oriTDB
The information of the oriT region
oriTDB accession number 100150
Name oriT_NAH7  insolico
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
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 experimental
GenBank accession number YP_534815
Family MOBF
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 insolico YP_534813 130 aa putative plasmid transfer protein TraA
Information of T4CP
ID 144
Name TraB_NAH7 insolico
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 insolico 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]

Microbial Bioinformatics Group in MML, SJTU