Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 102263
• Name: oriT_OLF-FSR1-STCopenhagen-53|unnamed1
• Organism: Salmonella enterica subsp. enterica serovar Copenhagen strain OLF-FSR1-STCopenhagen-53
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_PYUZ01000037 (54861..55130 [+], 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_OLF-FSR1-STCopenhagen-53|unnamed1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_C5H99_RS24815_OLF-FSR1-STCopenhagen-53|unnamed1

• ID: 1742
• GenBank: WP_107326555
• Name: traI_C5H99_RS24815_OLF-FSR1-STCopenhagen-53|unnamed1
• UniProt ID: _
• Length: 1752 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1752 a.a.
• Molecular weight: 191713.81 Da
• Isoelectric Point: 5.9311

>WP_107326555.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVVNVMQHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
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

No available structure.

Auxiliary protein

WP_001151546_OLF-FSR1-STCopenhagen-53|unnamed1

• ID: 684
• GenBank: WP_001151546
• Name: WP_001151546_OLF-FSR1-STCopenhagen-53|unnamed1
• 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_OLF-FSR1-STCopenhagen-53|unnamed1

• ID: 685
• GenBank: WP_001676655
• Name: WP_001676655_OLF-FSR1-STCopenhagen-53|unnamed1
• 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_C5H99_RS24720_OLF-FSR1-STCopenhagen-53|unnamed1

• ID: 1330
• GenBank: WP_000793310
• Name: traC_C5H99_RS24720_OLF-FSR1-STCopenhagen-53|unnamed1
• 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_C5H99_RS24800_OLF-FSR1-STCopenhagen-53|unnamed1

• ID: 1331
• GenBank: WP_107326554
• Name: traD_C5H99_RS24800_OLF-FSR1-STCopenhagen-53|unnamed1
• UniProt ID: _
• Length: 720 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 720 a.a.
• Molecular weight: 81473.04 Da
• Isoelectric Point: 5.0467

>WP_107326554.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR
QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQPTVV
SDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREE
VNINVHRGYGKDEPEPGDDF

