Mobile element type:
Transposon
Name:
Tn4662a
Synonyms:
Accession:
Tn4662a-NC_014124.1
Family:
Tn3
Group:
Tn3000
First isolate:
Yes
Partial:
ND
Evidence of transposition:
ND
Host Organism:
Pseudomonas putida HS
Date of Isolation:
2018
Country:
U.s.a.
Molecular Source:
plasmid pDK1
| Name | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|
| IRL | 1-38 | + | 38 | GGGGATGTAA GCCGGAACCC CAGAAATTTC CGTCACCC |
| IRR | 7163-7200 | - | 38 | GGGGTTGTAC GCCGGAATCC CAGAAATTTC CGTCAGCC |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| res | Tn4662a | 3376-3506 | + | 131 | CTGTTCAGGT AATGATGTAA ACGCGGCAAC CTCAAGGAGG TGTCGTAAAA CATTTGTTTT GCGACAGGCT GTCAGCCGCC GCTGTGCTAC CTGTGCAACC ACCCCCTCAA AAATGTACGG AAAACTCTAT C |
| res_site_I | Tn4662a | 3376-3405 | + | 30 | CTGTTCAGGT AATGATGTAA ACGCGGCAAC |
| res_site_II | Tn4662a | 3413-3443 | + | 31 | AGGTGTCGTA AAACATTTGT TTTGCGACAG G |
| res_site_III | Tn4662a | 3482-3506 | + | 25 | TCAAAAATGT ACGGAAAACT CTATC |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| rpfG | Tn4662a | 168-1472 | - | Passenger Gene | Other |
| pDK1_p018 | Tn4662a | 1590-1982 | - | Passenger Gene | Hypothetical |
| pDK1_p017 | Tn4662a | 1967-2293 | - | Passenger Gene | Hypothetical |
| WP_000741275.1 | Tn4662a | 2350-2652 | - | Passenger Gene | Hypothetical |
| HTH_37 | Tn4662a | 2667-3002 | - | Passenger Gene | Antitoxin |
| Gp49 | Tn4662a | 2983-3360 | - | Passenger Gene | Toxin |
| tnpR | Tn4662a | 3520-4155 | + | Accessory Gene | Resolvase |
| tnpA | Tn4662a | 4139-7168 | + | Transposase |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | rpfG | RpfG | Tn4662a | 434 | 168-1472 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Other | ||||||||||
| Comment: | metal dependent phosphohydrolase with conserved HD motif | ||||||||||
| Protein Sequence: | MVKRIPVSEL RLGMYIHKLA GSWVRHPFWR GSFLLTEPQD LSAIRECGVG EVWVDLAKSQ VDPESPESPE SPESPESPES PESPESPEPR AQSPEPRAQS PEPRELSEEQ SLPSSPLSKK SDGATSMESE MCYARKLCLA AKSQVMDMFQ EARLGKAVDP STTLPLVGEI AASVLRQPHA LISVARIKTH DDYTYLHSVA VCALMLSLAR HLDLDEEQTR LAGIGGLMHD LGKAAMPLEV LNKPGKLTDA EFAIMKRHPV EGAKMLRAGG AEPGVVDIAL HHHEKIDGTG YPDRLAGDAI SLLARMGAIC DVYDAVTSER AYKKPWDPSA AMRQMAKWEG HFDKRIFHAF VKAVGIYPVG SLVRLSSQRL AVVVEPGMES LLTPKVRVFF SLRSREPIPM QTIDLAATSC KDSITGPEDP TLWNFKNLDD LWME |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | pDK1_p018 | PDK1_p018 | Tn4662a | 130 | 1590-1982 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Hypothetical | ||||||||||
| Protein Sequence: | MDEQMNLSTI EALAIAWARI AEEAELPAGY EGTATPEAHR ACEVIQERIR EHVVATNDMR LFGLLHLLGQ ASLRMEQALW PEEYARMTRE VEEALREADD PNAKSYTHEE VMQAMQERID RARDKAMLIG |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | pDK1_p017 | PDK1_p017 | Tn4662a | 108 | 1967-2293 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Hypothetical | ||||||||||
| Protein Sequence: | MSRSRRKTPI VGHTTCRSER EDKKLWHQRW RTHERTALAS ASPEALCAHL PLLENQVSNV WSMGKDGRSY WPIKRQAATA DRIANHKGRN PQERASLKKR LLRKWMSK |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | WP_000741275.1 | WP_000741275.1 | Tn4662a | 101 | 2350-2652 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Hypothetical | ||||||||||
