oriTDB

The information of the oriT region

oriTDB accession number	100014
Name	oriT_R46
Sequence Completeness	intact
oriT length	650 nt
oriT sequence	AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAAGT TCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTCTTAAA CAAAAGATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTC ATTATAAAACAATGAGTTATTAGGTGTTTTTAATACCTAATTATTACCGAATATTGACGC TATTTATTTTTTTATTTTTTAAATCAGTGTGATAGCGTGATTTATGCCGCTGCGTTAGGT GTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGAGCGATCTACGTAGGTTA AGGACTAACTGACTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTA CAACACTATTACAACAAAAGTACATCAAAATTACATCAAAAGTACATCACTTGAAGGTTG ACAGTACAACAGAATTACATCATTATCTGGTACTGAGGTAGCCAGTACAACAAAAGTACA TCAAAAATACATCATAAATACATCAGAAATACATCAAAATTACATCATTCTAAATGAGGG TACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG
IR (inverted repeat)	IR1: [199-208] [212-221] nt (ATTAGGTGTT..AATACCTAAT) IR2:[320-325] [331-336] nt (AAAAAA..TTTTTT) IR3: [394-403] [406-415] nt (GTATTCATGC..GCATGAATAC)
Location of nic site	[302-303] nt
Conserved sequence flanking the nic site	GGTGT\|ATAGC
Note	_
	L:199-208;R:212-221;L:320-325;R:331-336;L:394-403;R:406-415;D:302-303

Visualization of oriT structure (The oriT was characterized experimentally)

1...5....10....15....20....25....30....35....40....45....50....55....60

1

AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAAGT

61

TCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTCTTAAA

121

CAAAAGATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTC

181

ATTATAAAACAATGAGTTATTAGGTGTTTTTAATACCTAATTATTACCGAATATTGACGC

241

TATTTATTTTTTTATTTTTTAAATCAGTGTGATAGCGTGATTTATGCCGCTGCGTTAGGT

301

GTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGAGCGATCTACGTAGGTTA

361

AGGACTAACTGACTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTA

421

CAACACTATTACAACAAAAGTACATCAAAATTACATCAAAAGTACATCACTTGAAGGTTG

481

ACAGTACAACAGAATTACATCATTATCTGGTACTGAGGTAGCCAGTACAACAAAAGTACA

541

TCAAAAATACATCATAAATACATCAGAAATACATCAAAATTACATCATTCTAAATGAGGG

601

TACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Reference

[1] Coupland GM et al (1987) The origin of transfer (oriT) of the conjugative plasmid R46: characterization by deletion analysis and DNA sequencing. Mol Gen Genet. 208(1-2):219-25. [PMID:3039307]

[2] Llosa M et al (1991) Structural and functional analysis of the origin of conjugal transfer of the broad-host-range IncW plasmid R388 and comparison with the related IncN plasmid R46. Mol Gen Genet. 226(3):473-83. [PMID:2038309]

I. Information of Relaxase

ID	13
Name	TraI_R46
GenBank accession number	NP_511201
Family	MOB_F
Length	1078 aa
UniProt ID	Q56053
PDB ID	_
Pfam	TrwC [PF08751.10], Evalue: 8.20E-80, Aligned region: 12..288 AAA_30 [PF13604.5], Evalue: 4.30E-42, Aligned region: 477..663 Viral_helicase1 [PF01443.17], Evalue: 5.00E-07, Aligned region: 774..899 UvrD_C_2 [PF13538.5], Evalue: 1.10E-08, Aligned region: 851..897
Note	relaxase
Protein sequence [Download]	MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLV GEIDTFTHMQRHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREA EKLAQARTTRQGKSVTQNTNNLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALK NDELMRNKMHLGDVYKQELALELAKAGYELRYNSKNNTFDMAHFSDEQIRAFSRRSEQIE KGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQEWASRAKTLGIDFDNREWQGH GKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIANKQVLGHATI ADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLSGKTLKK EQMRAVTEIVTSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALED DGLPARTVAAFLKAKDKKLDEKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQ TKAVEAGKPFEQLIKAGMQTSYMKDIQRQKNEVLLEAVKYAAEGNAARALKNITGVNELK EEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDYIRGNLGLAGTGETFTLLDRV DSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVESISGEQIAFSP RTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTD DKKSLASSVSRDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFN QKPDEHNMTTGTDYQPVSNAEDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQ RSAQEYADYEHYAEASDYDFDSSIYDDYAMPQTSQAEQSHTGKEHTHEHEHEEGGHEI

Reference

[1] Paterson ES et al (1999) Genetic analysis of the mobilization and leading regions of the IncN plasmids pKM101 and pCU1. J Bacteriol. 181(8):2572-83. [PMID:10198024]

II. Auxiliary DNA-binding protein(s) of the relaxosome

#	ID	Name	GenBank	Length	Note
1	20	TraK_R46	NP_511203	138 aa	_

Information of T4CP

ID	13
Name	TraJ_R46
SecReT4 accesion number	17530604
GenBank accession number	NP_511202
Family	TrwB/TraD
Length	509
UniProt ID	Q79SD7
PDB ID	_
Pfam	TrwB_AAD_bind [PF10412.8], Evalue: 7.00E-84, Aligned region: 112..491 TraG-D_C [PF12696.6], Evalue: 3.50E-19, Aligned region: 350..472 T4SS-DNA_transf [PF02534.13], Evalue: 1.30E-09, Aligned region: 297..500 DUF87 [PF01935.16], Evalue: 2.70E-05, Aligned region: 109..272
Note	Type IV Secretion System Coupling Protein
Protein sequence [Download]	MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIA GWFIGVGGLIAFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPI PTYAENLHFSIAGTTGTGKTTIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNA YDKRTEGWVFFNEIRRSYDYERLVNSIVQESPDMATEEWFGYGRLIFSEVSKKLHSLYST VTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGSARFVLSKNLAPHLKMPEGNF SLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESRINVFIDELES LQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALP GDMPVAKFKAKHVKYHRKNPVPGIELREI

Reference

[1] Paterson ES et al (1999) Structural and functional analysis of the origin of conjugal transfer of the broad-host-range IncW plasmid R388 and comparison with the related IncN plasmid R46. J Bacteriol. 181(8):2572-83. [PMID:10198024]

Information of plasmid

ID	13
Plasmid name	R46
GenBank accession number	NC_003292.1
Incompatibility group	IncN
Genome size	50969 bp
Coordinate of oriT [Strand]	19903..20551 [+]
Drug resistance	resistance to ampicillin, spectinomycin, streptomycin and tetracycline
Heavy-metal resistance	arsenical resistance
Virulence factor	_
Xenobiotic degradation	_
Host bacterium [NCBI Taxonomy ID]	Salmonella enterica serovar Typhimurium [90371]

Reference

[1] Paterson ES et al (1992) The oriT region of the conjugative transfer system of plasmid pCU1 and specificity between it and the mob region of other N tra plasmids. J Bacteriol. 174(2):499-507. [PMID:1309528]

[2] Hall RM et al (1987) The region of the IncN plasmid R46 coding for resistance to beta-lactam antibiotics, streptomycin/spectinomycin and sulphonamides is closely related to antibiotic resistance segments found in IncW plasmids and in Tn21-like transposons. Nucleic Acids Res. 15(18):7491-501. [PMID:2821509]

[3] Bruhn DF et al (1996) The arsenical resistance operon of IncN plasmid R46. FEMS Microbiol Lett. 139(2-3):149-53. [PMID:8674982]