oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	104694
Name	oriT_pVIRBov
Organism	Salmonella enterica subsp. enterica serovar Bovismorbificans str. 3114
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_HF969016 (74105..74374 [-], 270 nt)
oriT length	270 nt
IRs (inverted repeats)	247..253, 262..268 (CCCCTGG..CCAGGGG) 95..101, 109..115 (TTTAAAT..ATTTAAA) 81..89, 97..105 (ACAGATTTA..TAAATCTGT) 31..38, 41..48 (GCAAAATT..AATTTTGC)
*Location of nic* site**	_
Conserved sequence flanking the nic site	_
Note	Predicted by oriTfinder 2.0

oriT sequence

Download Length: 270 nt

                        >oriT_pVIRBov
GTCCTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTGCTGATTTTTATTTATTATCAATAGATTGCTGTTACAGATTTATATTGTTTAAATCTGTTTTATTTAAAATAGCGGTGTCAACGCGTCGCCGGCACCGCTATGACGACGCTATACAGGGGCAGTACTGACTATTTTTATAAAAAACATTGCATTATATCAGGGGCGCTGCTAGCGTCGCTGTGCCTGTTTTTAAGTAACCCCCCTGGGGGCGCTGCCAGGGGTG                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_BN855_RS22955_pVIRBov

ID	3358	GenBank	WP_021003386
Name	traI_BN855_RS22955_pVIRBov	UniProt ID	A0A5U9TSK7
Length	1751 a.a.	PDB ID
Note	Predicted by oriTfinder 2.0

Relaxase protein sequence

Download Length: 1751 a.a. Molecular weight: 190988.97 Da Isoelectric Point: 5.8095

          >WP_021003386.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]

MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGAVDKEVFTRVLEGRLPDGADLSRQQ

DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV

MALFNHDTSRDQEPQLHTHAVVANVTLHDGEWKTLSSDKVGKTGFIENIYANQIAFGKIYRAVLKEKVEA

LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPAVKMAEWMQT

LKDTGFDISAYREAADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA

GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD

AVSVLARDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIAADRRSQTNLKQDERLSGELITGRR

QLQEGMTFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ

GGQQTPATVISEPDRNVRYARLAGDFVAAVKTGEESVAQVSGVREQAILAGMIRSELKTQGILGQQDTMM

TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGGTQMVRISALDSS

WSLFRPEKIPVADGERLMVTGKIPGLRVSGGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE

NGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDEIRTAEKLSRHPSFTVVSEQIK

ARAGEVSLETAISLQKAGLHTPAQQALHLAIPVVESKNLAFSQVELLTEAKSFAAEGTGFADLGREIDAQ

IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL

ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPEDERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ

LQQRSGEAPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQARSAA

DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA

QEAEKKGEAFPDVPVTLYEAIVRDYTGRMPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGEQQADI

PVLTTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTL

YNPETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTCVVRPGQDRAEQHIDLAYAIT

AHGAQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLE

PKSEREMMNAERLFSTARELRDVAVGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGI

WLNPLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIAGDG

RPWNPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPE

EKTAQAVREIAGQEQDRMTPPEREPALPESVLREPQRERETIREVARENRGRERLQEMVCDLQKEKTPGG

D

Protein domains

Predicted by InterproScan.

TrwC relaxase (TrwC)

(11-282)

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

(574-626)

DNA helicase TraI (TraI_C)

(1433-1556)

AAA domain (AAA_30)

(967-1158)

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

(632-711)

Protein structure

No available structure.

Auxiliary protein

WP_001151546_pVIRBov

ID	1494	GenBank	WP_001151546
Name	WP_001151546_pVIRBov	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	3296	GenBank	WP_021003388
Name	traD_BN855_RS22970_pVIRBov	UniProt ID	_
Length	735 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 735 a.a. Molecular weight: 83261.95 Da Isoelectric Point: 5.1044

                        >WP_021003388.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]

MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGCIYWWCTTLEGMR

DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMVTWILGRQGKQ

QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVSTGKSEIIRRLANYAR

QRGDMVVMYDRSCEFVKSYYDPSIDKILNPCDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDSDRSYSKLVDTLLSIKIEKLRTYLRDSPAANLVEEKIEKTAISIRAVLTNYVKA

VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHSSLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA

DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLAL

KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEGRQMSSLFEPDTEAVAPTAAEAQSEQPQQPQQPQQ

PQQPQQPQQPQPTVVSDKKSAAASTAVNTPAGGVGQELKMKPEDEEQPLPPGINASGEVVDMAAYERWRQ

EQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

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.