| Protein Sequence: | MAARITDDEW DELTPENFDT TALLRAVDAV DVLRGDLNDS ADGAPPQLRT DLLKLHQLAM AAFNERSRSR VAELFDLAVD LQDQVDHLMT SLEQVQETLS R |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | HTH_37 | HTH_37 | Tn4662a | 111 | 2667-3002 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antitoxin | ||||||||||
| Sequence Family: | HTH_37 (Pfam:PF13744) | ||||||||||
| Protein Sequence: | MQKRIIEGVE VQRSSGNVFA DLGLPDAEKL KIKTGLVVEI RRAMRALGLT QQAAAKRMGI PQPKVSGMMR GDFTNLSERK LMDCLNRLGY DIEIKVRPAA EPIGHLTLAT A |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | Gp49 | Gp49 | Tn4662a | 125 | 2983-3360 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Toxin | ||||||||||
| Sequence Family: | Gp49 (Pfam:PF05973) | ||||||||||
| Target: | ribosome associated mRNA | ||||||||||
| Protein Sequence: | MTNKEKPLEW IASSHKDLMA LPSDVRRRFG YALSLAQIGD QDDAAKVLKG FGGAGVLEVV EDDAGGTYRA VYTVKFAEAV FVLHCFQKKS KSGIATPKAD MDIIRARLKV AEVLAQELRN AKTNH |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpR | TnpR | Tn4662a | 211 | 3520-4155 | + |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Resolvase | ||||||||||
| Sequence Family: | Serine Site-Specific Recombinase | ||||||||||
| Transposase Chemistry: | Serine | ||||||||||
| Protein Sequence: | MRKPVFDGYP PMLVGYMRVS SDSDRQSTDL QRDALLAAGV DPRHLFEDRA SGAKDDRAGL ARALEFVRAG DVLVVWKLDR LGRSLSHLLA IVTSLKDKRV AFRSLTENLD TTTPSGEFLF QVFGALAQYE RALIQERVVA GLAAARKRGR IGGRPQAITG EKLDAIVAAL DGGMSKAAVC RNFNVKRTTL IETLTRAGWR GAGRTVDEQQ E |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpA | TnpA | Tn4662a | 1009 | 4139-7168 | + |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Protein Sequence: | MSNKNKLLTV FSDAEQEALY RLPDFDDAQR LEYLALAESE LAFASSRPSL QAQVYCVLQI GYFKAKHAFF RFDWHEVEDD CAFVLSRYFH GEAFERKAIT KHEHYSQRGQ IAELFGYRSW AASFLPQLAQ QAEQIVRRDV MPGFVAAELI VWLSEHKIIR PGHTTLQELV SEALSTERRR LGGLLAEVLD ESAKAALGQL LVRDDTLSQL AALKQDAKDF GWRQMAGERE KRATLKSLHG IAKALLPKLG ISQQNLLYYA SLANFYTVHD LRHLKAEQTR LYLLCYAWVR YRQLTDNLVD AMAFHMKKLE DESRTGAKQS FVAEQLRRHQ ETPQVGRLLS LYVDDSVADP TPFGEVRQRA YKIMSRELLQ NTAQRMSVKP LNKLALHWQA VDGLAERIRR HLRPLYVALD FAGTAPDNPW LAALTWAKSV FAKQQRLSQR PLDECPAATL PKRLRPYLLM FDAEGTPTGL HADRYEFWLY RQVRKRFQAG ELYIDDSLQH RHLSDELVSM DEKAAVLAQM DIPFLRQPVS AQLDALAAEL RAQWVAFNRE LKQGKLTHLE YDKDTQRLTW RKPKGENQKA REQALYEQLP YCDVADVFRF VNGQCQFLSA LTPLQPRYAK KVADADSLMA VIIAQAMNHG NQVMARTSDI PYHVLESTYQ QYLRQATLHV ANDCISNAIA ALPIFPHYSF DLDSLYGAVD GQKFGVERPT VKARYSRKYF GRGKGVVAYT LLCNHVPLNG YLIGAHEYEA HHVFDIWYRN TSDIVPSAIT GDMHSINKAN FAILHWFGLR FEPRFTDLDD QLQELYCADD LALYEKCLIR PAGQIDRQLI VGEKANIDRI VATLGLKEMT QGTLIRKLCT YTAPNPTRRA IFEFDKLIRS IYTLRYLRDP QLERNVHRSQ NRIESYHQLR STIAQVGGKK ELTGRTDIEI EISNQCARLI GNAIIFYNSA ILSLLLTKYE AAGNAKALAL ITQMSPAAWR HILLNGHYTF QTDGKFIDLD ALVAGLELG |
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1. Miyakoshi M, Shintani M, Inoue K, Terabayashi T, Sai F, Ohkuma M, Nojiri H, Nagata Y, Tsuda M.
ParI, an orphan ParA family protein from Pseudomonas putida KT2440-specific genomic island, interferes with the partition system of IncP-7 plasmids.. Environ Microbiol. 2012 Nov;14(11):2946-59. doi: 10.1111/j.1462-2920.2012.02861.x. Epub 2012 Aug 28. PubMed ID:
22925377
.
2. Yano H, Miyakoshi M, Ohshima K, Tabata M, Nagata Y, Hattori M, Tsuda M. Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids.. J Bacteriol. 2010 Sep;192(17):4337-47. doi: 10.1128/JB.00359-10. Epub 2010 Jun 25. PubMed ID: 20581207 .
