oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	104055
Name	oriT_pATCC14028_1
Organism	Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 14028
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_CP117245 (58738..59007 [+], 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_pATCC14028_1
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_PQQ30_RS24215_pATCC14028_1

ID	3000	GenBank	WP_000986921
Name	traI_PQQ30_RS24215_pATCC14028_1	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	1265	GenBank	WP_001151546
Name	WP_001151546_pATCC14028_1	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	1266	GenBank	WP_001676655
Name	WP_001676655_pATCC14028_1	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_PQQ30_RS24120_pATCC14028_1
traD_PQQ30_RS24200_pATCC14028_1

ID	2874	GenBank	WP_000793310
Name	traC_PQQ30_RS24120_pATCC14028_1	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	2875	GenBank	WP_000009318
Name	traD_PQQ30_RS24200_pATCC14028_1	UniProt ID	_
Length	720 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 720 a.a. Molecular weight: 81447.01 Da Isoelectric Point: 5.1045

                        >WP_000009318.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Salmonella]

MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGGIYWWCTTLEGMR

DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMTTWILGRQGKQ

QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR

QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA

VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA

DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL

KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEVRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQPTVV

SDKKSAAAGTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREE

VNINVHRGHGKDEPEPGDDF

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: 58197..84553

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
PQQ30_RS24015 (PQQ30_24015)	53353..55350	+	1998	WP_000117513	ParB/RepB/Spo0J family partition protein	-
PQQ30_RS24020 (PQQ30_24020)	55390..55824	+	435	WP_010999943	conjugation system SOS inhibitor PsiB	-
PQQ30_RS24025 (PQQ30_24025)	55821..56558	+	738	WP_000581933	plasmid SOS inhibition protein A	-
PQQ30_RS24030 (PQQ30_24030)	56593..56721	+	129	WP_000372429	hypothetical protein	-
PQQ30_RS24035 (PQQ30_24035)	56807..56965	+	159	WP_001704449	hypothetical protein	-
PQQ30_RS24040 (PQQ30_24040)	57068..57886	+	819	Protein_72	DUF932 domain-containing protein	-
PQQ30_RS24045 (PQQ30_24045)	58197..58667	-	471	WP_001526856	transglycosylase SLT domain-containing protein	virB1
PQQ30_RS24050 (PQQ30_24050)	59082..59462	+	381	WP_001151546	conjugal transfer relaxosome DNA-binding protein TraM	-
PQQ30_RS24055 (PQQ30_24055)	59655..60341	+	687	WP_000336297	PAS domain-containing protein	-
PQQ30_RS24060 (PQQ30_24060)	60435..60662	+	228	WP_001676655	conjugal transfer relaxosome protein TraY	-
PQQ30_RS24065 (PQQ30_24065)	60704..61066	+	363	WP_001274201	type IV conjugative transfer system pilin TraA	-
PQQ30_RS24070 (PQQ30_24070)	61081..61392	+	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
PQQ30_RS24075 (PQQ30_24075)	61414..61980	+	567	WP_000399768	type IV conjugative transfer system protein TraE	traE
PQQ30_RS24080 (PQQ30_24080)	61967..62707	+	741	WP_001230719	type-F conjugative transfer system secretin TraK	traK
PQQ30_RS24085 (PQQ30_24085)	62707..64128	+	1422	WP_000146700	F-type conjugal transfer pilus assembly protein TraB	traB
PQQ30_RS24090 (PQQ30_24090)	64118..64714	+	597	WP_000527896	conjugal transfer pilus-stabilizing protein TraP	-
PQQ30_RS24095 (PQQ30_24095)	64692..64937	+	246	WP_010999944	DUF2689 domain-containing protein	virb4
PQQ30_RS24100 (PQQ30_24100)	64934..65449	+	516	WP_001079995	type IV conjugative transfer system lipoprotein TraV	traV
PQQ30_RS24105 (PQQ30_24105)	65584..65805	+	222	WP_001278699	conjugal transfer protein TraR	-
PQQ30_RS24110 (PQQ30_24110)	65798..66265	+	468	WP_000549562	hypothetical protein	-
PQQ30_RS24115 (PQQ30_24115)	66382..66645	+	264	WP_001239255	hypothetical protein	-
PQQ30_RS24120 (PQQ30_24120)	66661..69309	+	2649	WP_000793310	type IV secretion system protein TraC	virb4
PQQ30_RS24125 (PQQ30_24125)	69284..69670	+	387	WP_000105164	type-F conjugative transfer system protein TrbI	-
PQQ30_RS24130 (PQQ30_24130)	69667..70299	+	633	WP_000871995	type-F conjugative transfer system protein TraW	traW
PQQ30_RS24135 (PQQ30_24135)	70296..71288	+	993	WP_000833320	conjugal transfer pilus assembly protein TraU	traU
PQQ30_RS24140 (PQQ30_24140)	71307..71615	+	309	WP_010999945	hypothetical protein	-
PQQ30_RS24145 (PQQ30_24145)	71600..72238	+	639	WP_000554823	type-F conjugative transfer system pilin assembly protein TrbC	trbC
PQQ30_RS24150 (PQQ30_24150)	72275..72694	+	420	WP_001229397	HNH endonuclease signature motif containing protein	-
PQQ30_RS24155 (PQQ30_24155)	72691..74517	+	1827	WP_000827528	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
PQQ30_RS24160 (PQQ30_24160)	74528..74743	+	216	WP_000700023	conjugal transfer protein TrbE	-
PQQ30_RS24165 (PQQ30_24165)	74755..75504	+	750	WP_001226854	type-F conjugative transfer system pilin assembly protein TraF	traF
PQQ30_RS24170 (PQQ30_24170)	75718..76011	+	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
PQQ30_RS24175 (PQQ30_24175)	75998..76546	+	549	WP_000055840	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
PQQ30_RS24180 (PQQ30_24180)	76536..77918	+	1383	WP_001161719	conjugal transfer pilus assembly protein TraH	traH
PQQ30_RS24185 (PQQ30_24185)	77915..80737	+	2823	WP_001007086	conjugal transfer mating-pair stabilization protein TraG	traG
PQQ30_RS24190 (PQQ30_24190)	80753..81247	+	495	WP_010999946	entry exclusion protein	-
PQQ30_RS24195 (PQQ30_24195)	81283..82014	+	732	WP_000782438	conjugal transfer complement resistance protein TraT	-
PQQ30_RS24200 (PQQ30_24200)	82391..84553	+	2163	WP_000009318	type IV conjugative transfer system coupling protein TraD	virb4
PQQ30_RS24205 (PQQ30_24205)	84562..84960	-	399	WP_000911322	type II toxin-antitoxin system VapC family toxin	-
PQQ30_RS24210 (PQQ30_24210)	84960..85187	-	228	WP_000450265	toxin-antitoxin system antitoxin VapB	-

Host bacterium

ID	4494	GenBank	NZ_CP117245
Plasmid name	pATCC14028_1	Incompatibility group	IncFIB
Plasmid size	93832 bp	Coordinate of oriT [Strand]	58738..59007 [+]
Host baterium	Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 14028

Cargo genes

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