oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	101994
Name	oriT_STy01\|unnamed1
Organism	Salmonella enterica subsp. enterica serovar Typhimurium strain STy01
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_MATJ01000058 (36912..37181 [-], 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_STy01|unnamed1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_BBC55_RS23240_STy01|unnamed1

ID	1593	GenBank	WP_022743192
Name	traI_BBC55_RS23240_STy01\|unnamed1	UniProt ID	A0A484WVL1
Length	1752 a.a.	PDB ID
Note	Predicted by oriTfinder 2.0

Relaxase protein sequence

Download Length: 1752 a.a. Molecular weight: 191680.70 Da Isoelectric Point: 5.9879

          >WP_022743192.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]

MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGTVDKEVFTRVLEGRLPDGADLSRQQ

DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV

MALFNHDTSRDQEPQLHTHAVVVNVTQHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA

LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT

LKDTGFDISAYRESADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA

GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD

AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIVADRRSQTNLKQDERLSGELITGRR

QLQEGMLFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ

GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGMREQAILAGMIRSELKTQGILGQQDTMM

TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS

WSLFRPEKMPVADGERLMVTGKIPGLRVSVGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE

NGWVETPGHSVSDSAKVFASVTQMAMDNATLNSLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK

ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTGFADLGREIDAQ

IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL

ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPESERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ

LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA

DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA

QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL

TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP

ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHS

AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS

EREMKNAERLFSTARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN

PLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIVGDGRPW

NPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPEEKT

AQAVREIAGQEQDRMTPPEREPPLPESVLREPQRERETIREVARENRGRERLQQMEQEMVRDLQKEKTPG

GD

Protein domains

Predicted by InterproScan.

AAA domain (AAA_30)

(967-1158)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(632-711)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(574-626)

TrwC relaxase (TrwC)

(11-282)

DNA helicase TraI (TraI_C)

(1430-1553)

Protein structure

No available structure.

ID	647	GenBank	WP_001676655
Name	WP_001676655_STy01\|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

ID	648	GenBank	WP_001151546
Name	WP_001151546_STy01\|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

T4CP

traD_BBC55_RS23255_STy01|unnamed1
traC_BBC55_RS23335_STy01|unnamed1

ID	1256	GenBank	WP_023139332
Name	traD_BBC55_RS23255_STy01\|unnamed1	UniProt ID	_
Length	756 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 756 a.a. Molecular weight: 85634.49 Da Isoelectric Point: 5.0447

                        >WP_023139332.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]

MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR

DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ

QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR

QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA

VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFCSPSYKIA

DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL

KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQQPQQ

PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQPTVVSDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPL

PPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

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.

ID	1257	GenBank	WP_000793310
Name	traC_BBC55_RS23335_STy01\|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.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 11257..37722