3. Assinder SJ, De Marco P, Osborne DJ, Poh CL, Shaw LE, Winson MK, Williams PA. A comparison of the multiple alleles of xylS carried by TOL plasmids pWW53 and pDK1 and its implications for their evolutionary relationship.. J Gen Microbiol. 1993 Mar;139(3):557-68. doi: 10.1099/00221287-139-3-557. PubMed ID: 8473862 .
4. Assinder SJ, de Marco P, Sayers JR, Shaw LE, Winson MK, Williams PA. Identical resolvases are encoded by Pseudomonas TOL plasmids pWW53 and pDK1.. Nucleic Acids Res. 1992 Oct 25;20(20):5476. doi: 10.1093/nar/20.20.5476. PubMed ID: 1331988 .
5. Benjamin RC, Voss JA, Kunz DA. Nucleotide sequence of xylE from the TOL pDK1 plasmid and structural comparison with isofunctional catechol-2,3-dioxygenase genes from TOL, pWW0 and NAH7.. J Bacteriol. 1991 Apr;173(8):2724-8. doi: 10.1128/jb.173.8.2724-2728.1991. PubMed ID: 1672868 .
6. Voss JA, Khedairy H, Baker RF, Benjamin RC. Molecular cloning of the xylL-xylE region from the P. putida TOL plasmid, pDK1.. SAAS Bull Biochem Biotechnol. 1990 Jan;3:54-7. PubMed ID: 1366507 .
7. Shaw LE, Williams PA. Physical and functional mapping of two cointegrate plasmids derived from RP4 and TOL plasmid pDK1.. J Gen Microbiol. 1988 Sep;134(9):2463-74. doi: 10.1099/00221287-134-9-2463. PubMed ID: 3076182 .
8. Kunz DA, Ribbons DW, Chapman PJ. Metabolism of allylglycine and cis-crotylglycine by Pseudomonas putida (arvilla) mt-2 harboring a TOL plasmid.. J Bacteriol. 1981 Oct;148(1):72-82. doi: 10.1128/jb.148.1.72-82.1981. PubMed ID: 7287632 .
9. Kunz DA, Chapman PJ. Isolation and characterization of spontaneously occurring TOL plasmid mutants of Pseudomonas putida HS1.. J Bacteriol. 1981 Jun;146(3):952-64. doi: 10.1128/jb.146.3.952-964.1981. PubMed ID: 7240090 .
2. Yano H, Miyakoshi M, Ohshima K, Tabata M, Nagata Y, Hattori M, Tsuda M. Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids.. J Bacteriol. 2010 Sep;192(17):4337-47. doi: 10.1128/JB.00359-10. Epub 2010 Jun 25. PubMed ID: 20581207 .
3. Assinder SJ, De Marco P, Osborne DJ, Poh CL, Shaw LE, Winson MK, Williams PA. A comparison of the multiple alleles of xylS carried by TOL plasmids pWW53 and pDK1 and its implications for their evolutionary relationship.. J Gen Microbiol. 1993 Mar;139(3):557-68. doi: 10.1099/00221287-139-3-557. PubMed ID: 8473862 .
4. Assinder SJ, de Marco P, Sayers JR, Shaw LE, Winson MK, Williams PA. Identical resolvases are encoded by Pseudomonas TOL plasmids pWW53 and pDK1.. Nucleic Acids Res. 1992 Oct 25;20(20):5476. doi: 10.1093/nar/20.20.5476. PubMed ID: 1331988 .
5. Benjamin RC, Voss JA, Kunz DA. Nucleotide sequence of xylE from the TOL pDK1 plasmid and structural comparison with isofunctional catechol-2,3-dioxygenase genes from TOL, pWW0 and NAH7.. J Bacteriol. 1991 Apr;173(8):2724-8. doi: 10.1128/jb.173.8.2724-2728.1991. PubMed ID: 1672868 .
6. Voss JA, Khedairy H, Baker RF, Benjamin RC. Molecular cloning of the xylL-xylE region from the P. putida TOL plasmid, pDK1.. SAAS Bull Biochem Biotechnol. 1990 Jan;3:54-7. PubMed ID: 1366507 .
7. Shaw LE, Williams PA. Physical and functional mapping of two cointegrate plasmids derived from RP4 and TOL plasmid pDK1.. J Gen Microbiol. 1988 Sep;134(9):2463-74. doi: 10.1099/00221287-134-9-2463. PubMed ID: 3076182 .
8. Kunz DA, Ribbons DW, Chapman PJ. Metabolism of allylglycine and cis-crotylglycine by Pseudomonas putida (arvilla) mt-2 harboring a TOL plasmid.. J Bacteriol. 1981 Oct;148(1):72-82. doi: 10.1128/jb.148.1.72-82.1981. PubMed ID: 7287632 .
9. Kunz DA, Chapman PJ. Isolation and characterization of spontaneously occurring TOL plasmid mutants of Pseudomonas putida HS1.. J Bacteriol. 1981 Jun;146(3):952-64. doi: 10.1128/jb.146.3.952-964.1981. PubMed ID: 7240090 .