ISfinder

ISMsm12

Family IS1380
Group

MGE type ISRelated element(s) :
Isoform IS220Synonym(s)

Accession number	Transposition	Origin	Host
NC_008596	ND	Mycobacterium smegmatis	Mycobacterium smegmatis MC2 155

DNA section

IS Length : 3256 bp

Ends

IR Length : 17/19

IRL : CCTCGATCCACCGACTGTTGTGGATCGAGTGCGGTTCCCGCTGAAGAAAT
IRR : CCTCGATCCACCGACGGGTTCTGTGTCTGCGGCTGTGGCGGCTGTGGCTA

Insertion site

Left flank	Direct repeat	Right flank	DR Length
CCGTTTCCTG	TTTAG	AGCGGCTGGC	5

DNA sequence

CCTCGATCCACCGACTGTTGTGGATCGAGTGCGGTTCCCGCTGAAGAAATGCTGGCCCTGATCTGGGCTGATTCGTACTTGGGCTGGTTGTGCCGGTCGC
TGCGGTTCGGCACTGCGAGTGCCCGTGGGTTGTACGGCCCCGGTGCAATCCGCGCTTAGCGACTCGTGGGCAGCGAATCCACGTGAAGTCGCAAGATCTT
GGCGATGGTGGTCGGCTTTCGGGGGCCGTGCGCTGTCACAGCGTCGAGGGCGAGGCCGGACAGAAGTGACGCTAGGCGTTGGGCTTCCAGGCTGGGCTGT
GGCACCGACATGCCCTTCAGGGCTGTGACCAGCACGTCATCCAGGTCGGTGGCCATTTGCGCTGTCGCTGCCCGGAATGCTTCAGTAGTTCGGGAGGCAG
CGATGACTTCCATGAGGATCACTGCCTCGCTATGCCGTTCGGCGTCAAGGGGAACGAGTTCTTCAAGTAGTGCGATCAGATGTTGTCGTTGTCGCGAGAG
GTCGCGCGATTGCGGTGGTGTGTGTTTCATCAGCCGCTGGCCCATGCGGTTTCCGGCCTCGGTAACTACTGCGACGACGAGGGATTCGTGATCTGCGAAG
TAGTGCCGGACTGACCCGATGTTCAACTGCGATTCCGCCGCAACACGGCGGAACGTCGCGGCGGACAGCCCCTCCTTCAGCACCAGACGTAGCGCGGCCT
CGACGATGTGACTTCGGCGTTCCACGGGGTCGATACGTGCTGGCATCGTCAAAGTCTAACGACAGCAGACGGCGGCCTATCACGGGTGTGATAAAAAGAA
TGCACGGTTGGCGGGCAGTCGCCGAGCAGACGGAGAGTACCTCGATGAATCATGTTGATGCGCTGGCCTGTAACCGAGAGAACTGGGACGAACGCGCAGA
TATCCATGCCCGGTCGCAGATGTATGACGTGGAGGGTTTCCTGGCGGACCGGTCCTTGATTTCGTCGGTGGTCCGAAATGACCTGACCGTGCTGCAACCG
CACCTGCCCTCCTCGAAGATCAGCGGTCAATCCCTGCTGCATCTGCAATGTCACATCGGGACCGATACCGTGTCATGGGCGCGGCTGGGCGCCGTCAACG
TCACCGGCTTGGATCTGTCGCCGAACTCACTACGTCACGCTCGACGCATCGCCGAGCAAGACGGCCAGGTGATCACATGGGTACAGGGCGATGCCCGGGT
CGCTTCCTCACTGATCGACGAGCAGTTCGATGTTGTTGTCACCAGCGCAGGAACCATCGTGTGGCTGCCAGAGCTGTCGGCGTGGGCGCGCTCCATCCAT
GACCTGCTGACACCCGGCGGTGTTTTCATGATTCGCGACGACCATCCGATATTGGCGGCGATGGAGTTCCAGCCGTGGACGATCAGCGATGACTACCTCT
CTGGTGGCGGTACCCGGACCTATGACGACGCCAGCACCTACACCGAGAACACCGACGTGGTGATCCGTCAGACAACGAATTACGAGTGGCGCCACGATCT
CAGTGAAGTCCTCACCGCGCTCTTGGAAGCAGACCTGCGTATCGAGGCCGTCCACGAGCTTGCTTACATGGATTGGCCAGCATTCCCGGCGTTGATTCCC
GATCCACGCGGCTGGACATTGCCCGCAGATGCGCCACGCATTCCGTTGAACTTCGCGATCGTCGCCCGCAGAGCCAGCTAAGTTCAACACGGGCACAGCG
ACTTCGAGCGCCGCGGATGGAACTATCGCACAGGTTTGCCGCGTCGTCGGCGGTCTTCGACGATGATCATCTCGTGTCAATCGCCGGTTTGGTGCCCGTG
ATGACGCTGGCCACCCAGACCGGTTTGTCGGCGCTATTGGCCGACAAGGTTCGGATCAGCGAACCGAGGATCAAGTCCGGTTCGGCCAACCCGTCACCGA
AGTTGACTACGCTGATCGCCGGGATGTGCGCCGGTGCCGACAGCATCGACGACCTCGACATCGTGCGCTCGGGCGGGATGAAGACCCTCTTCGACGACGT
GTACGCACCCTCAACCATCGGCACACTGTTGCGTGAGTTCACTTTCGGGCACGCCCGACAACTCGAAGCAGTACTTCGGGCTCACCTGGCCGAACTATGC
CAGCGAGCCGACCTGCTGCCAGGCATCGACGGGCGGACGTTCGTCGACATCGACTCATTGCTTCGCCCGGTCTACGGCCACGCCAAACAGGGCGCCTCCT
ACGGGCATACCAAGATCGCGGGAAAACAAATCCTGCGTAAAGGCCTGTCGCCGTTGATCACCACCATCAGCTCTAGTACGAGCGCTCCGGTGATCGCCGG
CGCACGGCTACGAGCAGGCAAGACCAACTCCGGCAAGGGCGCGGCCCGGATGATTGCCCAAGCGGTCGCGACCGCGCGCGCCGCCGGAGTCACCGGGCCG
ATCTTGGTGCGCGGCGACTCTGCCTACGGCAACAGCACCGTGGCCGCGGCCTGTCGTCGGGCCGGCGCCCAGTTCTCGCTGGTGCTGACCAAGACGCCCG
CCGTCACTGCGGCCATTGATGCCATCAGTGACGGTGCCTGGATCCCGGTGAACTACCCCGGCGCAGTGCGCGACCCCGACACCGGCGCCTGGATCTCCGA
CGCCGAGGTCGCCGAAACCACCTACACCGCTTTCAGTTCCACCAAGACCCCCATCACTGCACGCTTGATCGTGCGCCGGGTCAAAGACGCCAGATTCCTC
GACGCACTGTTCCCGGTGTGGCGCTATCACCCCTTCTTCACCGACTCCGACGAGCCTGTCGACGCCGCCGACATCACCCATCGCCGCCACGCCATCATCG
AAACCGTCTTCGCCGACCTCATCGACGGACCCCTAGCCCACATGCCCTCAGGACGTTTCGGCGCGAACTCGGCCTGGATCCTCTGCGCGGCGATCGCCCA
CAACCTACTGCGCGCCGCAGGCGTCCTGGCCGGCACCGCCAACGCGGTCGCACGGGGATCCACATTGCGGCGACGCATCGTTACAGTTCCGGCCCGGCTC
GCCCGACCCCAGCGCCGACCCGTCCTGCATCTACCCACGCACTGGCCGTGGACAGATCAATGGCTCATGCTGTGGCGTAACACCATCGGATACAGCCCAC
CCGCGACCCCCTGCCACTGACTATCCCGCCGAAAGGCCCCGACCGGAGCACATAGGAAAAGCTGGACAGACCAGCCAGTACTGCCTGCCCGCGACCAGAT
ACCGCCTAGCCACAGCCGCCACAGCCGCAGACACAGAACCCGTCGGTGGATCGAGG

