oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	104031
Name	oriT_SO_8752_Stm\|pSLT
Organism	Salmonella enterica subsp. enterica serovar Typhimurium strain SO_8752_Stm
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_CP074093 (60664..60933 [+], 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_SO_8752_Stm|pSLT
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_KFK83_RS24010_SO_8752_Stm|pSLT

ID	2987	GenBank	WP_000986921
Name	traI_KFK83_RS24010_SO_8752_Stm\|pSLT	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

ID	1255	GenBank	WP_001151546
Name	WP_001151546_SO_8752_Stm\|pSLT	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	1256	GenBank	WP_001676655
Name	WP_001676655_SO_8752_Stm\|pSLT	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_KFK83_RS23915_SO_8752_Stm|pSLT
traD_KFK83_RS23995_SO_8752_Stm|pSLT

ID	2850	GenBank	WP_000793310
Name	traC_KFK83_RS23915_SO_8752_Stm\|pSLT	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	2851	GenBank	WP_000009320
Name	traD_KFK83_RS23995_SO_8752_Stm\|pSLT	UniProt ID	_
Length	747 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 747 a.a. Molecular weight: 84627.41 Da Isoelectric Point: 5.1045

                        >WP_000009320.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]

MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR

DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ

QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR

QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA

VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA

DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL

KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQQPQQ

PQQPQQPQQPQQPQQPQQPQQPQPTVVSDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGE

VVDMAAYERWRQEQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

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: 60123..86560

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
KFK83_RS23815 (KFK83_23815)	55279..57276	+	1998	WP_000117513	ParB/RepB/Spo0J family partition protein	-
KFK83_RS23820 (KFK83_23820)	57316..57750	+	435	WP_010999943	conjugation system SOS inhibitor PsiB	-
KFK83_RS23825 (KFK83_23825)	57747..58484	+	738	WP_000581933	plasmid SOS inhibition protein A	-
KFK83_RS24275	58519..58647	+	129	WP_000372429	hypothetical protein	-
KFK83_RS23830 (KFK83_23830)	58733..58891	+	159	WP_001704449	hypothetical protein	-
KFK83_RS23835 (KFK83_23835)	58994..59812	+	819	Protein_79	DUF932 domain-containing protein	-
KFK83_RS23840 (KFK83_23840)	60123..60593	-	471	WP_001526856	transglycosylase SLT domain-containing protein	virB1
KFK83_RS23845 (KFK83_23845)	61008..61388	+	381	WP_001151546	conjugal transfer relaxosome DNA-binding protein TraM	-
KFK83_RS23850 (KFK83_23850)	61581..62267	+	687	WP_000336297	PAS domain-containing protein	-
KFK83_RS23855 (KFK83_23855)	62361..62588	+	228	WP_001676655	conjugal transfer relaxosome protein TraY	-
KFK83_RS23860 (KFK83_23860)	62630..62992	+	363	WP_001274201	type IV conjugative transfer system pilin TraA	-
KFK83_RS23865 (KFK83_23865)	63007..63318	+	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
KFK83_RS23870 (KFK83_23870)	63340..63906	+	567	WP_000399769	type IV conjugative transfer system protein TraE	traE
KFK83_RS23875 (KFK83_23875)	63893..64633	+	741	WP_001230719	type-F conjugative transfer system secretin TraK	traK
KFK83_RS23880 (KFK83_23880)	64633..66054	+	1422	WP_000146700	F-type conjugal transfer pilus assembly protein TraB	traB
KFK83_RS23885 (KFK83_23885)	66044..66640	+	597	WP_000527896	conjugal transfer pilus-stabilizing protein TraP	-
KFK83_RS23890 (KFK83_23890)	66618..66863	+	246	WP_010999944	DUF2689 domain-containing protein	virb4
KFK83_RS23895 (KFK83_23895)	66860..67375	+	516	WP_001079995	type IV conjugative transfer system lipoprotein TraV	traV
KFK83_RS23900 (KFK83_23900)	67510..67731	+	222	WP_001278699	conjugal transfer protein TraR	-
KFK83_RS23905 (KFK83_23905)	67724..68191	+	468	WP_000549562	hypothetical protein	-
KFK83_RS23910 (KFK83_23910)	68308..68571	+	264	WP_001239256	hypothetical protein	-
KFK83_RS23915 (KFK83_23915)	68587..71235	+	2649	WP_000793310	type IV secretion system protein TraC	virb4
KFK83_RS23920 (KFK83_23920)	71210..71596	+	387	WP_000105164	type-F conjugative transfer system protein TrbI	-
KFK83_RS23925 (KFK83_23925)	71593..72225	+	633	WP_000871995	type-F conjugative transfer system protein TraW	traW
KFK83_RS23930 (KFK83_23930)	72222..73214	+	993	WP_000833320	conjugal transfer pilus assembly protein TraU	traU
KFK83_RS23935 (KFK83_23935)	73233..73541	+	309	WP_010999945	hypothetical protein	-
KFK83_RS23940 (KFK83_23940)	73526..74164	+	639	WP_000554823	type-F conjugative transfer system pilin assembly protein TrbC	trbC
KFK83_RS23945 (KFK83_23945)	74201..74620	+	420	WP_001229397	HNH endonuclease signature motif containing protein	-
KFK83_RS23950 (KFK83_23950)	74617..76443	+	1827	WP_000827528	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
KFK83_RS23955 (KFK83_23955)	76454..76669	+	216	WP_000700023	conjugal transfer protein TrbE	-
KFK83_RS23960 (KFK83_23960)	76681..77430	+	750	WP_001226854	type-F conjugative transfer system pilin assembly protein TraF	traF
KFK83_RS23965 (KFK83_23965)	77644..77937	+	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
KFK83_RS23970 (KFK83_23970)	77924..78472	+	549	WP_000055840	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
KFK83_RS23975 (KFK83_23975)	78462..79844	+	1383	WP_001161719	conjugal transfer pilus assembly protein TraH	traH
KFK83_RS23980 (KFK83_23980)	79841..82663	+	2823	WP_001007086	conjugal transfer mating-pair stabilization protein TraG	traG
KFK83_RS23985 (KFK83_23985)	82679..83173	+	495	WP_010999946	entry exclusion protein	-
KFK83_RS23990 (KFK83_23990)	83209..83940	+	732	WP_000782438	conjugal transfer complement resistance protein TraT	-
KFK83_RS23995 (KFK83_23995)	84317..86560	+	2244	WP_000009320	type IV conjugative transfer system coupling protein TraD	prgC
KFK83_RS24000 (KFK83_24000)	86569..86967	-	399	WP_000911322	type II toxin-antitoxin system VapC family toxin	-
KFK83_RS24005 (KFK83_24005)	86967..87194	-	228	WP_000450265	toxin-antitoxin system antitoxin VapB	-

Host bacterium

ID	4470	GenBank	NZ_CP074093
Plasmid name	SO_8752_Stm\|pSLT	Incompatibility group	IncFII
Plasmid size	93933 bp	Coordinate of oriT [Strand]	60664..60933 [+]
Host baterium	Salmonella enterica subsp. enterica serovar Typhimurium strain SO_8752_Stm

Cargo genes

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