ISJp4

  • Family IS5
  • Group IS427
MGE type ISRelated element(s) :
Isoform Synonym(s) ISJP4
Accession numberTranspositionOriginHost
U16782 Y Ralstonia eutropha
Ralstonia eutropha JMP134 plasmid pJP4
DNA section
IS Length : 915 bp

Ends


IR Length : 18/19

IRL : GAGACCGTTTCAAAAAGAGCCCCGGGGGGCTGTTAACCTTTTCGGCAAGC
IRR : GAGACTGTTTCAAAAAGACGGCTCAGCGCGCCTGAAGATGTTCCAGCAGA

Insertion site


Left flankDirect repeatRight flankDR Length
TCGCAATTTCTAAGGAAGGATAG3

DNA sequence

GAGACCGTTTCAAAAAGAGCCCCGGGGGGCTGTTAACCTTTTCGGCAAGCTGTTAACCTTGGCCATCTGAACAACTGGAACCGAGGGGATGAGCGCGCCG
ATCATTGATGATGAACTGTGGGCACTGATCGAACCTTTGCTGCCGCCGCCGAAACCGCGACGCAAGAAATATCCAGGGCGGCTCCCGGTTTCGAACCGGG
CTGCACTGAACGGCATCCTGTTCGTGTTCAAGACTGGCATACGCTGGTGCGACCTGTCGACCAAGTTGGGATTCGGGTCGGGGCCGACCTGCTGGAGGCG
CTTGCGCGATTGGCAGAAGGCCGGCGTTTGGAAGCGATTGCACGAGCTACTGCTGGCGAAGTTACGCGAGGCCGGCGAACTCGACTTCTCCCGAGCAGCC
GTCGATTCATCGTCTGTGCGAGCCGTTGGGGCGGGCGAAAAACTGGTCCGAACCCCACGGATCGCTCGCGACCAGGTTCCAAGCATCACATCCTCGTCGA
CGCAAATGGCGTCCCCATCAGCGCAATCCTGACCGGGGCGAACCGCAACGACGTCACCCAACTGCTGCCGCTCGTCGACGCGATCCCGCCAATTCGCGGC
GTGCGCGGTCGCCCGCTTCAAAAGCCCAAAGTCATCTACGCAGACCGTGGCTACGACTCCGAGCCGCATCGTCAGCGGCTTCGCGAGCGCGGCATCAAAC
CGGTGCTCGCCAAGCGCCGGACAGAACACGGCAGTGGCTTGGGCAAATTCCGCTGGGTTGTCGAACGTACTCACGCGTGGCTTCACAACTTTCGTCGTCT
TCGCATTCGCTTCGAACGTCGAGCCGACATTCACGAAGCGTTCCTAAAACTCGGCTGCTCTCTCGTCTGCTGGAACATCTTCAGGCGCGCTGAGCCGTCT
TTTTGAAACAGTCTC
Recoding section
  • Recoding by frameshift
  • Frame
  • Type
  • Experimentally demonstrated

Stimulators :

  • Shine-Dalgarno sequence :
  • Secondary structure :

Recoding motif :

Protein section
ORF number : 1

 

ORF 1
LengthBeginEndStrandFusion ORF
818 bp273 aa89906+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MSAPIIDDELWALIEPLLPPPKPRRKKYPGRLPVSNRAALNGILFVFKTGIRWCDLSTKLGFGSGPTCWRRLRDWQKAGVWKRLHELLLAKLREAGELDF
SRAAVDSSSVRAVGAGEKKTGPNPTDRSRPGSKHHILVDANGVPISAILTGANRNDVTQLLPLVDAIPPIRGVRGRPLQKPKVIYADRGYDSEPHRQRLR
ERGIKPVLAKRRTEHGSGLGKFRWVVERTHAWLHNFRRLRIRFERRADIHEAFLKLGCSLVCWNIFRRAEPSF

 

Blast result :
Comments
Note that Ralstonia eutropha was formerly named Alcaligenes eutrophus. ISJp4 is located within (hence inactivating) the tfdT (lysR-type transcriptional regulator) gene, downstream of tfdK (a putative transport protein gene), tfdBII (chlorophenol monooxygenase), tfdFII (maleylacetate reductase) and other genes involved in the chlorocatechol degradation pathway. Based on comparison with other elements from the IS5 family, the limits of ISJp4 have been redefined, removing the first and last bp. Although ISJp4 displays two ORFs, a fused ORF is considered here (89-442) and (439-906). However, at position 437, the sequence 5'-CAAAAACTGGTCC-3' is reminiscent of what is found in other related elements, such as IS402 (The same observation has also been made by Leveau and van der Meer, 1997). The involvement of a putative -1 translational frameshift around position 437 remains to be confirmed. ISJp4 and IS402 transposases are 81 % identical. ISJp4 is present as a single copy on the pJP4 plasmid and as a single copy in the Ralstonia eutropha JMP134 chromosome.
References
1] Leveau, J., and van der Meer J.R. (1996) J. Bacteriol. 178, 6824-6832.
2] Leveau, J., and van der Meer J.R. (1997) Gene.