Mobile element type:
Transposon
Name:
Tn4652
Synonyms:
Accession:
Tn4652-AF151431.1
Family:
Tn3
Group:
Tn4651
First isolate:
Yes
Partial:
ND
Evidence of transposition:
Yes
Host Organism:
Pseudomonas putida Strain KT2440
Date of Isolation:
1999
Country:
Singapore
Molecular Source:
genomic DNA
| Name | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|
| IRL | 1-46 | + | 46 | GGGGTTATGC CGAGATAAGG CAAAAATTAG GACATTCGTT CTGTAA |
| IRR | 16984-17029 | - | 46 | GGGGTCATGC CGAGATAAGG CAAAAATTAG GACATTCGTT CTCTAA |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| res | Tn4652 | 13598-13800 | + | 203 | GACGTCTTTC ATCGCCCGAG GTTGCCCTTT GTGTACTGGA AAACGGCTGC CAAACGACCG TTTTTGCCTT TCGTATTGAA TAACACTCCA TTATTTTATC TGATTTATTT GCTTTTAACT GGCTTTACAT CAATCAAATT TAGTATGTAA ATACATACTA TGTAATCTAC TACGAAATCG TAGGAGCAGA CCATGGCCCG CGG |
| res_site_6 | Tn4652 | 13663-13686 | + | 24 | GCCTTTCGTA TTGAATAACA CTCC |
| res_core_IRR | Tn4652 | 13688-13700 | - | 13 | TCAGATAAAA TAA |
| res_site_3 | Tn4652 | 13708-13728 | + | 21 | GCTTTTAACT GGCTTTACAT C |
| res_site_2 | Tn4652 | 13732-13769 | + | 38 | CAAATTTAGT ATGTAAATAC ATACTATGTA ATCTACTA |
| res_acc_IR1 | Tn4652 | 13738-13746 | + | 9 | TAGTATGTA |
| res_acc_IR1 | Tn4652 | 13749-13757 | - | 9 | TAGTATGTA |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| tnpA | Tn4652 | 143-3157 | + | Transposase | |
| tnpC | Tn4652 | 3166-3528 | + | Accessory Gene | Inhibitor/Regulator |
| rcnA | Tn4652 | 4084-5223 | - | Passenger Gene | Heavy Metal Resistance |
| tnp | IS1246 | 6288-7130 | - | Transposase | |
| itaS | Tn4652 | 8697-9599 | + | Passenger Gene | Other |
| tnpA | ISPpu33 | 10034-10345 | + | Accessory Gene | Regulator |
| tnpB | ISPpu33 | 10342-11247 | + | Transposase | |
| tnpS | Tn4652 | 12638-13609 | - | Accessory Gene | Resolvase |
| tnpT | Tn4652 | 13790-14803 | + | Accessory Gene | Resolvase |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpA | TnpA | Tn4652 | 1004 | 143-3157 | + |
|---|
| Class: | Transposase | ||||||||||
| Function: | transposase activity (GO:0004803) | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Comment: | possibly regulated by integration host factor upstream of feature | ||||||||||
| Protein Sequence: | MCSMASVERT AYPILPSQLP AKELHRSYSL SDSEIEWVNN TAKSPALSIG LAIQLKVFQQ LHYFVPFEEL PQELISHVRQ CLRYGARIAP RYSNPRTLYR HQAAVRQYLQ VTPFYSSDGL AVTEQIARDC AVVLEQRVDL INAMLDELIQ RGYELPAYST LNNLAETALA SAQEVTFNLV VTRAPIEVIY KLKELLDTDF GRRQSDFNAL KQAPKKPSRK HLEVLIDHLA WLESFGDLEA IFEGIVDAKI RHFAAQAAAA DVSELKDCSL PKRHTLMLAL IYRMRVRTRD HLAEMFIRRI STIHKRAKEE LEQIQARQRQ KLEQLAATLD GVVQILVQEP DDQEAGSLIR EYLSPDGNLD RLRETCAEVQ ATGGNNYLPL IWKHFRSHRS LLFRLSHLLQ LEPTTQDRSL TQALQLIQDS ENLHREWIDE HVDLSFASER WVKVVRRPSS EGPPTNRRYL EVCVFSYLAS ELRSGDMCVQ GSVSFADYRK QLLPWEECLQ RLPAYCEKMG LPGTAKEFVA SLKTQLEETA QQLDEKFPSC RGDVSINEAG EPVLRRVAAR DIPPSAISLQ TALMQRMPAR HVLDIMANIE HWIQFTRHFG PMSGNEPKLK EPAERYLMTI FAMGCNLGPS QAARHLTGNV TPHMLSYTNR RHLSLEKLDK ANRELVELYL QLDLPKLWGD GKAVAADGTQ FDFYDDNLLA GYHFRYRKMG AVAYRHVANN YIAVFQHFIP PGIWEAIYVI EGLLKADLSV EADTVYSDTQ GQSATVFAFT HLLGINLMPR IRNWRDLVMC RPDRGASYKH INRLFTDTAD WNLIETHWQD LMQVALSIQA GKISSPMLVR KLGSYSRRNK LYHAAQALGS VIRTIFLLNW IGSRELRQEV TANTNKIESY NGFSKWLSFG GDVIAENDPD EQQKRLRYND MVASSVILQN TVDMMRILHK LAREGWQFTD EDVSFLSPYL TSNVKRFGEF NLKLNRPPEP WIKDSVFQQA AGSLRANTAS KTGA |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpC | TnpC | Tn4652 | 120 | 3166-3528 | + |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Inhibitor/Regulator | ||||||||||
| Function: | tpnA repressor protein, at post-transcriptional level | ||||||||||
| Sequence Family: | Tn3_family | ||||||||||
| Comment: | similarity to an ORF of Tn5041encoding a putative 120-amino-acid-long polypeptide | ||||||||||
| Protein Sequence: | MIEIPPATFR VTPYGEVDGV ALDKLRASFD TSQLLRLVDQ FDACLAELGG VVAVRDELLK LHAMALTLVE GVPLTVPTEN ACIWTEAESL QQNLETLAGW VRSAQAGIIP LVNLAPDHEQ |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | rcnA | RcnA | Tn4652 | 379 | 4084-5223 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Heavy Metal Resistance | ||||||||||
| Function: | Nickel cation transmembrane transport (GO:0035444) | ||||||||||
| Target: | Nickel | ||||||||||
| Comment: | conserved domain Pfam: PF03824 | ||||||||||
| Protein Sequence: | MSSFAELLQQ GASQAWLYFP SAILLGALHG LEPGHSKTMM AAFIVAIRGT VKQAVLLGLA STLSHTAVVW LVAMAGMYLG QNLNAETTEP YFQLASAAII ITIALWMLWR TWRGEQMWRF EEGDDLQHDY HHHDEMQRID TGHGRIELSI FEEGVPPRWR LNILTGHAWS AAEMSLLTTR PDGLAQQFRF VDRGDYLESV DEIPEPHEFT ARLSLGHAGH SHDYDLEFHE HGHGHGHDHA ELEGLELSLE GYQDAHERAH ANDIRKRFSN RNVTTGQIIL FGLTGGLIPC PAAITVLLLC LQVKEVALGA VLVLCFSIGL AITLVTVGAA AAIGARQASN RWPWLGAVAR RAPYLSSLLI IGVGIYVGVH GWIGPERLA |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnp | Tnp | IS1246 | 280 | 6288-7130 | - |
|---|
| Class: | Transposase | ||||||||||
| Function: | Transposase activity (GO:0004803) | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Comment: | two transposase domains PF01609 and PF05598||similar to open reading frames of insertion sequences IS1168 and IS1186 andto protein encoded by GenBank Accession Number M11585 | ||||||||||
