Mobile element type:
Transposon
Name:
Tn4656
Synonyms:
Accession:
Tn4656-NC_008275.1
Family:
Tn3
Group:
Tn21
First isolate:
Yes
Partial:
ND
Evidence of transposition:
ND
Host Organism:
Pseudomonas putida MT53
Date of Isolation:
2001
Country:
Molecular Source:
plasmid pWW53
| Name | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|
| IRL | 1-38 | + | 38 | GGGGAGCCCG CAGAATTCGG AAAATAACGT ACGCTAAG |
| IRR | 5661-5699 | - | 39 | GGGGAGCCTA CAGAATTCGG AAAAAATCGT ACGCTAAGG |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| res | Tn4656 | 1937-2065 | + | 129 | AAGGCCGTCA GGTTGGGCTA TACCCTAACT GGATGTCAGG AAAGGCCGCG CCACGCCGTC AGAATAGAGT CGCCTTTTGC ATTCTTTGAC ACCTGCTTGC CAAGGTCATA GATTTTAGCC TGACAAATT |
| res_site_I | Tn4656 | 1938-1976 | + | 39 | AGGCCGTCAG GTTGGGCTAT ACCCTAACTG GATGTCAGG |
| res_site_II | Tn4656 | 1989-2033 | + | 45 | ACGCCGTCAG AATAGAGTCG CCTTTTGCAT TCTTTGACAC CTGCT |
| res_site_III | Tn4656 | 2038-2065 | + | 28 | AAGGTCATAG ATTTTAGCCT GACAAATT |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| mcp | Tn4656 | 136-1794 | - | Passenger Gene | Other |
| tnpR | Tn4656 | 2082-2696 | + | Accessory Gene | Resolvase |
| tnpA | Tn4656 | 2700-5666 | + | Transposase |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | mcp | Mcp | Tn4656 | 552 | 136-1794 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Other | ||||||||||
| Function: | methyl-accepting chemotaxis protein | ||||||||||
| Sequence Family: | Methyl-Accepting Chemotaxis Protein | ||||||||||
| Protein Sequence: | MSGWLARFSI KTRLIGLLVL LASMAVGLPM AGLNGMRTSN AVIDRLYNNM LLPIDKLGDI NNHMHNARAQ LLLALQHEPG SAFEKAHDHP SSMHFDRVDK SVSIIRERLS DYQRIPMSKE QQRLSTELQN KLSDYLDNGV LPTLNAMRQG DYAGGNQILL TRLDPAFMTT YASLRTLIES EASAAELSFQ NADKQFERLV AMIGLALVVA LSLVTVTALA TVPSITKGVR ELQVGGQQLA DGNLGYRVTY QGRDELGEIS SAFNEMASRF HHTFQELAGA VEQLAAAAEQ TAQASSQTSD GIRRQQLETD LIATAMNEMS ATVQDVAGNA ASAARAAQEA DQQSESGMRV VHQTIASIDS LASEVEHAAT VIHELEADSA GISSVVDVIR SITEQTNLLA LNAAIEAAHA GEHGRGFAVV ADEVRSLASR TQQSANEIQA MIEKLQSGAN RAVAVMESSC SKAQAGKQQV ASAGHMLEQI SNAVATINDM NAMIASAAEE QSSVAEEISR NVTNVSQIAE KTSEASRQNV ATSTQLASLA SQLQRLMHMF RL |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpR | TnpR | Tn4656 | 204 | 2082-2696 | + |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Resolvase | ||||||||||
| Sequence Family: | Serine Site-Specific Recombinase | ||||||||||
| Transposase Chemistry: | Serine | ||||||||||
