oriTDB
The information of the oriT region
oriTDB accession number 100238
Name oriT_pDTG1  insolico
Sequence Completeness intact
oriT length 428 nt
oriT sequence GGTGGTCCTCTCTGAGCCAAATATGGGACTAATTCAGGATAACGATAACTTCCGAAATAG CGTATAGCAAATGCAATACATAAAATGCTTGATTTTATTGGTCTAAATGATAATTTTGTA ATACATATGTATAGCGCATGAAATTCATGAATTTGCTCTGTAAGCCGCTCCCAGCGCGGC TTTAACCTACCGCTAGGGGGGTGCGTGTTGTGTATTGAGACTTTGACCCTGTTAAGGGGA AAAGTTGAAGCTCTTGTTAAGGGCGTATCCACTAGTCAGGCCGCAGGCCGTAGGGGGGTA GCACAGATGGTATGCAGAAAGGGTGCAGGAAGGGTGCTAAGAGAGTGCAAGAGGGGTGCA ACTTGACTACAGGTAGGGGGCGATTAAGATGCACCTAGAGTGCAATAGGGGTGCAGATAG GGTGCAAA
IR (inverted repeat)IR1: [121-126] [127-132] nt  (ATACAT..ATGTAT)
IR2: [137-142] [144-149] nt  (CATGAA..TTCATG)
IR3: [162-170] [174-182] nt  (AAGCCGCTC..GCGCGGCTT)
Location of nic site [213-214] nt
Conserved sequence flanking the
  nic site 		_
Note predicted by the oriTfinder
L:121-126;R:127-132;L:137-142;R:144-149;L:162-170;R:174-182;D:213-214
Visualization of oriT structure
Reference
 N/A
I. Information of Relaxase
ID 309
Name TraC_pDTG1 insolico
GenBank accession number NP_863125
Family MOBF
Length 981 aa
UniProt ID Q847F0
PDB ID _
Pfam TrwC [PF08751.10], Evalue: 6.70E-82, Aligned region: 9..290
AAA_30 [PF13604.5], Evalue: 4.60E-40, Aligned region: 476..674
Viral_helicase1 [PF01443.17], Evalue: 1.60E-05, Aligned region: 829..918
AAA_19 [PF13245.5], Evalue: 5.10E-07, Aligned region: 481..617
UvrD_C_2 [PF13538.5], Evalue: 3.50E-07, Aligned region: 870..917
Note putative relaxase
Protein sequence [Download] MFNVTSIKGSNQYAAAGYYTAADDYYAKESPGEWQGIGAELLGLDGPIDQKELAKLFDGK
LPNGELMPKPVNKETGQIVNRRMGLDLTFSAPKSVSMQALIAGDKDVVAAHDRAVTKAME
HVEKLAQTRRKEHGKSMLERTGNLIIGKFRHELSRAKDPQLHTHAVVMNATRRADGKWRA
IHNDDIFKIQPQIDAMYKGELAKELRELGYEIRVLDKDGNFELAHISRDQIEAFSSRSKV
IEEALAKDGKTRSNATALEKQIIAMATRPRKDERDRHLVKEYWVIKARDLGIEFGGRSQL
DNREYGRRSESIHAEHNLPEGITAGQAVVQYAINHLTEREQVVGESDLRTAALRRAVGLA
SPSEVDDEIKRLVKQGTLIESPPTYTMATGKDGTALSPAGWRALLKEQKGWTDKEAQQYV
KMAITRGSLVEAEKRYTTQRALKREKAILAIERSGRGLVAPLLSKEQVAKALEGSTLSAG
QYQAVEVIVSTSNRFVGIQGDAGTGKTYSVDRAVKLIESVNNAMTERTTTTDAVFRVVAL
APYGNQVTALKNEGLDAHTLASFFHTKDKKLDERTIVVLDEAGVVGARQMEHLMRIIEQS
GARLVQLGDTKQTEAIEAGKPFAQLQQNGMQTARIKEIQRQKNQELKIAVQHAADGNPGK
SLEHVNHVEEFREPGQRHQAIVRDYMSLTPEERKEVLIVAGTNKDRKQINAMTRESLGLV
GNGKELPTLNRVDTTQAERRYAPSYKKGMIVQPEKDYIRTGLSRGELYTVDQALPGNVLV
VKDKNGNRVEFNPRKLTKLSVYNLEKPEFSVGDLVRITRNDQKLDLTNGDRMRVVGNANG
VIELASLKEKDGTPERVVALPTNRPLHLEHAYSATVHSAQGLTNDRVMISINTKSRTTSQ
NLWYVAISRARHEARIYTDSIAGLPAAIANRYDKTTALSLQQARERQRNESIKPRTVLDG
KALERKQRSALDGPSAGKSGV
Reference
 N/A

II. Auxiliary DNA-binding protein(s) of the relaxosome
 N/A
 N/A
Information of plasmid
ID 700
Plasmid name pDTG1
GenBank accession number NC_004999.1
Genome size 83042 bp
Coordinate of oriT  [Strand] 63861..64288 [-]
Drug resistance _
Heavy-metal resistance _
Virulence factor _
Xenobiotic degradation experimental degradation of naphthalene
Host bacterium [NCBI Taxonomy ID] Pseudomonas putida NCIB 9816-4 [303]
Reference
[1] Dennis JJ et al (2004) Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4. J Mol Biol. 341(3):753-68. [PMID:15288784]
[2] Park W et al (2002) nahR, encoding a LysR-type transcriptional regulator, is highly conserved among naphthalene-degrading bacteria isolated from a coal tar waste-contaminated site and in extracted community DNA. Microbiology. 148(Pt 8):2319-29. [PMID:12177326]
[3] Simon MJ et al (1993) Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene. 127(1):31-7. [PMID:8486285]

Microbial Bioinformatics Group in MML, SJTU