oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	102252
Name	oriT_OLF-FSR1-STCopenhagen-52\|unnamed1
Organism	Salmonella enterica subsp. enterica serovar Copenhagen strain OLF-FSR1-STCopenhagen-52
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_PYUY01000037 (54856..55125 [+], 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

Download Length: 270 nt

                        >oriT_OLF-FSR1-STCopenhagen-52|unnamed1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_C5H98_RS24850_OLF-FSR1-STCopenhagen-52|unnamed1

ID	1733	GenBank	WP_000986921
Name	traI_C5H98_RS24850_OLF-FSR1-STCopenhagen-52\|unnamed1	UniProt ID	Q93GL4
Length	1752 a.a.	PDB ID
Note	Predicted by oriTfinder 2.0

Relaxase protein sequence

Download 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

Source	ID	Structure
AlphaFold DB	Q93GL4

Auxiliary protein

WP_001151546_OLF-FSR1-STCopenhagen-52|unnamed1
WP_001676655_OLF-FSR1-STCopenhagen-52|unnamed1

ID	675	GenBank	WP_001151546
Name	WP_001151546_OLF-FSR1-STCopenhagen-52\|unnamed1	UniProt ID	Q93GP1
Length	126 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download 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

Source	ID	Structure
AlphaFold DB	Q93GP1

ID	676	GenBank	WP_001676655
Name	WP_001676655_OLF-FSR1-STCopenhagen-52\|unnamed1	UniProt ID	H3JT82
Length	75 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download 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

Source	ID	Structure
AlphaFold DB	H3JT82

T4CP

traC_C5H98_RS24755_OLF-FSR1-STCopenhagen-52|unnamed1
traD_C5H98_RS24835_OLF-FSR1-STCopenhagen-52|unnamed1

ID	1315	GenBank	WP_000793310
Name	traC_C5H98_RS24755_OLF-FSR1-STCopenhagen-52\|unnamed1	UniProt ID	_
Length	882 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download 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.

ID	1316	GenBank	WP_080076934
Name	traD_C5H98_RS24835_OLF-FSR1-STCopenhagen-52\|unnamed1	UniProt ID	_
Length	720 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 720 a.a. Molecular weight: 81443.01 Da Isoelectric Point: 5.0467

                        >WP_080076934.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]

MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQAFVNGGIYWWCTTLEGMR

DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ

QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR

QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA

VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA

DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL

KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQPTVV

SDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREE

VNINVHRGYGKDEPEPGDDF

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: 54315..80671

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
C5H98_RS24655 (C5H98_24630)	49471..51468	+	1998	WP_000117513	ParB/RepB/Spo0J family partition protein	-
C5H98_RS24660 (C5H98_24635)	51508..51942	+	435	WP_010999943	conjugation system SOS inhibitor PsiB	-
C5H98_RS24665 (C5H98_24640)	51939..52676	+	738	WP_000581933	plasmid SOS inhibition protein A	-
C5H98_RS25815	52711..52839	+	129	WP_000372429	hypothetical protein	-
C5H98_RS25465	52925..53083	+	159	WP_001704449	hypothetical protein	-
C5H98_RS24670 (C5H98_24645)	53186..54004	+	819	Protein_69	DUF932 domain-containing protein	-
C5H98_RS24675 (C5H98_24650)	54315..54785	-	471	WP_001526856	transglycosylase SLT domain-containing protein	virB1
C5H98_RS24685 (C5H98_24660)	55200..55580	+	381	WP_001151546	conjugal transfer relaxosome DNA-binding protein TraM	-
C5H98_RS24690 (C5H98_24665)	55773..56459	+	687	WP_000336297	PAS domain-containing protein	-
C5H98_RS24695 (C5H98_24670)	56553..56780	+	228	WP_001676655	conjugal transfer relaxosome protein TraY	-
C5H98_RS24700 (C5H98_24675)	56822..57184	+	363	WP_001274201	type IV conjugative transfer system pilin TraA	-
C5H98_RS24705 (C5H98_24680)	57199..57510	+	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
C5H98_RS24710 (C5H98_24685)	57532..58098	+	567	WP_000399768	type IV conjugative transfer system protein TraE	traE
C5H98_RS24715 (C5H98_24690)	58085..58825	+	741	WP_001230719	type-F conjugative transfer system secretin TraK	traK
C5H98_RS24720 (C5H98_24695)	58825..60246	+	1422	WP_000146700	F-type conjugal transfer pilus assembly protein TraB	traB
C5H98_RS24725 (C5H98_24700)	60236..60832	+	597	WP_000527896	conjugal transfer pilus-stabilizing protein TraP	-
C5H98_RS24730 (C5H98_24705)	60810..61055	+	246	WP_010999944	DUF2689 domain-containing protein	virb4
C5H98_RS24735 (C5H98_24710)	61052..61567	+	516	WP_001079995	type IV conjugative transfer system lipoprotein TraV	traV
C5H98_RS24740 (C5H98_24715)	61702..61923	+	222	WP_001278699	conjugal transfer protein TraR	-
C5H98_RS24745 (C5H98_24720)	61916..62383	+	468	WP_000549562	hypothetical protein	-
C5H98_RS24750 (C5H98_24725)	62500..62763	+	264	WP_001239255	hypothetical protein	-
C5H98_RS24755 (C5H98_24730)	62779..65427	+	2649	WP_000793310	type IV secretion system protein TraC	virb4
C5H98_RS24760 (C5H98_24735)	65402..65788	+	387	WP_000105164	type-F conjugative transfer system protein TrbI	-
C5H98_RS24765 (C5H98_24740)	65785..66417	+	633	WP_000871995	type-F conjugative transfer system protein TraW	traW
C5H98_RS24770 (C5H98_24745)	66414..67406	+	993	WP_000833320	conjugal transfer pilus assembly protein TraU	traU
C5H98_RS24775 (C5H98_24750)	67425..67733	+	309	WP_010999945	hypothetical protein	-
C5H98_RS24780 (C5H98_24755)	67718..68356	+	639	WP_000554823	type-F conjugative transfer system pilin assembly protein TrbC	trbC
C5H98_RS24785 (C5H98_24760)	68393..68812	+	420	WP_001229397	HNH endonuclease signature motif containing protein	-
C5H98_RS24790 (C5H98_24765)	68809..70635	+	1827	WP_000827528	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
C5H98_RS24795 (C5H98_24770)	70646..70861	+	216	WP_000700023	conjugal transfer protein TrbE	-
C5H98_RS24800 (C5H98_24775)	70873..71622	+	750	WP_001226854	type-F conjugative transfer system pilin assembly protein TraF	traF
C5H98_RS24805 (C5H98_24780)	71836..72129	+	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
C5H98_RS24810 (C5H98_24785)	72116..72664	+	549	WP_000055840	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
C5H98_RS24815 (C5H98_24790)	72654..74036	+	1383	WP_001161719	conjugal transfer pilus assembly protein TraH	traH
C5H98_RS24820 (C5H98_24795)	74033..76855	+	2823	WP_080076933	conjugal transfer mating-pair stabilization protein TraG	traG
C5H98_RS24825 (C5H98_24800)	76871..77365	+	495	WP_010999946	entry exclusion protein	-
C5H98_RS24830 (C5H98_24805)	77401..78132	+	732	WP_000782438	conjugal transfer complement resistance protein TraT	-
C5H98_RS24835 (C5H98_24810)	78509..80671	+	2163	WP_080076934	type IV conjugative transfer system coupling protein TraD	virb4
C5H98_RS24840 (C5H98_24815)	80680..81078	-	399	WP_000911322	type II toxin-antitoxin system VapC family toxin	-
C5H98_RS24845 (C5H98_24820)	81078..81305	-	228	WP_000450265	toxin-antitoxin system antitoxin VapB	-

Host bacterium

ID	2696	GenBank	NZ_PYUY01000037
Plasmid name	OLF-FSR1-STCopenhagen-52\|unnamed1	Incompatibility group	IncFIB
Plasmid size	91751 bp	Coordinate of oriT [Strand]	54856..55125 [+]
Host baterium	Salmonella enterica subsp. enterica serovar Copenhagen strain OLF-FSR1-STCopenhagen-52

Cargo genes

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