ISAs9

  • Family IS3
  • Group IS3
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
CP000644 ND Aeromonas salmonicida
Aeromonas salmonicida subsp. salmonicida A449
Aeromonas salmonicida subsp. salmonicida A449 plasmid 4
DNA section
IS Length : 1626 bp

Ends


IR Length : 16/24

IRL : CCCCCAGTGGCAGGGTAGTTGTCGCCTGATTTTTTCACTGGGGGCTGGAG
IRR : CGGCGTTTTTCAAGGTAGTTGTCGTTTTTTATGCTGCCCGGCGTTCATTT

Insertion site


Left flankDirect repeatRight flankDR Length
TGAACGCTCATTCCGGCTCAACCT4
AGGTTGAGCCGGAATGAGCGTTCA4
AGGTTGAACCGGAATGAGCGTTCA4
TGAGCCGGAATTCACGTTGA0

DNA sequence

CCCCCAGTGGCAGGGTAGTTGTCGCCTGATTTTTTCACTGGGGGCTGGAGCTGTAAAATGGCTAATCACAGGATTGCGCCTGAGCTTAGGGAGAGAGCCA
TCATGCATATGATGCCACCCTATAACTGGAGCCTCAGACAGGTTGCTGATGATATTGGTGTTGGCATTGCAACTGTTCATGGCTGGCGAAAACAACTGGA
ACTAGAGGGGCTGATCATCCGAAAAATCGAACCCGACTCGGAGCATTCTACAGAGCAAATTTTTACGATCCTGCTTGAAACGGCCGCATTGTCTGAACAT
GAGTTGGCTGAGTATTGTCGGAAACATGGTCTGTACCCTGAGCATCTTGTGGCATGGAAGCAAAATTGCCTGGCGGCCAATCAGCCTAAGCATCGCCAAT
TGGTTGATGAACAGCGAGCTGTTCGTTCAGAGAAAGCCCGCATCCGAGCGCTTGAAAAAGAGCTACGTCGAAAAGACAAGGCTCTAGCCGAATTGGCTGC
ACTGCTGGTGCTTCAGGAAAAGTTATCAGCCCTCCGGGACAACGAAGAGGACGACTGACCTCTTACCCGGAGAGGCAACGGATAATTGCACTGATAGAGG
AAGCTGTAGACCACGGGGCTCGCTATGCGCAGGCCTGCCGAGTTGCGGGTATCACACACAGGACTTTTCAGCGATGGTTCTGTGACGGCAGGCTAAAACC
AGATGGAAGACCATTAGCCAGACGGCCAGTGCCAGCCAATAAGCTGACAGAACATGAGCGAACACGGGTACTACAGGTATGCTCTGAGGCTGAGTACGCG
TCTTTACCTCCGTCGAGGATCGTCCCCATGCTTGCTGACAGGGGCATATACCTTGCGTCGGAAGCAACATTCTATCGGCTCCTGAAGGCAGAAGATCAAT
TGCACCACAGAGCCGGTGGGAAACCCCGTGGTACTTATAGCCGTCCGACCAGCTATACAGCACATGGTCCGAACCAAGTCTGGTCTTGGGACATAACCCA
TTTGCCAGGAGAGGTTAAAGGGGAGCGGTATTATCTATACATGCTCATGGATGTATATAGCCGTAAAATTGTGGCAGCGGAAGTGAGGGAGGTTGAGCGC
GGTGAATATGCCGCAGCCTTGTTACAGCGGGCCGTCATCATGGAAAACTGCCGGAATAGCGGATTAATTTTACACTCAGATAACGGGGCTCCGATGAAGA
GCTTCACAATGCTGGCCAAAATGTATGAACTGGGTGTCTGCTCGTCATTCAGTAGACCCCGGGTCAGCAATGATAACCCCTACTCGGAGTCGCTGTTCCG
AACACTGAAATATTGCCCTGCATGGCCTGCCGATGGCTTTAGCGATATAAGCAAAGCACGGGCATGGGTACACAGCTTCATACGCTGGTACAACACCCAA
CATCGTCATAGCGGGATTAAGTTTGTCACACCAGAACAAAGGCACCAGGGTTTGGATAAGCCCCTGCTTAAACAACGGGAAGCAGTCTATGAAGCCGCAC
GATGCCAGCATCCTGAACGCTGGTCTGGTAAAACAAGGAACTGGACACCAGTAAGTATGGTGGCGCTCAATCCGGAAAATGAACGCCGGGCAGCATAAAA
AACGACAACTACCTTGAAAAACGCCG
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
450 bp149 aa109558+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MMPPYNWSLRQVADDIGVGIATVHGWRKQLELEGLIIRKIEPDSEHSTEQIFTILLETAALSEHELAEYCRKHGLYPEHLVAWKQNCLAANQPKHRQLVD
EQRAVRSEKARIRALEKELRRKDKALAELAALLVLQEKLSALRDNEEDD

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
1143 bp380 aa4561598+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

KRATSKRQGSSRIGCTAGASGKVISPPGQRRGRLTSYPERQRIIALIEEAVDHGARYAQACRVAGITHRTFQRWFCDGRLKPDGRPLARRPVPANKLTEH
ERTRVLQVCSEAEYASLPPSRIVPMLADRGIYLASEATFYRLLKAEDQLHHRAGGKPRGTYSRPTSYTAHGPNQVWSWDITHLPGEVKGERYYLYMLMDV
YSRKIVAAEVREVERGEYAAALLQRAVIMENCRNSGLILHSDNGAPMKSFTMLAKMYELGVCSSFSRPRVSNDNPYSESLFRTLKYCPAWPADGFSDISK
ARAWVHSFIRWYNTQHRHSGIKFVTPEQRHQGLDKPLLKQREAVYEAARCQHPERWSGKTRNWTPVSMVALNPENERRAA

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1490 bp496 aa1091598+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MMPPYNWSLRQVADDIGVGIATVHGWRKQLELEGLIIRKIEPDSEHSTEQIFTILLETAALSEHELAEYCRKHGLYPEHLVAWKQNCLAANQPKHRQLVD
EQRAVRSEKARIRALEKELRRKDKALAELAALLVLQEKVISPPGQRRGRLTSYPERQRIIALIEEAVDHGARYAQACRVAGITHRTFQRWFCDGRLKPDG
RPLARRPVPANKLTEHERTRVLQVCSEAEYASLPPSRIVPMLADRGIYLASEATFYRLLKAEDQLHHRAGGKPRGTYSRPTSYTAHGPNQVWSWDITHLP
GEVKGERYYLYMLMDVYSRKIVAAEVREVERGEYAAALLQRAVIMENCRNSGLILHSDNGAPMKSFTMLAKMYELGVCSSFSRPRVSNDNPYSESLFRTL
KYCPAWPADGFSDISKARAWVHSFIRWYNTQHRHSGIKFVTPEQRHQGLDKPLLKQREAVYEAARCQHPERWSGKTRNWTPVSMVALNPENERRAA

 

Blast result :
Comments
ISAs9 is 70% (orfAB) aa similar to IS1240.
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible -1 frameshift.
The ends as defined are not typical of the IS3 family, the proposed ends are based on the similarities with closely relative elements.
References
1] Reith,M.E., Singh,R.K., Curtis,B., Boyd,J., Bouevitch,A., Kimball,J., Munholland,J., Murphy,C., Sarty,D., Williams,J., Nash,J., Johnson,S. and Brown,L. (2007) Direct submission to GenBank