| Protein Sequence: | MVRILVLKRL YNLSDEQMEY QLLDRMSYKR FCGLASAVNI PDRTTVWTFE NRIGDAGAKV LFDGVTAQLL RHGFIARGGQ IVDATLVPAP KQRNSREENK LVREGAMPAN WKPAKRRQKD TDATWTQKHG KNHFGYKLSV NVDKKYKIIR KFETDTASVH DSKHFDALID RSNTSRDVYA DRGHTSADRE GWLKDHGYRN QIQRKGYRNK PLSECQQRRN HRIAKTRARV EHVFASIEQM GGKLIRTIGQ GRANFAMTMM AACYNLKRLV YFQKAGIKAF |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | itaS | ItaS | Tn4652 | 300 | 8697-9599 | + |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Other | ||||||||||
| Function: | Sulfuric ester hydrolase activity (GO:0008484) | ||||||||||
| Sequence Family: | sulphate esters (Interpro: IPR000917) | ||||||||||
| Comment: | similar match with LTA Synthase (WP_023445412.1) | ||||||||||
| Protein Sequence: | MPADQATTLT RDLLFTEHDR LADQNTAAIR RDFQPPQDRR LPIRNVVVIL MESFAGHFVG ALGSEAGITP NFDRLAQEGV LFRRFFANGT HTHQGMFASM ACFPNLPGFE YLMQTPEGGH QFSGLAQLLS TRDFDDLYVY NGDFAWDNQR GFFSNQGMTR FIGRNDFVDP VVSDPTWGVA DQDMFDRAAE ELFKQDPKKP FYALLQTLSN HTPYALPGVL PVEPVTGQGS LDQHLTAMRY SDWALGRFFE KARKAPYFKD TLFVVVGDHG FGAQEQLTEM DLYPVIPPEN QALVRSRIFS |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpA | TnpA | ISPpu33 | 103 | 10034-10345 | + |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Regulator | ||||||||||
| Function: | transposase activity (GO:0004803) | ||||||||||
| Comment: | similar to transposase subunit of insertion sequence IS401 from Burkholderia cepacia 17616 | ||||||||||
| Protein Sequence: | MSKHTKFSPE VRDRAIRMVY EVRESRTSQW AAIEAVASKI GCTAQTLSSW IRKAAAPAAP SASGTDARVK ELEREVRELK RANEILKVAS AFSAQAELDR RLK |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpB | TnpB | ISPpu33 | 301 | 10342-11247 | + |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Comment: | 100% match to end 226 amino acids referenced in ORF2 of ISFinder||orfB | ||||||||||
| Protein Sequence: | VIWQLIDKHR QSFGVEPLCR VLQVSPSAYR RHAARLRDRS RRSARAIRDE ELAVQIHRVW QENYEVYGAR KVWRQMHREH QVVARCTVER LMREMGLCGV TRGKTVKTTQ PDPDNANPRD LVKRQFTAER PNQLWVADFT FVSTWQGFAY VAFIVDVYSR FIVGWRVSRH MRTEFVLDAL EQALHTRRPE PHRLVHHSDR GSQYLSIRYS ERLGEAGIEP SVGNTGDSYD NALAETINGL YKTELIHKRG PWKSVDSLEW ETLKWVTWFN HQRLLEPIGN RPPAEFEALY EQSQATISVA A |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpS | TnpS | Tn4652 | 323 | 12638-13609 | - |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Resolvase | ||||||||||
| Function: | DNA binding (GO:0003677)||DNA integration (GO:0015074)||DNA recombination (GO:0006310) | ||||||||||
| Sequence Family: | TyrosineSite-Specific Recombinase | ||||||||||
| Transposase Chemistry: | Tyrosine | ||||||||||
| Comment: | orfS | ||||||||||