| Protein Sequence: | MEPKTNVSPA AHPAHGGILQ GQRIGYVRVS SYDQNPERQL EQVEVGKLFT DKASGKDTQR PQLEAMLGFV REGDTVVVHS MDRLARNLDD LRRLVQKLTK RGVRIEFLKE GLVFTGEDSP MANLMLSVMG AFAEFERALI RERQREGIAL AKQRGAYRGR KKALSDEQAA TLRQRAAAGE PKAQLAREFN ISRETLYQYL RTDD |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpA | TnpA | Tn4656 | 988 | 2700-5666 | + |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Protein Sequence: | MPRRLILSAT ERDTLLALPE SQDDLIRYYT FNDSDLSLIR QRRGDANRLG FAVQLSLLRY PGYALGTDSE LPEPVIQWVA KQVQADPESW AKYGERDVTR REHTQELRTY LQLAPFGLSD FRALVRELTE LAQQTDKGLL LAGQALESLR QKRRILPALS VIDRACSEAI ARANRRVYRA LVEPLTDSHR AKLDELLKLK AGSSITWLTW LRQAPLKPNS RHMLEHIERL RTFQLVDLPE GLGRHIHQNR LLKLAREGGQ MTPKDLGKFE PQRRYATLAA VVLESTATVI DELVDLHDRI LVKLFSSAKH KHQQQFQKQG KAINDKVRLY SKIGQALLEA KETGSDPYAA IEAVIPWDEF TESVSEAELL ARPEGFDHLH LVGENFATLR RYTPALLEVL ELRAAPAAQG VLAAVQTLRE MNADNLRKVP ADAPTAFIKP RWKPLVITPE GLDRRFYEIC ALSELKNALR SGDIWVKGSR QFRDFDDYLL PAEKFAALKR EQALPLAINP SSDQYLEERL QLLDEQLATV TRLAKDNELP DAILTESGLK ITPLDSAVPN TAQALIDQTS QLLPRIKITE LLMDVDDWTG FSRHFTHLKD GAEAKDRTLL LSAILGDAIN LGLTKMAESS PGLTYAKLSW LQAWHIRDET YSAALAELVN HQYRHTFAAH WGDGTTSSSD GQRFRAGGRG ESTGHVNPKY GSEPGRLFYT HISDQYAPFS TRVVNVGVRD STYVLDGLLY HESDLRIEEH YTDTAGFTDH VFALMHLLGF RFAPRIRDLG ETKLYVPNSV QDYPTLRPMV GGTLNIKHVR AHWDDILRLA SSIKQGTVTA SLMLRKLGSY PRQNGLAVAL RELGRIERTL FILDWLQSVE LRRRVHAGLN KGEARNSLAR AVFFNRLGEI RDRSFEQQRY RASGLNLVTA AIVLWNTVYL ERSTQAMGEA GKQVNGELLQ YLSPLGWEHI NLTGDYVWRQ SRRLEDGKFR PLRLPGKP |
||||||||||
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, Garruto CE, Sota M, Ohtsubo Y, Nagata Y, Zylstra GJ, Williams PA, Tsuda M. Complete sequence determination combined with analysis of transposition/site-specific recombination events to explain genetic organization of IncP-7 TOL plasmid pWW53 and related mobile genetic elements.. J Mol Biol. 2007 May 25;369(1):11-26. doi: 10.1016/j.jmb.2007.02.098. Epub 2007 Mar 14. PubMed ID: 17408691 .
3. Tsuda M, Genka H. Identification and characterization of Tn4656, a novel class II transposon carrying a set of toluene-degrading genes from TOL plasmid pWW53.. J Bacteriol. 2001 Nov;183(21):6215-24. doi: 10.1128/JB.183.21.6215-6224.2001. PubMed ID: 11591664 .
4. Sentchilo VS, Perebituk AN, Zehnder AJ, van der Meer JR. Molecular diversity of plasmids bearing genes that encode toluene and xylene metabolism in Pseudomonas strains isolated from different contaminated sites in Belarus.. Appl Environ Microbiol. 2000 Jul;66(7):2842-52. doi: 10.1128/AEM.66.7.2842-2852.2000. PubMed ID: 10877777 .