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: 54320..80675

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
C5H99_RS24620 (C5H99_24605)	49476..51473	+	1998	WP_000117513	ParB/RepB/Spo0J family partition protein	-
C5H99_RS24625 (C5H99_24610)	51513..51947	+	435	WP_010999943	conjugation system SOS inhibitor PsiB	-
C5H99_RS24630 (C5H99_24615)	51944..52681	+	738	WP_000581933	plasmid SOS inhibition protein A	-
C5H99_RS25500	52716..52844	+	129	WP_000372429	hypothetical protein	-
C5H99_RS25175	52930..53088	+	159	WP_001704449	hypothetical protein	-
C5H99_RS24635 (C5H99_24620)	53191..54009	+	819	Protein_69	DUF932 domain-containing protein	-
C5H99_RS24640 (C5H99_24625)	54320..54790	-	471	WP_001526856	transglycosylase SLT domain-containing protein	virB1
C5H99_RS24650 (C5H99_24635)	55205..55585	+	381	WP_001151546	conjugal transfer relaxosome DNA-binding protein TraM	-
C5H99_RS24655 (C5H99_24640)	55778..56464	+	687	WP_000336297	PAS domain-containing protein	-
C5H99_RS24660 (C5H99_24645)	56558..56785	+	228	WP_001676655	conjugal transfer relaxosome protein TraY	-
C5H99_RS24665 (C5H99_24650)	56827..57189	+	363	WP_107326551	type IV conjugative transfer system pilin TraA	-
C5H99_RS24670 (C5H99_24655)	57204..57515	+	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
C5H99_RS24675 (C5H99_24660)	57537..58103	+	567	WP_000399768	type IV conjugative transfer system protein TraE	traE
C5H99_RS24680 (C5H99_24665)	58090..58830	+	741	WP_001230719	type-F conjugative transfer system secretin TraK	traK
C5H99_RS24685 (C5H99_24670)	58830..60251	+	1422	WP_000146700	F-type conjugal transfer pilus assembly protein TraB	traB
C5H99_RS24690 (C5H99_24675)	60241..60837	+	597	WP_107339037	conjugal transfer pilus-stabilizing protein TraP	-
C5H99_RS24695 (C5H99_24680)	60815..61059	+	245	Protein_80	DUF2689 domain-containing protein	-
C5H99_RS24700 (C5H99_24685)	61056..61571	+	516	WP_001079995	type IV conjugative transfer system lipoprotein TraV	traV
C5H99_RS24705 (C5H99_24690)	61706..61927	+	222	WP_001278699	conjugal transfer protein TraR	-
C5H99_RS24710 (C5H99_24695)	61920..62387	+	468	WP_000549562	hypothetical protein	-
C5H99_RS24715 (C5H99_24700)	62504..62767	+	264	WP_001239255	hypothetical protein	-
C5H99_RS24720 (C5H99_24705)	62783..65431	+	2649	WP_000793310	type IV secretion system protein TraC	virb4
C5H99_RS24725 (C5H99_24710)	65406..65792	+	387	WP_000105164	type-F conjugative transfer system protein TrbI	-
C5H99_RS24730 (C5H99_24715)	65789..66421	+	633	WP_000871995	type-F conjugative transfer system protein TraW	traW
C5H99_RS24735 (C5H99_24720)	66418..67410	+	993	WP_000833320	conjugal transfer pilus assembly protein TraU	traU
C5H99_RS24740 (C5H99_24725)	67429..67737	+	309	WP_010999945	hypothetical protein	-
C5H99_RS24745 (C5H99_24730)	67722..68360	+	639	WP_000554823	type-F conjugative transfer system pilin assembly protein TrbC	trbC
C5H99_RS24750 (C5H99_24735)	68397..68816	+	420	WP_001229397	HNH endonuclease signature motif containing protein	-
C5H99_RS24755 (C5H99_24740)	68813..70639	+	1827	WP_000827528	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
C5H99_RS24760 (C5H99_24745)	70650..70865	+	216	WP_000700023	conjugal transfer protein TrbE	-
C5H99_RS24765 (C5H99_24750)	70877..71626	+	750	WP_001226854	type-F conjugative transfer system pilin assembly protein TraF	traF
C5H99_RS24770 (C5H99_24755)	71840..72133	+	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
C5H99_RS24775 (C5H99_24760)	72120..72668	+	549	WP_000055840	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
C5H99_RS24780 (C5H99_24765)	72658..74040	+	1383	WP_107326553	conjugal transfer pilus assembly protein TraH	traH
C5H99_RS24785 (C5H99_24770)	74037..76859	+	2823	WP_001007086	conjugal transfer mating-pair stabilization protein TraG	traG
C5H99_RS24790 (C5H99_24775)	76875..77369	+	495	WP_010999946	entry exclusion protein	-
C5H99_RS24795 (C5H99_24780)	77405..78136	+	732	WP_000782438	conjugal transfer complement resistance protein TraT	-
C5H99_RS24800 (C5H99_24785)	78513..80675	+	2163	WP_107326554	type IV conjugative transfer system coupling protein TraD	virb4
C5H99_RS24805 (C5H99_24790)	80684..81082	-	399	WP_000911322	type II toxin-antitoxin system VapC family toxin	-
C5H99_RS24810 (C5H99_24795)	81082..81309	-	228	WP_000450265	toxin-antitoxin system antitoxin VapB	-

Host bacterium

• ID: 2707
• GenBank: NZ_PYUZ01000037
• Plasmid name: OLF-FSR1-STCopenhagen-53|unnamed1
• Incompatibility group: IncFIB
• Plasmid size: 91755 bp
• Coordinate of oriT [Strand]: 54861..55130 [+]
• Host baterium: Salmonella enterica subsp. enterica serovar Copenhagen strain OLF-FSR1-STCopenhagen-53

Cargo genes

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