oriTDB

The information of the oriT region

oriTDB accession number	100150
Name	oriT_NAH7
Sequence Completeness	intact
oriT length	430 nt
oriT sequence	GGTGTTCCTCTCTGAGCCCAAAATGGGACATATTCAGGCTAACGATAACTGCCGAAACAG TGTATAGCAAATGTAATACACAAAAAGCTTGATTTTGCTGATCTAGACTGTACTTTTGTA ATACATATGTATAGCGCATAAAAACACCACTTTTTCTCTGCAGGCCGCGCACAGCGCGGC TGTCACCTCCCGCTAGGGGGGTGCGTATTGTGTATTGAGACTTTGAATTGAGACTTTGAC CCTGTTAAGGGGAAAAGTTGAAGCTCTTGTTAAGGGCGTATCCACTAGCCAGGCCGAAGG CCGTAGGGGGGTAGCACAGATGGTATGCAGAAAGGGTGCTAGAAGAGAGCAGGAAGAGTG CAACTTGACTACAGGTAGGGGGCGAGTAAGATGCACATAGAGTGCAATAGGGGTGCAGAT AGGGTGCAAA
IR (inverted repeat)	IR1: [60-65] [76-81] nt (GTGTAT..ATACAC) IR2: [121-126] [127-132] nt (ATACAT..ATGTAT) IR3: [140-144] [151-155] nt (AAAAA..TTTTT) IR4: [171-175] [179-183] nt (ACAGC..GCTGT)
Location of nic site	[213-214] nt
Conserved sequence flanking the nic site	_
Note
	L:60-65;R:76-81;L:121-126;R:127-132;L:140-144;R:151-155;L:171-175;R:179-183;D:213-214

Visualization of oriT structure

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

1

GGTGTTCCTCTCTGAGCCCAAAATGGGACATATTCAGGCTAACGATAACTGCCGAAACAG

61

TGTATAGCAAATGTAATACACAAAAAGCTTGATTTTGCTGATCTAGACTGTACTTTTGTA

121

ATACATATGTATAGCGCATAAAAACACCACTTTTTCTCTGCAGGCCGCGCACAGCGCGGC

181

TGTCACCTCCCGCTAGGGGGGTGCGTATTGTGTATTGAGACTTTGAATTGAGACTTTGAC

241

CCTGTTAAGGGGAAAAGTTGAAGCTCTTGTTAAGGGCGTATCCACTAGCCAGGCCGAAGG

301

CCGTAGGGGGGTAGCACAGATGGTATGCAGAAAGGGTGCTAGAAGAGAGCAGGAAGAGTG

361

CAACTTGACTACAGGTAGGGGGCGAGTAAGATGCACATAGAGTGCAATAGGGGTGCAGAT

421

AGGGTGCAAA

Reference

[1] Sota M et al (2006) Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. J Bacteriol. 188(11):4057-67. [PMID:16707697]

I. Information of Relaxase

ID	144
Name	TraC_NAH7
GenBank accession number	YP_534815
Family	MOB_F
Length	978 aa
UniProt ID	Q1XGM7
PDB ID	_
Pfam	TrwC [PF08751.10], Evalue: 5.60E-82, Aligned region: 9..287 AAA_30 [PF13604.5], Evalue: 3.00E-40, Aligned region: 473..672 Viral_helicase1 [PF01443.17], Evalue: 1.50E-05, Aligned region: 826..915 AAA_19 [PF13245.5], Evalue: 8.70E-07, Aligned region: 478..614 UvrD_C_2 [PF13538.5], Evalue: 1.10E-06, Aligned region: 867..914
Note	relaxase
Protein sequence [Download]	MFNVTSIKGSNQYAAAGYYTAADDYYAKESPGEWQGIGAELLGLAGPIDQKELAKLFDGK LPNGEVMPKTFDKETGNRRMGLDLTFSAPKSVSMQALIAGDKDVVAAHDRAVTKAMEHVE KLAQARRKEHGKSMLERTGNLIIGKFRHELSRAKDPQLHTHAVVMNATRREDGKWRAIHN DDIFKIQPQIDAMYKGELAKELRELGYEIRVLDKDGNFELAHISRDQIEAFSSRAKVIEE ALAKDGKTRSNATALEKQIIAMATRPRKDERDRHLVKEYWVTKARDLGIEFGGRSQLDNQ EYGRRSESIHAEHNLPEGITAGQAVVQYAINHLTEREQVVGESDLRTAALRRAVGLASPS EVDDEIKRLVKQGTLIESPPTYRMATGKDGAALSPAGWRALLKEQKGWSEKEAQQYVKMA INRGSLVEAEKRYTTQRALKREKAILAIERSGRGQVAPLLSKEQVAKALESSTLSAGQYQ AVEVIVSTSNRFVGIQGDAGTGKTYSVDRAVKLIESVNNAMTERSTTTDAVFRVVALAPY GNQVTALKNEGLDAHTLASFFHTKDKKLDERTIVVLDEAGVVGARQMEQLMRIIEQSGAR LVQLGDTKQTEAIEAGKPFAQLQQNGMQTARIKEIQRQKNQELKIAVQHAADGNPGKSLE HVNHVEELREPGQRHQAIVRDYMSLTPQERKEVLIVAGTNKDRKQINAMTRESLGLVGNG KELPTLNRVDTTQAERRYAPSYKKGMIVQPEKDYIRAGLSRGELYTVDQALPGNVLVVKD KNGNRVEFNPRKLTKLSVYNLEKPEFSVGDLVRITRNDQKLDLTNGDRMRVVGNANGVIE LASLKEKDGTPERVVALPTNRPLHLEHAYSATVHSAQGLTNDRVMISINTKSLTTSQNLW YVAISRARHEARIYTDSIAGLPAAIANRYDKTTALSLQQARERQRNESIKPRTVLDGKEL ERKQRSALDGAGLGKSGV

