oriTDB
The information of the oriT region
oriTDB accession number 100221
Name oriT_pNoc614  insolico
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
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 insolico
GenBank accession number AAV52093
Family MOBF
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 _ insolico
 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 experimental 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]

Microbial Bioinformatics Group in MML, SJTU