IS5564

  • Family IS481
  • Group
MGE type ISRelated element(s) :
Isoform Synonym(s) Tn5564
Accession numberTranspositionOriginHost
AF024666 Y Corynebacterium striatum
Corynebacterium striatum M82B plasmid pTP10
DNA section
IS Length : 2437 bp

Ends


IR Length : 22

IRL : TGTGATGTCCAGGGACGTTGTTCTGGCCCCGCCCGTAATGACACCGTGCC
IRR : TGTGATGTCCAGGGACGTTGTTGAGTCGGTCGAAGGGTACGCCGCCAATC

Insertion site


Left flankDirect repeatRight flankDR Length
NNAGATCTGTCCTAGGGGAAACGCTA6

DNA sequence

TGTGATGTCCAGGGACGTTGTTCTGGCCCCGCCCGTAATGACACCGTGCCGATTCAAGAAGTATCTGTCCAGACCGCTTGCCATTGAAGGCATGTTAGAG
TTTGGGGCATGTCGAGTCCCGAATCAGACAGGTCAGGGGTTGTCGGTCACACCGCCAGCCCCTTGAACCACTAGTTACGACGCCCACGATCTGTGTGGGC
GTATGTCTGGCGTACCCGGGGCGCTGGCCGTGGTGACAAGAAGAACCATTTCTTGATCTCACACCTCGGAGTACTCGATGCCTTTTGCCCTCTACATGCT
TGCCCTGGCGGTCTTCGTCATGGGCACTTCAGAATTCATGCTCGCGGGATTGCTCCCCGCGATCGCGACCGAACTTGACGTCTCGGTCGGCACTGCGGGC
CTGCTGACCTCCGCATTCGCAGTCGGTATGGTCGTCGGCGCGCCAGTGATGGCGGCATTCGCTCGCCGTTGGCCACCGCGGCTCACATTGATCGTTTGCC
TTCTCGTGTTCGCGGGAAGCCACGTCATCGGAGCGATGACACCAGTGTTCTCTCTCCTGCTCATCACCCGGGTGCTCAGCGCTCTCGCAAACGCAGGATT
CCTCGCCGTAGCACTGAGCACGGCCACTACCCTCGTGCCAGCGAACCAGAAGGGGCGTGCACTGTCGATCCTGCTCTCCGGCACGACGATCGCAACCGTC
GTGGGCGTCCCCGCCGGGGCACTGCTCGGCACAGCGCTGGGCTGGCGAACGACGTTCTGGGCGATCGCCATCCTCTGTATTCCCGCGGCCGTTGGAGTCA
TTCGTGGCGTCACGAACAATGTTGGTCGGAGCGAGACTAGCGCGACCTCACCAAGGCTCCGTGTCGAGCTCAGCCAGTTGGCGACGCCGCGGCTCATCCT
GGCCATGGCACTCGGAGCGCTGATCAACGGAGGGACCTTTGCGGCATTCACCTTCCTGGCACCCATCGTGACCGAGACCGCGGGCTTGGCCGAAGCGTGG
GTGTCCGTCGCGCTGGTGATGTTCGGCATCGGATCGTTCCTTGGCGTCACGATCGCAGGACGACTATCAGATCAACGACCTGGCCTCGTGCTCGCAGTCG
GCGGACCGCTATTGCTGACAGGCTGGATCGTGTTGGCAGTGGTCGCATCTCATCCCGTTGCGCTTATCGTCCTCGTCCTCGTTCAGGGATTCCTGTCGTT
CGGCGTCGGCAGTACTCTGATCACGCGTGTGCTGTATGCAGCATCGGGTGCGCCAACGATGGGCGGTTCGTACGCAACCGCAGCATTGAATATCGGAGCT
GCAGCGGGGCCCGTGCTTGGTGCGCTCGGGCTCGCGACCGGGCTGGGGCTGCTCGCGCCGGTTTGGGTCGCTTCGGTGCTGACAGCGATCGCTCTCGTCA
TCATGCTTCTCACCAGACGCGCGCTTACGAAGACCGCGGCGGAGGCCAATTGATGACCCATCCGAACGCTCTTCTCACTCCTCGTGCCCGTCTCCGGTTA
GCTCGGCTGATTGTCGAAGACGGCTATCCGGCCACGATCGCCGCAAAGATGTTCATGGTCTCCCCGATCACTGCCCGGAAATGGGCAGGCCGCTACCGGG
AAGAGGGTGAGTTTGGGATGCAGGATCGCTCCAGCAAGCCGCACCGGATCCCAGGCAGGACGCCCGAGCATGTCAAGAAGAAGATCATCAACCTGCGCTG
GCGGCTTCGACTGGGGCCAGCCCAGATCGCTGCGCGACTTGGTCTCTCGACGTCGACTGTTCACGCGGTCCTCGTCCGTTGCCGCGTGAACCGCCTCTCG
CATATCGATCGTGTCACTGGCGAGCCATTGCGGCGATATGAGCATCCTCATCCGGGATCGTTGATTCATGTCGATGTCACGAAGTTCGGCAACATCCCCG
ACGGCGGTGGACATCGTTACGTAGGTCGGCAGCAAGGCGCACGGAACAAGCTCGCGACTCCGGGATTACCACGAGGAAAAGATCACAAGCCGCGCACCGG
GACGGCGTTCGTTCACACAGTCATCGACGACCACTCCCGCGTCGCATACGCAGAAATCTGGTCGGATGAGCAGGCGAGCACAGCGGTGGGAGTTCTCGAA
CGCGCCGTGGCCTGGTTCGCCGAACGAGGCGTGACCGTCGAGCGAGTCCTATCCGACAACGGGTCGGCATACAGATCCCACGCATGGAGGGACTTCTGCG
CTCGGCTCGGCATCCGACACAAGCGGACACGCCCCTACCGGCCGCAGACGAACGGGAAGATCGAGCGATTCCACCGCACGCTCGGGGACGGCTGGGCCTA
TGCCAGGTTTTACGGTTCAGAGGCCGAACGACGCCTGGCGCTGCCCGGCTGGCTCCACTTCTACAACCACCACCGACACCACTCTGCGATTGGCGGCGTA
CCCTTCGACCGACTCAACAACGTCCCTGGACATCACA
Protein section
ORF number : 2

