oriTDB

oriT

The information of the oriT region

oriTDB ID	113634
Name	oriT_ZCX\|unnamed2
Organism	Salmonella sp. strain ZCX
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_OP927725 (5386..5655 [+], 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_ZCX|unnamed2
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTTCTGATTTGTTTTTAGTAACAGTGAGTTATGTTCATAATAATGTAATTTAATTTATTTTAATGTATTAAATAGCGGTGCAGGCACGTCGCCGGCACCGCTATGACGACGCTATACAGGGGTAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACACCCCTGGGGGCGCTGCCAGGGGTG                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_QZJ79_RS00205_ZCX|unnamed2

ID	8732	GenBank	WP_000986921
Name	traI_QZJ79_RS00205_ZCX\|unnamed2	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	5112	GenBank	WP_001151546
Name	WP_001151546_ZCX\|unnamed2	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	5113	GenBank	WP_001676655
Name	WP_001676655_ZCX\|unnamed2	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_QZJ79_RS00110_ZCX|unnamed2
traD_QZJ79_RS00190_ZCX|unnamed2

ID	10109	GenBank	WP_000793310
Name	traC_QZJ79_RS00110_ZCX\|unnamed2	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	10110	GenBank	WP_000009318
Name	traD_QZJ79_RS00190_ZCX\|unnamed2	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: 7728..31200

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
QZJ79_RS00020	3241..3369	+	129	WP_000372429	hypothetical protein	-
QZJ79_RS00025	3443..3613	+	171	WP_000229547	hypothetical protein	-
QZJ79_RS00030	3716..4534	+	819	Protein_5	DUF932 domain-containing protein	-
QZJ79_RS00035	4845..5315	-	471	WP_014344446	transglycosylase SLT domain-containing protein	-
QZJ79_RS00040	5730..6110	+	381	WP_001151546	conjugal transfer relaxosome DNA-binding protein TraM	-
QZJ79_RS00045	6303..6988	+	686	Protein_8	PAS domain-containing protein	-
QZJ79_RS00050	7082..7309	+	228	WP_001676655	conjugal transfer relaxosome protein TraY	-
QZJ79_RS00055	7351..7713	+	363	WP_001274201	type IV conjugative transfer system pilin TraA	-
QZJ79_RS00060	7728..8039	+	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
QZJ79_RS00065	8061..8627	+	567	WP_000399768	type IV conjugative transfer system protein TraE	traE
QZJ79_RS00070	8614..9354	+	741	WP_001230719	type-F conjugative transfer system secretin TraK	traK
QZJ79_RS00075	9354..10775	+	1422	WP_000146700	F-type conjugal transfer pilus assembly protein TraB	traB
QZJ79_RS00080	10765..11361	+	597	WP_000527896	conjugal transfer pilus-stabilizing protein TraP	-
QZJ79_RS00085	11339..11584	+	246	WP_010999944	DUF2689 domain-containing protein	virb4
QZJ79_RS00090	11581..12096	+	516	WP_001079995	type IV conjugative transfer system lipoprotein TraV	traV
QZJ79_RS00095	12231..12452	+	222	WP_001278699	conjugal transfer protein TraR	-
QZJ79_RS00100	12445..12912	+	468	WP_000549562	hypothetical protein	-
QZJ79_RS00105	13029..13292	+	264	WP_001239255	hypothetical protein	-
QZJ79_RS00110	13308..15956	+	2649	WP_000793310	type IV secretion system protein TraC	virb4
QZJ79_RS00115	15931..16317	+	387	WP_000105164	type-F conjugative transfer system protein TrbI	-
QZJ79_RS00120	16314..16946	+	633	WP_023139304	type-F conjugative transfer system protein TraW	traW
QZJ79_RS00125	16943..17935	+	993	WP_000833320	conjugal transfer pilus assembly protein TraU	traU
QZJ79_RS00130	17954..18262	+	309	WP_010999945	hypothetical protein	-
QZJ79_RS00135	18247..18885	+	639	WP_000554823	type-F conjugative transfer system pilin assembly protein TrbC	trbC
QZJ79_RS00140	18922..19341	+	420	WP_001229397	HNH endonuclease	-
QZJ79_RS00145	19338..21164	+	1827	WP_000827529	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
QZJ79_RS00150	21175..21390	+	216	WP_000700023	conjugal transfer protein TrbE	-
QZJ79_RS00155	21402..22151	+	750	WP_001226854	type-F conjugative transfer system pilin assembly protein TraF	traF
QZJ79_RS00160	22365..22658	+	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
QZJ79_RS00165	22645..23193	+	549	WP_000055840	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
QZJ79_RS00170	23183..24565	+	1383	WP_001161719	conjugal transfer pilus assembly protein TraH	traH
QZJ79_RS00175	24562..27384	+	2823	WP_001007086	conjugal transfer mating-pair stabilization protein TraG	traG
QZJ79_RS00180	27400..27894	+	495	WP_010999946	entry exclusion protein	-
QZJ79_RS00185	27930..28661	+	732	WP_000782438	conjugal transfer complement resistance protein TraT	-
QZJ79_RS00190	29038..31200	+	2163	WP_000009318	type IV conjugative transfer system coupling protein TraD	virb4
QZJ79_RS00195	31209..31607	-	399	WP_000911322	type II toxin-antitoxin system VapC family toxin	-
QZJ79_RS00200	31607..31834	-	228	WP_000450265	toxin-antitoxin system antitoxin VapB	-

Host bacterium

ID	14069	GenBank	NZ_OP927725
Plasmid name	ZCX\|unnamed2	Incompatibility group	IncFII
Plasmid size	108892 bp	Coordinate of oriT [Strand]	5386..5655 [+]
Host baterium	Salmonella sp. strain ZCX

Cargo genes

Drug resistance gene	qnrS2, oqxB, oqxA
Virulence gene	rck, pefD, pefC, pefA, pefB, fdeC, spvC, spvB
Metal resistance gene	-
Degradation gene	-
Symbiosis gene	-
Anti-CRISPR	-

Detailed information of oriT

oriT

The information of the oriT region

oriT sequence

oriT secondary structure

Relaxase

Relaxase protein sequence

Protein domains

Protein structure

Auxiliary protein

Auxiliary protein sequence

Protein domains

Protein structure

Auxiliary protein sequence

Protein domains

Protein structure

T4CP

T4CP protein sequence

Protein domains

Protein structure

T4CP protein sequence

Protein domains

Protein structure

T4SS

Host bacterium

Cargo genes