ISPpu4

  • Family IS3
  • Group IS3
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
AJ233397 ND Pseudomonas putida
Pseudomonas putida P1
Pseudomonas migulae D2RT plasmid pD2RT
DNA section
IS Length : 1663 bp

Ends


IR Length : 23/33

IRL : CCCCCGGTGTCAGGCTAGTTGTCGCCTGAGCTGATTTATCAAAACGATAG
IRR : GGCGTTTTGCAAGGTAGTTGTCGCGTCAGCTGTGTTTTTATGCGGCTATT

Insertion site


Left flankDirect repeatRight flankDR Length
CACAGATTTCGCGTACGGCA0
ACCATCCGTAGACCCCCGGC0

DNA sequence

CCCCCGGTGTCAGGCTAGTTGTCGCCTGAGCTGATTTATCAAAACGATAGATCGGGGGCGCCAAAGAGAGCTGTAATGTCGAGCTATTCACCTGAGCGTA
AAGTGGCCCTTATCAACAAATTGCTGCCGCCTCAAAACATGTCCGTGGCCGAGTTGTCGCGTCAAGAAGGCATCTCTCAAGCCACCCTGTATGCTTGGCG
AACCAAGCTCAAAGCAGGAGGCGCAGTGGTGCCCGGAGATAAAAGCAGTGCCGATAACTGGTCGGCTGAAGCCAAGTTCGCAGCGGTGTTGCACACGGCC
ACGTTGAGCGAGATCGAGCTTAGCGAATACTGTCGCAGCAAGGGTTTGTACCCCGAGCAAATTGGCGCTTGGCGACAGGCCTGCATCAGTGGCCAGCTAA
CAGCCCAGGCACAGCGCCAGGCCGAGCGAGAACAGGCGCGCGCCGACAAAAAACGCATCGCCGAGTTGGAGCGTGAACTGCGGCGCAAGGACAAGGCGCT
CGCAGAAACCACCGCGATTCTGGTGCTGCGAAAAAGATGAATGCCTTCTGGGGAAACGACAGCGAGGACGTCTGACCTCGCTGCCAGAACGGCAACAACT
CGTTGAACGTTTTAACCAAGCCGTTGCTTCTGGTGCACGCAAAACTATTGCCAGCGCGGAGATCGGGCTGTCGCTGCGCAGCCTGCAACGCTGGGCGCTG
ACGCCTGTGATGCAGGCCGACGTGCGCACCACCACGTCACGTCCGCGACCACTTAATGCCCTGAGTGAACAGGAGCGTTGCGCTATTTTAGAGGTCTGCA
ACAGTCCGCCATTCGTCAGCCTGCCGCCCAGCCAGATCGTCCCGATACTGGCCGATCAAGGCCGTTATCTGGCCTCAGAGGCAACCTTTTACCGCGTCCT
GAAGGAAGCTGATCAGCAGCACCGACGTGGCCGCAGCCATGCACCGCACAAGCATGCTGCGCCGACAACTCACAGCGCAACCACAGCCAATAAGGTCTGG
TCTTGGGACATCACCTACTTGCCATCGCCAGTGCGTGGGAAGTACTACTATCTGTATTTGATCGAGGACATCTACAGCCGAAAGGCCGTGGGCTGGGAAG
TTTACGAGCAAGAAAGTGGCGAGCTGGCGGCCGAACTGATGCAGCGCACCGTGCTCACCGAACGCTGCGCCGGACGGCCCTTAGTGCTGCACTCGGACAA
CGGTGCACCGATGAAATCGGTGACGTTGCTGAGCAAACTGTACGAACTCGGCATCACCCCGTCACGCGGACGACCACGGGTGAGTAACGATAATCCCTAC
TCAGAATCGCTGTTTAGAACCCTGAAATATTGCCCGCAATGGCCTCCTGGTGGTTTTGCAGATTTGGACGCGGCACGCAGCTGGGTGCGCGATTTTATCC
GCTGGTACAACCACCACACCGCCACAGCCGCATCCGCTTCGTGACCCCGGCACAGCGTCATCGAGGCGAGGATCAAGAGATCTTAGCCAAGCGTCATGCG
CTGTATCAGCAAGCCCGCAATCAGCATCCACACCGCTGGTCGGGTGCGACACGCAATTGGCAGCCCATCGGTGCTGTCACACTCAATCCGGAAAGGGACT
TACCGACACTGAAAATAGCCGCATAAAAACACAGCTGACGCGACAACTACCTTGCAAAACGCC
Recoding section
  • Recoding by frameshift
  • Frame
  • Type
  • Experimentally demonstrated

