oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	102283
Name	oriT_OLF-FSR1-STCopenhagen-55\|unnamed1
Organism	Salmonella enterica subsp. enterica serovar Copenhagen strain OLF-FSR1-STCopenhagen-55
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_PYVA01000040 (54852..55121 [+], 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-55|unnamed1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_C5I07_RS24810_OLF-FSR1-STCopenhagen-55|unnamed1

ID	1751	GenBank	WP_000986921
Name	traI_C5I07_RS24810_OLF-FSR1-STCopenhagen-55\|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-55|unnamed1
WP_001676655_OLF-FSR1-STCopenhagen-55|unnamed1

ID	689	GenBank	WP_001151546
Name	WP_001151546_OLF-FSR1-STCopenhagen-55\|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	690	GenBank	WP_001676655
Name	WP_001676655_OLF-FSR1-STCopenhagen-55\|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_C5I07_RS24715_OLF-FSR1-STCopenhagen-55|unnamed1
traD_C5I07_RS24795_OLF-FSR1-STCopenhagen-55|unnamed1

ID	1340	GenBank	WP_000793310
Name	traC_C5I07_RS24715_OLF-FSR1-STCopenhagen-55\|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	1341	GenBank	WP_080076934
Name	traD_C5I07_RS24795_OLF-FSR1-STCopenhagen-55\|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: 54311..80667

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
C5I07_RS24615 (C5I07_24600)	49467..51464	+	1998	WP_000117513	ParB/RepB/Spo0J family partition protein	-
C5I07_RS24620 (C5I07_24605)	51504..51938	+	435	WP_010999943	conjugation system SOS inhibitor PsiB	-
C5I07_RS24625 (C5I07_24610)	51935..52672	+	738	WP_000581933	plasmid SOS inhibition protein A	-
C5I07_RS25465	52707..52835	+	129	WP_000372429	hypothetical protein	-
C5I07_RS25160	52921..53079	+	159	WP_001704449	hypothetical protein	-
C5I07_RS25165 (C5I07_24615)	53182..54000	+	819	Protein_69	DUF932 domain-containing protein	-
C5I07_RS24635 (C5I07_24620)	54311..54781	-	471	WP_001526856	transglycosylase SLT domain-containing protein	virB1
C5I07_RS24645 (C5I07_24630)	55196..55576	+	381	WP_001151546	conjugal transfer relaxosome DNA-binding protein TraM	-
C5I07_RS24650 (C5I07_24635)	55769..56455	+	687	WP_000336297	PAS domain-containing protein	-
C5I07_RS24655 (C5I07_24640)	56549..56776	+	228	WP_001676655	conjugal transfer relaxosome protein TraY	-
C5I07_RS24660 (C5I07_24645)	56818..57180	+	363	WP_001274201	type IV conjugative transfer system pilin TraA	-
C5I07_RS24665 (C5I07_24650)	57195..57506	+	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
C5I07_RS24670 (C5I07_24655)	57528..58094	+	567	WP_000399768	type IV conjugative transfer system protein TraE	traE
C5I07_RS24675 (C5I07_24660)	58081..58821	+	741	WP_001230719	type-F conjugative transfer system secretin TraK	traK
C5I07_RS24680 (C5I07_24665)	58821..60242	+	1422	WP_000146700	F-type conjugal transfer pilus assembly protein TraB	traB
C5I07_RS24685 (C5I07_24670)	60232..60828	+	597	WP_000527896	conjugal transfer pilus-stabilizing protein TraP	-
C5I07_RS24690 (C5I07_24675)	60806..61051	+	246	WP_010999944	DUF2689 domain-containing protein	virb4
C5I07_RS24695 (C5I07_24680)	61048..61563	+	516	WP_001079995	type IV conjugative transfer system lipoprotein TraV	traV
C5I07_RS24700 (C5I07_24685)	61698..61919	+	222	WP_001278699	conjugal transfer protein TraR	-
C5I07_RS24705 (C5I07_24690)	61912..62379	+	468	WP_000549562	hypothetical protein	-
C5I07_RS24710 (C5I07_24695)	62496..62759	+	264	WP_001239255	hypothetical protein	-
C5I07_RS24715 (C5I07_24700)	62775..65423	+	2649	WP_000793310	type IV secretion system protein TraC	virb4
C5I07_RS24720 (C5I07_24705)	65398..65784	+	387	WP_000105164	type-F conjugative transfer system protein TrbI	-
C5I07_RS24725 (C5I07_24710)	65781..66413	+	633	WP_000871995	type-F conjugative transfer system protein TraW	traW
C5I07_RS24730 (C5I07_24715)	66410..67402	+	993	WP_000833320	conjugal transfer pilus assembly protein TraU	traU
C5I07_RS24735 (C5I07_24720)	67421..67729	+	309	WP_010999945	hypothetical protein	-
C5I07_RS24740 (C5I07_24725)	67714..68352	+	639	WP_000554823	type-F conjugative transfer system pilin assembly protein TrbC	trbC
C5I07_RS24745 (C5I07_24730)	68389..68808	+	420	WP_001229397	HNH endonuclease signature motif containing protein	-
C5I07_RS24750 (C5I07_24735)	68805..70631	+	1827	WP_000827528	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
C5I07_RS24755 (C5I07_24740)	70642..70857	+	216	WP_000700023	conjugal transfer protein TrbE	-
C5I07_RS24760 (C5I07_24745)	70869..71618	+	750	WP_001226854	type-F conjugative transfer system pilin assembly protein TraF	traF
C5I07_RS24765 (C5I07_24750)	71832..72125	+	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
C5I07_RS24770 (C5I07_24755)	72112..72660	+	549	WP_000055840	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
C5I07_RS24775 (C5I07_24760)	72650..74032	+	1383	WP_001161719	conjugal transfer pilus assembly protein TraH	traH
C5I07_RS24780 (C5I07_24765)	74029..76851	+	2823	WP_080076933	conjugal transfer mating-pair stabilization protein TraG	traG
C5I07_RS24785 (C5I07_24770)	76867..77361	+	495	WP_010999946	entry exclusion protein	-
C5I07_RS24790 (C5I07_24775)	77397..78128	+	732	WP_000782438	conjugal transfer complement resistance protein TraT	-
C5I07_RS24795 (C5I07_24780)	78505..80667	+	2163	WP_080076934	type IV conjugative transfer system coupling protein TraD	virb4
C5I07_RS24800 (C5I07_24785)	80676..81074	-	399	WP_000911322	type II toxin-antitoxin system VapC family toxin	-
C5I07_RS24805 (C5I07_24790)	81074..81301	-	228	WP_000450265	toxin-antitoxin system antitoxin VapB	-

Host bacterium

ID	2727	GenBank	NZ_PYVA01000040
Plasmid name	OLF-FSR1-STCopenhagen-55\|unnamed1	Incompatibility group	IncFIB
Plasmid size	91747 bp	Coordinate of oriT [Strand]	54852..55121 [+]
Host baterium	Salmonella enterica subsp. enterica serovar Copenhagen strain OLF-FSR1-STCopenhagen-55

Cargo genes

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