Reference

[1] Sota M et al (2006) Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. J Bacteriol. 188(11):4057-67. [PMID:16707697]

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

#	ID	Name	GenBank	Length	Note
1	209	TraA_NAH7	YP_534813	130 aa	putative plasmid transfer protein TraA

Information of T4CP

ID	144
Name	TraB_NAH7
SecReT4 accesion number	90576572
GenBank accession number	YP_534814
Family	TrwB/TraD
Length	519
UniProt ID	Q1XGM8
PDB ID	_
Pfam	TrwB_AAD_bind [PF10412.8], Evalue: 1.10E-103, Aligned region: 124..500 TraG-D_C [PF12696.6], Evalue: 4.90E-21, Aligned region: 363..481 T4SS-DNA_transf [PF02534.13], Evalue: 3.70E-15, Aligned region: 240..512
Note	Type IV secretion-system coupling protein DNA-binding domain; pfam10412
Protein sequence [Download]	MHKREVDSAVMTAGFGLPIAGWAAGVYFAQMPLTPFPAAFKETLHNGWHNPIVLGATIAT SAVAASLVYYLYEYCDDGFRGEQYQEFLRGSEIKNWHTVKAKVRRRNEKTNRERKKWGLA KSEPIMIGKLPMPLHLEDRNTMICASIGAGKSVTMEGMIASALKRGDRLAVVDPNGTFYS KFSFKGDSILNPFDERSVGWTIFNEIRGIHDFNRMAKSIIPPQVDPSDEQWCAYARDVLS DTMRKLKETNNPDQDTLVNLLVREDGDTIRAFLANTDSEGYFRDNAEKAIASIQFMMNKY IRPLRYMSKGEFSIYKWVNDPNAGNLFITWREDMRDTMKPLVATWIDTICATILSSEPMT GKRLWLFLDELQSLGKLESFVPAATKGRKHGLRMVGSLQDWSQLNASYGRDDAETLLSCF RNYVILAAANAKNAGMASEILGSHDVKRWRKSYTAGKLTRTEEVTRDEPVVQASEISNLP DLVAYVKFGEDFPITKVKTPYIDYKERAQAIMLTGQAAA

Reference

[1] Sota M et al (2006) Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. J Bacteriol. 188(11):4057-67. [PMID:16707697]

Information of plasmid

ID	144
Plasmid name	NAH7
GenBank accession number	NC_007926.1
Incompatibility group	IncP9
Genome size	82232 bp
Coordinate of oriT [Strand]	19758..20187 [-]
Drug resistance	_
Heavy-metal resistance	_
Virulence factor	_
Xenobiotic degradation	naphthalene degradation
Host bacterium [NCBI Taxonomy ID]	Pseudomonas putida G7 [303]

Reference

[1] Sota M et al (2006) Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. J Bacteriol. 188(11):4057-67. [PMID:16707697]

[2] Tsuda M et al (1990) Naphthalene degrading genes on plasmid NAH7 are on a defective transposon. Mol Gen Genet. 223(1):33-9. [PMID:2175388]