| Protein Sequence: | MKDVGRYLQA GTRENTRRSY QSAIEHFEVT WGGFLPATSD NIVRYLVEYA DTLSLSTLKQ RLAALAQWHI TQGFPDPTKT PTVRQVLKGI RTLHPAQTKQ AAPLQLQHLE QAIQWLSREA EQAQQSGNLA SLLRSRRDAA LLLIGFWRGF RSDELCRLQV EHIQAEAGAG MSLFLPQSKG DRDNLGTTHY VPALKCLCPV QAYLDWISAA GIARGAVFCR LDRWGHLSDE ALHPGSLISL LRQILQRAGI SAELYTSHSL RRGFASWATA NGWDLKALMT YVGWKDIKSA MRYIDPAISF GGLAAKPVLE LHAGPLGQLS ASH |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpT | TnpT | Tn4652 | 337 | 13790-14803 | + |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Resolvase | ||||||||||
| Function: | possibly involved in cointegrate resolution | ||||||||||
| Comment: | orfT | ||||||||||
| Protein Sequence: | MARGGINKAL VQKARQAILA RGENPSIDAV RVELGNTGSK TTIHRYLKEL EDAERGRNTA AIPLSEQLAN LVGQLADQLE EDAQATVAQE REQLQRERLD YQNQARLAES RIQQLESQSS GLTEQLQAVQ QALQQEQQQR QQTEVENARL AQANGDQEVR LQDRDSQIRS LEEKHQHARD ALEHYRQASK EQREQEQRRH ESQVQQLQLE LRQLQQTLII KQDELTQLNR DNARLLTEAR QLQKEQHAQQ QLLAQKNQAM EALQSVLAGS ERSNEALEQR CRTLQEEVSR LGEASATLAQ QAQGLQERLV EANTQLKLLR APLANSDGAP EHMNRHT |
||||||||||
| TnCentral Accession | TE Name | Type | Coordinates | Strand | Length |
|---|---|---|---|---|---|
| IS1246-L11583 | IS1246 | insertion sequence | 6125-7399 | + | 1275 |
| ISPpu33-AF151431 | ISPpu33 | insertion sequence | 9981-11286 | + | 1306 |
| Name | Associated TE | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|---|
| IRR | IS1246 | 6125-6174 | + | 50 | GGGCACCTCG AATAACGCGA GGTTTTCAGT GAATCCGACC GCCAAATGAT |
| IRL | IS1246 | 7350-7399 | - | 50 | GGGCACCTCG AAAAACCTCG GCCCCCTGCG ATTGGTAAAA TTGCGTTGTC |
| IRL | ISPpu33 | 9981-10006 | + | 26 | TGAACCGCCC CGGGTTTCGC GGAGGC |
| IRR | ISPpu33 | 11261-11286 | - | 26 | TGAACCGCCC CGGGTTTCGC GGAGGC |
1. Horak R, Kivisaar M.
Regulation of the transposase of Tn4652 by the transposon-encoded protein TnpC.. J Bacteriol. 1999 Oct;181(20):6312-8. doi: 10.1128/JB.181.20.6312-6318.1999. PubMed ID:
10515920
.
2. Horak R, Kivisaar M. Expression of the transposase gene tnpA of Tn4652 is positively affected by integration host factor.. J Bacteriol. 1998 Jun;180(11):2822-9. doi: 10.1128/JB.180.11.2822-2829.1998. PubMed ID: 9603867 .
3. Kivistik PA, Kivisaar M, Horak R. Target site selection of Pseudomonas putida transposon Tn4652.. J Bacteriol. 2007 May;189(10):3918-21. doi: 10.1128/JB.01863-06. Epub 2007 Mar 9. PubMed ID: 17351034 .
2. Horak R, Kivisaar M. Expression of the transposase gene tnpA of Tn4652 is positively affected by integration host factor.. J Bacteriol. 1998 Jun;180(11):2822-9. doi: 10.1128/JB.180.11.2822-2829.1998. PubMed ID: 9603867 .
3. Kivistik PA, Kivisaar M, Horak R. Target site selection of Pseudomonas putida transposon Tn4652.. J Bacteriol. 2007 May;189(10):3918-21. doi: 10.1128/JB.01863-06. Epub 2007 Mar 9. PubMed ID: 17351034 .