Stimulators :

  • Shine-Dalgarno sequence :
  • Secondary structure :

Recoding motif :

Protein section
ORF number : 3

 

ORF 1
LengthBeginEndStrandFusion ORF
465 bp154 aa76540+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MSSYSPERKVALINKLLPPQNMSVAELSRQEGISQATLYAWRTKLKAGGAVVPGDKSSADNWSAEAKFAAVLHTATLSEIELSEYCRSKGLYPEQIGAWR
QACISGQLTAQAQRQAEREQARADKKRIAELERELRRKDKALAETTAILVLRKR

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
1223 bp414 aa4011623+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

QPRHSARPSENRRAPTKNASPSWSVNCGARTRRSQKPPRFWCCEKDECLLGKRQRGRLTSLPERQQLVERFNQAVASGARKTIASAEIGLSLRSLQRWAL
TPVMQADVRTTTSRPRPLNALSEQERCAILEVCNSPPFVSLPPSQIVPILADQGRYLASEATFYRVLKEADQQHRRGRSHAPHDAKHAAPTTHSATTANK
VWSWDITYLPSPVRGKYYYLYLIEDIYSRKAVGWEVYEQESGELAAELMQRTVLTERCAGRPLVLDAHSDNGAPMKSVTLLSKLYELGITPSRGRPRVSN
DNPYSESLFRTLKYCPQWPPGGFADLDAARSWVRDFIRWYNHHHRHSDARIRFVTPAQRHRGEDQEILAKRHALYQQARNQHPHRWSGATRNWQPIGAVT
LNPERDLPTLKIAA

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1548 bp523 aa761623+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MSSYSPERKVALINKLLPPQNMSVAELSRQEGISQATLYAWRTKLKAGGAVVPGDKSSADNWSAEAKFAAVLHTATLSEIELSEYCRSKGLYPEQIGAWR
QACISGQLTAQAQRQAEREQARADKKNASPSWSVNCGARTRRSQKPPRFWCCEKDECLLGKRQRGRLTSLPERQQLVERFNQAVASGARKTIASAEIGLS
LRSLQRWALTPVMQADVRTTTSRPRPLNALSEQERCAILEVCNSPPFVSLPPSQIVPILADQGRYLASEATFYRVLKEADQQHRRGRSHAPHDAKHAAPT
THSATTANKVWSWDITYLPSPVRGKYYYLYLIEDIYSRKAVGWEVYEQESGELAAELMQRTVLTERCAGRPLVLDAHSDNGAPMKSVTLLSKLYELGITP
SRGRPRVSNDNPYSESLFRTLKYCPQWPPGGFADLDAARSWVRDFIRWYNHHHRHSDARIRFVTPAQRHRGEDQEILAKRHALYQQARNQHPHRWSGATR
NWQPIGAVTLNPERDLPTLKIAA

 

Blast result :
Comments
Two copies of ISPpu4 flank the alk gene clusters of Pseudomonas putida P1. The ends of the insertion sequence could not be identified unambiguously, as the homology between ISPpu4 and IS1240 extends several bases beyond the inverted repeats, and direct repeats could not be identified. Southern blots indicate that other copies are present as well. ORF2 has a frameshift in a series of histidine codons. The sequence at the likely location of the frameshift is repetitive (CAACCACCACACC), and a shift to the -1 phase in this sequence would allow the synthesis of the full length protein.
ISPpu4 (ORF B) is 81% aa similar to IS1240 and 54% to IS1141.
File updated: September 19 2013. Extremities were modified, the proposed ends for this sequence are based on the similarities with closely relative elements.
References
1] van Beilen, J. B., Röthlisberger, M. and Witholt, B. Direct submission.
2] van Beilen,J.B., Panke,S., Lucchini,S., Franchini,A.G., Rothlisberger,M. and Witholt,B. (2001) Microbiology 147 (Pt 6), 1621-1630