 

ORF 1
LengthBeginEndStrandFusion ORF
1176 bp391 aa2881463+No
ORF function : Passenger Gene
Annotation : Chloramphenicol resistance geneDescription : Antibiotic resistance

ORF sequence :

MPFALYMLALAVFVMGTSEFMLAGLLPAIATELDVSVGTAGLLTSAFAVGMVVGAPVMAAFARRWPPRLTLIVCLLVFAGSHVIGAMTPVFSLLLITRVL
SALANAGFLAVALSTATTLVPANQKGRALSILLSGTTIATVVGVPAGALLGTALGWRTTFWAIAILCIPAAVGVIRGVTNNVGRSETSATSPRLRVELSQ
LATPRLILAMALGALINGGTFAAFTFLAPIVTETAGLAEAWVSVALVMFGIGSFLGVTIAGRLSDQRPGLVLAVGGPLLLTGWIVLAVVASHPVALIVLV
LVQGFLSFGVGSTLITRVLYAASGAPTMGGSYATAALNIGAAAGPVLGALGLATGLGLLAPVWVASVLTAIALVIMLLTRRALTKTAAEAN

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
990 bp329 aa14632452+No
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MTHPNALLTPRARLRLARLIVEDGYPATIAAKMFMVSPITARKWAGRYREEGEFGMQDRSSKPHRIPGRTPEHVKKKIINLRWRLRLGPAQIAARLGLST
STVHAVLVRCRVNRLSHIDRVTGEPLRRYEHPHPGSLIHVDVTKFGNIPDGGGHRYVGRQQGARNKLATPGLPRGKDHKPRTGTAFVHTVIDDHSRVAYA
EIWSDEQASTAVGVLERAVAWFAERGVTVERVLSDNGSAYRSHAWRDFCARLGIRHKRTRPYRPQTNGKIERFHRTLGDGWAYARFYGSEAERRLALPGW
LHFYNHHRHHSAIGGVPFDRLNNVPGHH

 

Blast result :
Comments
Corynebacterium striatum M82B was formerly named Corynebacterium xerosis M82B. IS5564 is a transposon. The ORF1 of IS5564 encodes the chloramphenicol resistance gene "cmx", specifying a transmembrane efflux protein, originally deposited as sequence with GenBank Accession Number A08113. ORF2 is a transposase which is 91% similar to U85507, 64% to IS1652 and ISAni1, 63% to IS1649, 62% to ISSco1, 56% to IS1122 and 55% to IS1121.
The IS5564 sequence was constructed by deletion in silico of IS1513 insertion sequence and one of the IS-DR (coordinates of insertion : DR : 84-86 ; IR : 87-113 ; Transposase : 574-1794 ; IR : 1775-1801 ; DR : 1802-1804).
The insertion sequence IS1513 encoding a putative transposase of the IS30 family is an integral part of Tn5564 and is located upstream of "cmx".

There is no stop codon at the end of the element, the transposase use the first Stop codon after the end of the IRR.
The transposase in the database is cut at the end of the IS.
References
1] Tauch,A., Zheng,Z., Puhler,A. and Kalinowski,J. (1998) Plasmid 40 (2), 126-139
2] Tauch,A., Kalinowski,J. and Puehler,A.(1998)Direct Submission GenBank.