5. Gallegos MT, Williams PA, Ramos JL. Transcriptional control of the multiple catabolic pathways encoded on the TOL plasmid pWW53 of Pseudomonas putida MT53.. J Bacteriol. 1997 Aug;179(16):5024-9. doi: 10.1128/jb.179.16.5024-5029.1997. PubMed ID: 9260942 .
6. 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 .
7. 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 .
8. Keil H, Keil S, Williams PA. Molecular analysis of regulatory and structural xyl genes of the TOL plasmid pWW53-4.. J Gen Microbiol. 1987 May;133(5):1149-58. doi: 10.1099/00221287-133-5-1149. PubMed ID: 3309179 .
9. Keil H, Saint CM, Williams PA. Gene organization of the first catabolic operon of TOL plasmid pWW53: production of indigo by the xylA gene product.. J Bacteriol. 1987 Feb;169(2):764-70. doi: 10.1128/jb.169.2.764-770.1987. PubMed ID: 3027047 .
10. Keil H, Keil S, Pickup RW, Williams PA. Evolutionary conservation of genes coding for meta pathway enzymes within TOL plasmids pWW0 and pWW53.. J Bacteriol. 1985 Nov;164(2):887-95. doi: 10.1128/jb.164.2.887-895.1985. PubMed ID: 2997136 .
2. Yano H, Garruto CE, Sota M, Ohtsubo Y, Nagata Y, Zylstra GJ, Williams PA, Tsuda M. Complete sequence determination combined with analysis of transposition/site-specific recombination events to explain genetic organization of IncP-7 TOL plasmid pWW53 and related mobile genetic elements.. J Mol Biol. 2007 May 25;369(1):11-26. doi: 10.1016/j.jmb.2007.02.098. Epub 2007 Mar 14. PubMed ID: 17408691 .
3. Tsuda M, Genka H. Identification and characterization of Tn4656, a novel class II transposon carrying a set of toluene-degrading genes from TOL plasmid pWW53.. J Bacteriol. 2001 Nov;183(21):6215-24. doi: 10.1128/JB.183.21.6215-6224.2001. PubMed ID: 11591664 .
4. Sentchilo VS, Perebituk AN, Zehnder AJ, van der Meer JR. Molecular diversity of plasmids bearing genes that encode toluene and xylene metabolism in Pseudomonas strains isolated from different contaminated sites in Belarus.. Appl Environ Microbiol. 2000 Jul;66(7):2842-52. doi: 10.1128/AEM.66.7.2842-2852.2000. PubMed ID: 10877777 .
5. Gallegos MT, Williams PA, Ramos JL. Transcriptional control of the multiple catabolic pathways encoded on the TOL plasmid pWW53 of Pseudomonas putida MT53.. J Bacteriol. 1997 Aug;179(16):5024-9. doi: 10.1128/jb.179.16.5024-5029.1997. PubMed ID: 9260942 .
6. 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 .
7. 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 .
8. Keil H, Keil S, Williams PA. Molecular analysis of regulatory and structural xyl genes of the TOL plasmid pWW53-4.. J Gen Microbiol. 1987 May;133(5):1149-58. doi: 10.1099/00221287-133-5-1149. PubMed ID: 3309179 .
9. Keil H, Saint CM, Williams PA. Gene organization of the first catabolic operon of TOL plasmid pWW53: production of indigo by the xylA gene product.. J Bacteriol. 1987 Feb;169(2):764-70. doi: 10.1128/jb.169.2.764-770.1987. PubMed ID: 3027047 .
10. Keil H, Keil S, Pickup RW, Williams PA. Evolutionary conservation of genes coding for meta pathway enzymes within TOL plasmids pWW0 and pWW53.. J Bacteriol. 1985 Nov;164(2):887-95. doi: 10.1128/jb.164.2.887-895.1985. PubMed ID: 2997136 .