oriTDB

The information of the oriT region

oriTDB accession number	100221
Name	oriT_pNoc614
Sequence Completeness	intact
oriT length	510 nt
oriT sequence	TTGAGGCCGCGGCCGCGAAGTCGCCGGCGGAACGCTGGGCCCCGCTGGCCCGCGAGGTCG ACCCGCGCCTGGCGGAGCAGGACGACTGGCCCGCCACCGCCGCGATGCTGCAACAGGCCC ACGAGCAAGGCCACGACGTCAGCGCCGCTACCCGCGCCCTGGTCGCAGCAGCACCCCTGG GCGACGCCCCCGCCCGCGAACTGCGCTACCGGCTGGTTCGGCAGGTTGGATTCGGCGAAC ACGACGCCGAATCCACCGACCGTGACGCCCCGAAGCGCCGGCGCGACGCGGGTACTGGAC ATGAGCTCGGCTCTTCGAACCCAGTGCACCGCAGCCGCCGCCGGTAGGCCTGGGCACAGG TTGAGACCTACAACGAGAGGGCTGTCGGACACTCAACGCGAGGTACCCGCGTGCAGACCT GCCACATTGCGGCCCACTGTGGGGCAGCGTCATGGCGCTCAAACGGGCGGGCTCCTTGTC CAGAGGTCTTCAAAGCGCCGGACTGGGCCG
IR (inverted repeat)	IR1: [179-183] [185-189] nt (GGGCG..CGCCC) IR2: [225-237] [245-257] nt (GTTGGATTCGGCG..CGCCGAATCCACC)
Location of nic site	[155-156] nt
Conserved sequence flanking the nic site	TACCCGCG\|CCCT
Note	The putative JS614 oriT region contains a sequence (TACCCGCG\|CCCT) very similar to the consensus oriT core sequence identified in RSF1010, pTF1, and Ti plasmids (TAAGTGCG\|CCCT)(Cook and Farrand 1992).
	L:179-183;R:185-189;L:225-237;R:245-257;D:155-156

Visualization of oriT structure

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

1

TTGAGGCCGCGGCCGCGAAGTCGCCGGCGGAACGCTGGGCCCCGCTGGCCCGCGAGGTCG

61

ACCCGCGCCTGGCGGAGCAGGACGACTGGCCCGCCACCGCCGCGATGCTGCAACAGGCCC

121

ACGAGCAAGGCCACGACGTCAGCGCCGCTACCCGCGCCCTGGTCGCAGCAGCACCCCTGG

181

GCGACGCCCCCGCCCGCGAACTGCGCTACCGGCTGGTTCGGCAGGTTGGATTCGGCGAAC

241

ACGACGCCGAATCCACCGACCGTGACGCCCCGAAGCGCCGGCGCGACGCGGGTACTGGAC

301

ATGAGCTCGGCTCTTCGAACCCAGTGCACCGCAGCCGCCGCCGGTAGGCCTGGGCACAGG

361

TTGAGACCTACAACGAGAGGGCTGTCGGACACTCAACGCGAGGTACCCGCGTGCAGACCT

421

GCCACATTGCGGCCCACTGTGGGGCAGCGTCATGGCGCTCAAACGGGCGGGCTCCTTGTC

481

CAGAGGTCTTCAAAGCGCCGGACTGGGCCG

Reference

[1] Mattes TE et al (2005) Physiological and molecular genetic analyses of vinyl chloride and ethene biodegradation in Nocardioides sp. strain JS614. Arch Microbiol. 183(2):95-106. [PMID:15599705]

