oriTDB

The information of the oriT region

oriTDB accession number	100013
Name	oriT_pCU1
Sequence Completeness	intact
oriT length	268 nt
oriT sequence	GTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTAGGTGTTTTTAA TACCTAATTATTACCGAATATTGACGCTATTTATTTTTTTATTTTTTAAATCAGTGTGAT AGCGTGATTTATGCCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTT TTTGGTAGGAGCGATCTACGTAGGTTAAGGACTAACTGACTAAAAAGCGTTCAATATTCC GTATTCATGCTTGCATGAATACCAGTAC
IR (inverted repeat)	IR1: [46-55] [59-68] nt (ATTAGGTGTT..AATACCTAAT) IR2: [107-113] [125-131] nt (TAAATCA..TGATTTA) IR3: [167-172] [178-183] nt (AAAAAA..TTTTTT) IR4: [241-250] [253-262] nt (GTATTCATGC..GCATGAATAC)
Location of nic site	[149-150] nt
Conserved sequence flanking the nic site	GGTGT\|ATAGC
Note	minimal oriT sequence
	L:46-55;R:59-68;L:107-113;R:125-131;L:167-172;R:178-183;L:241-250;R:253-262;D:149-150

Visualization of oriT structure (The oriT was characterized experimentally)

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

1

GTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTAGGTGTTTTTAA

61

TACCTAATTATTACCGAATATTGACGCTATTTATTTTTTTATTTTTTAAATCAGTGTGAT

121

AGCGTGATTTATGCCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTT

181

TTTGGTAGGAGCGATCTACGTAGGTTAAGGACTAACTGACTAAAAAGCGTTCAATATTCC

241

GTATTCATGCTTGCATGAATACCAGTAC

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]

[2] Paterson ES et al (1997) Localization of the nic site of IncN conjugative plasmid pCU1 through formation of a hybrid oriT. J Bacteriol. 179(18):5768-76. [PMID:9294433]

I. Information of Relaxase

ID	12
Name	TraI_pCU1
GenBank accession number	AAD27542
Family	MOB_F
Length	1078 aa
UniProt ID	Q9X4G2
PDB ID	3L57, 3L6T
Pfam	TrwC [PF08751.10], Evalue: 6.70E-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 NDELMRNKMHLGDVYKQELALELTKAGYELRYNSKNNTFDMAHFSDEQIRAFSRRSEQIE KGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQEWASRAKTLGIDFDNREWQGH GKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIANKQVLGHATI ADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLSGKTLKK EQMRAVTEIVTSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALED DGLPARTVAAFLKAKDKKLDEKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQ TKAVEAGKPFEQLIKAGMQTSYMKDIQRQKNEVLLEAVKYAAEGNAARALKNITGVNELK EEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDYIRGNLGLAGTGETFTLLDRV DSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVESISGEQIAFSP RTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTD DKKSLASSVSRDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFN QKPDEHNMTTGTDYQPVSNAEDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQ WSAQEYADYEHYAEASDYDFDSSIYDDYAMPQTSQAEQSHTGKEHTHEHEHEEGGHEI

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	19	TraK_pCU1	AAD27540	138 aa	_

Information of T4CP

ID	12
Name	TraJ_pCU1
SecReT4 accesion number	_
GenBank accession number	AAD27541
Family	TrwB/TraD
Length	509
UniProt ID	Q9X4G1
PDB ID	_
Pfam	TrwB_AAD_bind [PF10412.8], Evalue: 2.70E-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: 2.20E-05, Aligned region: 109..282
Note	Type IV secretion-system coupling protein
Protein sequence [Download]	MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIA GWFIGVGGLIAFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPI PTYAENLHFSIAGTTGTGKTTIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNA YDKRTEGWVFFNEIRRSYDYERLVNSIVQESPDMATEEWLAYGRLIFSEVSKKLHSLYST VTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGSARFVLSKNLAPHLKMPEGNF SLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESRINVFIDELES LQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALP GDMPVAKFKAKHVKYHRKNPVPGIELREI

Reference

[1] Paterson ES et al (1999) Localization of the nic site of IncN conjugative plasmid pCU1 through formation of a hybrid oriT. J Bacteriol. 181(8):2572-83. [PMID:10198024]

Information of plasmid

ID	12
Plasmid name	pCU1
GenBank accession number	AF109305.1
Incompatibility group	IncN
Genome size	_
Coordinate of oriT [Strand]	343..610 [+]
Drug resistance	resistance to spectinomycin, ampicillin and streptomycin
Heavy-metal resistance	_
Virulence factor	_
Xenobiotic degradation	_
Host bacterium [NCBI Taxonomy ID]	Escherichia coli [562]

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]