Protein section

ORF number : 3

ORF 1

Length		Begin	End	Strand	Fusion ORF
591 bp	156 aa	746	156	-	No

ORF function : Passenger Gene
Annotation : Transcriptional regulator, TetR familyDescription : Transcriptional Regulator factor

ORF sequence :

MPARIDPVERRSHIVEAALRLVLKEGLSAATFRRVAAESQLNIGSVRHYFADHESLVVAVVTEAGNRMGQRLMKHTPPQSRDLSRQRQHLIALLEELVPL
DAERHSEAVILMEVIAASRTTEAFRAATAQMATDLDDVLVTALKGMSVPQPSLEAQRLASLLSGLALDAVTAHGPRKPTTIAKILRLHVDSLPTSR

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
837 bp	278 aa	845	1681	+	No

ORF function : Passenger Gene
Annotation : Methyltransferase type12Description :

ORF sequence :

MNHVDALACNRENWDERADIHARSQMYDVEGFLADRSLISSVVRNDLTVLQPHLPSSKISGQSLLHLQCHIGTDTVSWARLGAVNVTGLDLSPNSLRHAR
RIAEQDGQVITWVQGDARVASSLIDEQFDVVVTSAGTIVWLPELSAWARSIHDLLTPGGVFMIRDDHPILAAMEFQPWTISDDYLSGGGTRTYDDASTYT
ENTDVVIRQTTNYEWRHDLSEVLTALLEADLRIEAVHELAYMDWPAFPALIPDPRGWTLPADAPRIPLNFAIVARRAS

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
1404 bp	467 aa	1717	3120	+	No

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MELSHRFAASSAVFDDDHLVSIAGLVPVMTLATQTGLSALLADKVRISEPRIKSGSANPSPKLTTLIAGMCAGADSIDDLDIVRSGGMKTLFDDVYAPST
IGTLLREFTFGHARQLEAVLRAHLAELCQRADLLPGIDGRTFVDIDSLLRPVYGHAKQGASYGHTKIAGKQILRKGLSPLITTISSSTSAPVIAGARLRA
GKTNSGKGAARMIAQAVATARAAGVTGPILVRGDSAYGNSTVAAACRRAGAQFSLVLTKTPAVTAAIDAISDGAWIPVNYPGAVRDPDTGAWISDAEVAE
TTYTAFSSTKTPITARLIVRRVKDARFLDALFPVWRYHPFFTDSDEPVDAADITHRRHAIIETVFADLIDGPLAHMPSGRFGANSAWILCAAIAHNLLRA
AGVLAGTANAVARGSTLRRRIVTVPARLARPQRRPVLHLPTHWPWTDQWLMLWRNTIGYSPPATPCH

Blast result :

Comments

ISMsm12 is 91% aa similar to ISMsm10 for the transposase(ORF3). The two first ORF are passenger genes annotated as transcriptional regulator, TetR family and methyltransferase.

References

1] ISfinder annotation (2009)
2] Fleischmann,R.D., Dodson,R.J., Haft,D.H., Merkel,J.S., Nelson,W.C. and Fraser,C.M. (2006) Direct submission GenBank.