I. Information of Relaxase

ID	214
Name	TraA_pNoc614
GenBank accession number	AAV52093
Family	MOB_F
Length	1818 aa
UniProt ID	Q5U9L8
PDB ID	_
Pfam	TrwC [PF08751.10], Evalue: 4.60E-73, Aligned region: 12..426 AAA_30 [PF13604.5], Evalue: 1.50E-54, Aligned region: 589..792 Toprim_N [PF08275.10], Evalue: 1.90E-27, Aligned region: 1529..1661 AAA_19 [PF13245.5], Evalue: 1.60E-08, Aligned region: 598..736 Toprim_2 [PF13155.5], Evalue: 6.80E-08, Aligned region: 1670..1757 Toprim_4 [PF13662.5], Evalue: 2.50E-05, Aligned region: 1668..1741
Note	putative TraA conjugation protein
Protein sequence [Download]	MPVTMSLHKLTAGSGYDYLTRQVAAMDATDKGHTGLASYYTEKGETPGVWVGSGMEGIEG LDAGDVVTADHMQNLFGAGHHPLATARTKELDLRVGRAGVGSPTAADYKAAARLGTPFKV YENDVSAFRVEVAKRLAAVNEAAGLPGDWPVPAEERARIRTEIGRDFFRAEHGREPADAR ELAATIAKHSRPKTNAVAGYDLTFSPVKSVSTLWALADPKTAAVIEGAHQSAIKDALNFI ETKALFTRQGTNGIRQVNVRGLLATAFTHRDSRAGDPDLHTHVAVANKVQTLDGKWLAID GRLLYKAKVSASETYNTALERHLGDALGGTVRGTAESRRPEAAGARDRRLSYPDLNHRFL QAPRSASKPAARSWPPSSRRPTAARRHRIETLQLAQRATLETREAKHEPRSLNDQREAWD REAVEVLGSPRGLQQMLHGTLNPTAAGTAPVADAAWFAKTGDRIVTTMEGGRATWQYWHV YAEAQRQVRAANVPTDQVSTVVGLLVSEVLDGRSVSITRPFDEISEPPELRKLDGASVYT VGGVHLFTSSKVLAAEERLVEAAGRRDGYAVDEQNVALALLESEANGVTLNAGQATLVKE MATSGARLQLAIAPAGSGKTTAMRALAQAWTDGGGSVIGLAPSAAAADALRVSMGSQIDT QTDTLAKLTHSLEQSQVTGAEVPDWVAGIGPQTLVVIDEAGMADTLSLDIAVQHVLERGG SVRLVGDDQQLAAIGAGGVLRDIRATHGALQLTELVRFTDPAEGAASLALREGKGEALGF YLDRDRVHVGDLATMTEDVFAAWQADRAAGLDAIMLAPTRELVSELNQQARAHRLEGADP ASVGPARRLADGNEASIGELIITRTNDRKLRTSATDWVKNGDRWTVLGLHEGGDLTVQHT QHGRTVRLPREYVETSTELGYACTVHTAQGVTTDTMHGLATGNESRQQLYTMLTRGKSGN HIYLQVVGDGDPHSVIHPTLVRPLTPTDILESMLARDDAQRSATSLMREQADPATQLGEA AQRYLDSLYVAAENHLRNTAGPDGSNVVEALDSTVDQLLPGLADEAAWPTLRAHLLLLGA AGENPVEAMRAAASDRELVSAEDRAAVLDWRLDASGMRNVGTGPLPWIPGVPERLADDPH WGAYLDQRAHLVDQLADEVRGRAAAQTSLPTWAQNGIRPDTDTVADVEVWRAAMQVPLDD RRPTGAPQLQKASSTYQRRLNRRITGDHTPALTEWRQLLYSLAPQVRGDEFTPLLAERLA AMSRAGVEAHQLLRTATAADTGAGPLPDEHAAAALWWRMARHLSPAVAAQVGDGSHGEGV TTSWAAQLPELLSDERSARIQASAWWPALVSNIDHGLQRGWQLEALLSAGSALPSDDIDE CQALVWRTSIALEPIPDEHEHDDHFDEPPVDMWDGVEPDPATLVDHPDDTEWPLPHDLEA DGDHLVDHPEPDEAIDQVDVAPAAADNVDEQQFVEGDLTLAAYIRDLGGTPLEPTAADIR LMYQRADEWYSFPVTRERMIEINEITQTFFESRFTDSWGRDYLTGRFGIDLAGHEHFRPG QAPAGWTNLVDHLRHRGVSGAEMLATGVATTASTGRLIDRFRDRVMFPVVHNGEVLGFVG RRRPELTDADQANGRGGPKYLNTADTPLFHKGAQLYGVVDELLAEGAVPVIVEGPMDAIA VTLASAARYVGVAPLGTSLTDEQASQLGGIGRDPIVATDADLAGEVAAERDFWMLTPHGL DPGYARFPEGLDPADLLAQRGPAALTASLASGQTLGDQLLSERLDNLAPEQARVAAMRVL AARPSRAWRRAPTWCAPD

Reference

[1] Mattes TE et al (2005) Physiological and molecular genetic analyses of vinyl chloride and ethene biodegradation in Nocardioides sp. strain JS614. Arch Microbiol. 183(2):95-106. [PMID:15599705]

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

#	ID	Name	GenBank	Length	Note
1	302	_

N/A

Information of plasmid

ID	683
Plasmid name	pNoc614
GenBank accession number	AY772007.1
Genome size	290 kb
Coordinate of oriT [Strand]	_
Drug resistance	_
Heavy-metal resistance	_
Virulence factor	_
Xenobiotic degradation	utilizing vinyl chloride and ethene
Host bacterium [NCBI Taxonomy ID]	Nocardioides sp. strain JS614 [1839]

Reference

[1] Mattes TE et al (2005) Physiological and molecular genetic analyses of vinyl chloride and ethene biodegradation in Nocardioides sp. strain JS614. Arch Microbiol. 183(2):95-106. [PMID:15599705]