ID	3297	GenBank	WP_025388521
Name	traC_BN855_RS23055_pVIRBov	UniProt ID	_
Length	882 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 882 a.a. Molecular weight: 100391.12 Da Isoelectric Point: 6.5616

                        >WP_025388521.1 type IV secretion system protein TraC [Salmonella enterica]

MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP

VNGANETIALSLDHLLRTKLPRGIPLCIHLMSSQLVGERIEYGLREFSWSGEQAERFNAITRAYYMKAAE

THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQTVDAQAFINIVG

EMINHNPESLHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDHGKNSTARIMSFHLARNPEIAFL

WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD

LRQRLASNQSSVVSYFFNITAFCRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG

LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA

GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERIRDQLSV

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)

(467-763)

TraC protein (TraC_F_IV)

(38-276)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 48041..74915

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
BN855_RS22960	47407..47634	+	228	WP_000450263	toxin-antitoxin system antitoxin VapB	-
BN855_RS22965 (BN855_p360)	47634..48032	+	399	WP_021003387	tRNA(fMet)-specific endonuclease VapC	-
BN855_RS22970 (BN855_p370)	48041..50248	-	2208	WP_021003388	type IV conjugative transfer system coupling protein TraD	virb4
BN855_RS22975 (BN855_p380)	50529..51008	-	480	WP_025388510	hypothetical protein	-
BN855_RS22980 (BN855_p390)	51260..51991	-	732	WP_021003390	conjugal transfer complement resistance protein TraT	-
BN855_RS22985	52090..52401	+	312	WP_025388511	heavy metal-binding domain-containing protein	-
BN855_RS22990	52367..55222	-	2856	WP_025388512	conjugal transfer mating-pair stabilization protein TraG	traG
BN855_RS22995	55219..56601	-	1383	WP_025388513	conjugal transfer pilus assembly protein TraH	traH
BN855_RS23000	56591..57139	-	549	WP_025388514	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
BN855_RS23005	57126..57419	-	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
BN855_RS23010 (BN855_p400)	57633..58382	-	750	WP_025388515	type-F conjugative transfer system pilin assembly protein TraF	traF
BN855_RS23015 (BN855_p410)	58394..58609	-	216	WP_000700023	conjugal transfer protein TrbE	-
BN855_RS23020	58620..60446	-	1827	WP_025388516	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
BN855_RS23025 (BN855_p420)	60443..60862	-	420	WP_021003392	HNH endonuclease signature motif containing protein	-
BN855_RS23030	60899..61537	-	639	WP_025388517	type-F conjugative transfer system pilin assembly protein TrbC	trbC
BN855_RS23035	61534..61830	-	297	WP_134813960	hypothetical protein	-
BN855_RS23040	61849..62841	-	993	WP_025388519	conjugal transfer pilus assembly protein TraU	traU
BN855_RS23045 (BN855_p430)	62838..63470	-	633	WP_025388520	type-F conjugative transfer system protein TraW	traW
BN855_RS23050 (BN855_p440)	63467..63853	-	387	WP_000105164	type-F conjugative transfer system protein TrbI	-
BN855_RS23055	63828..66476	-	2649	WP_025388521	type IV secretion system protein TraC	virb4
BN855_RS23060	66492..66875	-	384	WP_038389657	hypothetical protein	-
BN855_RS23065	66872..67339	-	468	WP_025388522	hypothetical protein	-
BN855_RS23070 (BN855_p450)	67332..67553	-	222	WP_001278699	conjugal transfer protein TraR	-
BN855_RS23075	67688..68203	-	516	WP_025388523	type IV conjugative transfer system lipoprotein TraV	traV
BN855_RS23080	68200..68445	-	246	WP_088734843	DUF2689 domain-containing protein	-
BN855_RS23085 (BN855_p460)	68423..68959	-	537	WP_021003394	conjugal transfer pilus-stabilizing protein TraP	-
BN855_RS23090	68973..70370	-	1398	WP_038389658	F-type conjugal transfer pilus assembly protein TraB	traB
BN855_RS23095	70370..71110	-	741	WP_025388525	type-F conjugative transfer system secretin TraK	traK
BN855_RS23100 (BN855_p470)	71097..71663	-	567	WP_021003395	type IV conjugative transfer system protein TraE	traE
BN855_RS23105 (BN855_p480)	71685..71996	-	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
BN855_RS23110 (BN855_p490)	72011..72373	-	363	WP_021003396	type IV conjugative transfer system pilin TraA	-
BN855_RS23115	72415..72642	-	228	WP_025388526	conjugal transfer relaxosome protein TraY	-
BN855_RS23120 (BN855_p500)	72779..73456	-	678	WP_025388527	conjugal transfer protein TrbJ	-
BN855_RS23125 (BN855_p510)	73650..74030	-	381	WP_001151546	conjugal transfer relaxosome DNA-binding protein TraM	-
BN855_RS23130 (BN855_p520)	74445..74915	+	471	WP_015056628	transglycosylase SLT domain-containing protein	virB1
BN855_RS23135	75229..76047	-	819	Protein_92	DUF932 domain-containing protein	-
BN855_RS23495 (BN855_p560)	76394..76522	-	129	WP_000372430	hypothetical protein	-
BN855_RS23140	76557..77213	-	657	Protein_94	plasmid SOS inhibition protein A	-
BN855_RS23455	77216..77317	-	102	Protein_95	conjugation system SOS inhibitor PsiB family protein	-
BN855_RS23150	77357..79078	-	1722	Protein_96	ParB/RepB/Spo0J family partition protein	-
BN855_RS23155	79379..79801	+	423	WP_000925628	translesion error-prone DNA polymerase V autoproteolytic subunit	-

Host bacterium

ID	5133	GenBank	NZ_HF969016
Plasmid name	pVIRBov	Incompatibility group	IncFIB
Plasmid size	93046 bp	Coordinate of oriT [Strand]	74105..74374 [-]
Host baterium	Salmonella enterica subsp. enterica serovar Bovismorbificans str. 3114

Cargo genes

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