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
BBC55_RS23245 (BBC55_23295)	10623..10850	+	228	WP_000450265	toxin-antitoxin system antitoxin VapB	-
BBC55_RS23250 (BBC55_23300)	10850..11248	+	399	WP_000911322	type II toxin-antitoxin system VapC family toxin	-
BBC55_RS23255 (BBC55_23305)	11257..13527	-	2271	WP_023139332	type IV conjugative transfer system coupling protein TraD	prgC
BBC55_RS23260 (BBC55_23310)	13904..14635	-	732	WP_022743186	conjugal transfer complement resistance protein TraT	-
BBC55_RS23265 (BBC55_23315)	14671..15165	-	495	WP_010999946	entry exclusion protein	-
BBC55_RS23270 (BBC55_23320)	15181..18003	-	2823	WP_001007086	conjugal transfer mating-pair stabilization protein TraG	traG
BBC55_RS23275 (BBC55_23325)	18000..19382	-	1383	WP_001161719	conjugal transfer pilus assembly protein TraH	traH
BBC55_RS23280 (BBC55_23330)	19372..19920	-	549	WP_022743183	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
BBC55_RS23285 (BBC55_23335)	19907..20200	-	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
BBC55_RS23290 (BBC55_23340)	20414..21163	-	750	WP_001226854	type-F conjugative transfer system pilin assembly protein TraF	traF
BBC55_RS23295 (BBC55_23345)	21175..21390	-	216	WP_000700023	conjugal transfer protein TrbE	-
BBC55_RS23300 (BBC55_23350)	21401..23227	-	1827	WP_000827528	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
BBC55_RS23305 (BBC55_23355)	23224..23643	-	420	WP_001229397	HNH endonuclease signature motif containing protein	-
BBC55_RS23310 (BBC55_23360)	23680..24318	-	639	WP_000554823	type-F conjugative transfer system pilin assembly protein TrbC	trbC
BBC55_RS23315 (BBC55_23365)	24303..24611	-	309	WP_010999945	hypothetical protein	-
BBC55_RS23320 (BBC55_23370)	24630..25622	-	993	WP_000833320	conjugal transfer pilus assembly protein TraU	traU
BBC55_RS23325 (BBC55_23375)	25619..26251	-	633	WP_000871995	type-F conjugative transfer system protein TraW	traW
BBC55_RS23330 (BBC55_23380)	26248..26634	-	387	WP_000105164	type-F conjugative transfer system protein TrbI	-
BBC55_RS23335 (BBC55_23385)	26609..29257	-	2649	WP_000793310	type IV secretion system protein TraC	virb4
BBC55_RS23340 (BBC55_23390)	29273..29536	-	264	WP_001239256	hypothetical protein	-
BBC55_RS23345 (BBC55_23395)	29653..30120	-	468	WP_000549562	hypothetical protein	-
BBC55_RS23350 (BBC55_23400)	30113..30334	-	222	WP_001278699	conjugal transfer protein TraR	-
BBC55_RS23355 (BBC55_23405)	30469..30984	-	516	WP_001079995	type IV conjugative transfer system lipoprotein TraV	traV
BBC55_RS23360 (BBC55_23410)	30981..31226	-	246	WP_010999944	DUF2689 domain-containing protein	virb4
BBC55_RS23365 (BBC55_23415)	31204..31800	-	597	WP_000527896	conjugal transfer pilus-stabilizing protein TraP	-
BBC55_RS23370 (BBC55_23420)	31790..33211	-	1422	WP_000146700	F-type conjugal transfer pilus assembly protein TraB	traB
BBC55_RS23375 (BBC55_23425)	33211..33951	-	741	WP_001230719	type-F conjugative transfer system secretin TraK	traK
BBC55_RS23380 (BBC55_23430)	33938..34504	-	567	WP_000399768	type IV conjugative transfer system protein TraE	traE
BBC55_RS23385 (BBC55_23435)	34526..34837	-	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
BBC55_RS23390 (BBC55_23440)	34852..35214	-	363	WP_001274201	type IV conjugative transfer system pilin TraA	-
BBC55_RS25955	35256..35483	-	228	WP_001676655	conjugal transfer relaxosome protein TraY	-
BBC55_RS23395 (BBC55_23445)	35578..36264	-	687	WP_000336297	PAS domain-containing protein	-
BBC55_RS23400 (BBC55_23450)	36457..36837	-	381	WP_001151546	conjugal transfer relaxosome DNA-binding protein TraM	-
BBC55_RS23405 (BBC55_23455)	37252..37722	+	471	WP_001526856	transglycosylase SLT domain-containing protein	virB1
BBC55_RS26980	38033..38851	-	819	Protein_45	DUF932 domain-containing protein	-
BBC55_RS26985	38954..39112	-	159	WP_001704449	hypothetical protein	-
BBC55_RS27375	39198..39326	-	129	WP_000372429	hypothetical protein	-
BBC55_RS23420 (BBC55_23470)	39361..40098	-	738	WP_000581933	plasmid SOS inhibition protein A	-
BBC55_RS23425 (BBC55_23475)	40095..40529	-	435	WP_010999943	conjugation system SOS inhibitor PsiB	-
BBC55_RS23430 (BBC55_23480)	40569..42566	-	1998	WP_000117513	ParB/RepB/Spo0J family partition protein	-

Host bacterium

ID	2438	GenBank	NZ_MATJ01000058
Plasmid name	STy01\|unnamed1	Incompatibility group	IncFII
Plasmid size	94170 bp	Coordinate of oriT [Strand]	36912..37181 [-]
Host baterium	Salmonella enterica subsp. enterica serovar Typhimurium strain STy01

Cargo genes

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