP_000336297	PAS domain-containing protein	-
QZJ82_RS00120 (OEDFHHLC_00020)	18888..19115	+	228	WP_001676655	conjugal transfer relaxosome protein TraY	-
QZJ82_RS00125 (OEDFHHLC_00021)	19157..19519	+	363	WP_001274201	type IV conjugative transfer system pilin TraA	-
QZJ82_RS00130 (OEDFHHLC_00022)	19534..19845	+	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
QZJ82_RS00135 (OEDFHHLC_00023)	19867..20433	+	567	WP_000399769	type IV conjugative transfer system protein TraE	traE
QZJ82_RS00140 (OEDFHHLC_00024)	20420..21160	+	741	WP_001230719	type-F conjugative transfer system secretin TraK	traK
QZJ82_RS00145 (OEDFHHLC_00025)	21160..22581	+	1422	WP_000146700	F-type conjugal transfer pilus assembly protein TraB	traB
QZJ82_RS00150 (OEDFHHLC_00026)	22571..23167	+	597	WP_000527896	conjugal transfer pilus-stabilizing protein TraP	-
QZJ82_RS00155 (OEDFHHLC_00027)	23145..23390	+	246	WP_010999944	DUF2689 domain-containing protein	virb4
QZJ82_RS00160 (OEDFHHLC_00028)	23387..23902	+	516	WP_001079995	type IV conjugative transfer system lipoprotein TraV	traV
QZJ82_RS00165 (OEDFHHLC_00029)	24037..24258	+	222	WP_001278699	conjugal transfer protein TraR	-
QZJ82_RS00170 (OEDFHHLC_00030)	24251..24718	+	468	WP_000549562	hypothetical protein	-
QZJ82_RS00175 (OEDFHHLC_00032)	24835..25098	+	264	WP_001239256	hypothetical protein	-
QZJ82_RS00180 (OEDFHHLC_00033)	25114..27762	+	2649	WP_000793310	type IV secretion system protein TraC	virb4
QZJ82_RS00185 (OEDFHHLC_00034)	27737..28123	+	387	WP_000105164	type-F conjugative transfer system protein TrbI	-
QZJ82_RS00190 (OEDFHHLC_00035)	28120..28752	+	633	WP_000871995	type-F conjugative transfer system protein TraW	traW
QZJ82_RS00195 (OEDFHHLC_00036)	28749..29741	+	993	WP_000833320	conjugal transfer pilus assembly protein TraU	traU
QZJ82_RS00200 (OEDFHHLC_00037)	29760..30068	+	309	WP_010999945	hypothetical protein	-
QZJ82_RS00205 (OEDFHHLC_00038)	30053..30691	+	639	WP_000554823	type-F conjugative transfer system pilin assembly protein TrbC	trbC
QZJ82_RS00210 (OEDFHHLC_00039)	30728..31147	+	420	WP_001229397	HNH endonuclease	-
QZJ82_RS00215 (OEDFHHLC_00040)	31144..32970	+	1827	WP_000827528	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
QZJ82_RS00220 (OEDFHHLC_00041)	32981..33196	+	216	WP_000700023	conjugal transfer protein TrbE	-
QZJ82_RS00225 (OEDFHHLC_00042)	33208..33957	+	750	WP_001226854	type-F conjugative transfer system pilin assembly protein TraF	traF
QZJ82_RS00230 (OEDFHHLC_00043)	34171..34464	+	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
QZJ82_RS00235 (OEDFHHLC_00044)	34451..34999	+	549	WP_000055840	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
QZJ82_RS00240 (OEDFHHLC_00045)	34989..36371	+	1383	WP_001161719	conjugal transfer pilus assembly protein TraH	traH
QZJ82_RS00245 (OEDFHHLC_00046)	36368..39190	+	2823	WP_001007086	conjugal transfer mating-pair stabilization protein TraG	traG
QZJ82_RS00250 (OEDFHHLC_00047)	39206..39700	+	495	WP_010999946	entry exclusion protein	-
QZJ82_RS00255 (OEDFHHLC_00048)	39736..40467	+	732	WP_000782438	conjugal transfer complement resistance protein TraT	-
QZJ82_RS00260 (OEDFHHLC_00049)	40844..43051	+	2208	WP_053299623	type IV conjugative transfer system coupling protein TraD	virb4
QZJ82_RS00265 (OEDFHHLC_00050)	43060..43458	-	399	WP_000911322	type II toxin-antitoxin system VapC family toxin	-
QZJ82_RS00270 (OEDFHHLC_00051)	43458..43685	-	228	WP_000450265	toxin-antitoxin system antitoxin VapB	-

Host bacterium

• ID: 14070
• GenBank: NZ_OP905632
• Plasmid name: pSH11G993-2
• Incompatibility group: IncFIB
• Plasmid size: 108575 bp
• Coordinate of oriT [Strand]: 17191..17460 [+]
• Host baterium: Salmonella enterica subsp. enterica serovar Typhimurium

Cargo genes

• Drug resistance gene: aac(6')-Il, sul1, aac(3)-IId
• Virulence gene: pefB, pefA, pefC, pefD, rck, spvB, spvC, fdeC
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -