ISH3C

  • Family ISH3
  • Group
MGE type ISRelated element(s) :
Isoform ISH27-2Synonym(s) ISH3A, ISH3D, ISH3E, ISH40
Accession numberTranspositionOriginHost
AF016485 ND Halobacterium sp.
Halobacterium sp. NRC-1 plasmid pNRC200
Halobacterium salinarum R1
Halobacterium sp. NRC-1 plasmid pNRC100
Halobacterium salinarum SD104
Halobacterium salinarum R1 plasmid pHS1
Halobacterium sp. NRC-1
Halobacterium salinarum R1 plasmid PHS3
Halobacterium salinarum R1 plasmid pHS2
DNA section
IS Length : 1389 bp

Ends


IR Length : 15/16

IRL : CAGTACATCACAAAGCCGCTTAGTTAGAACGTCTGCTTGCTGAAGGTGTG
IRR : CAGTACCTCACAAAGCATCGCCGGCTAATCCGACTTGAGCCATCTGTTCT

Insertion site


Left flankDirect repeatRight flankDR Length
AGCGTATCCCAATCTTCGTCGAAGA5
AGAGTTCTGGAATCTCATCTTCCCT5
ATATGATTCCAGTTTAGAACATAGT5
CTCAGAGACGAGGATAAGAGCGCAT5
GCTAATGCCAATGATCTCTTCATCA5
GTGATGCCCGAGTATAGTTAGAGAT5
TGGATTTCACAGTATGGACAATCCG5
ATGGAGAAAAAGTATGGTGAGTTCG5
CAGCAGCAACAGATTACGGTCTCCG5
AACACCGACGAGTCTCCCTACCAGT5
ACCGAGACGTACACTGGGTACTCGA5
TGCTGATCTGAATATCGTTGGGACT5
AGGTGAGTCTATAATGAGTCGGATA5
GGATTACCCAATGATCTACCAGAGT5
GCAAAAACGAATGGTGGGACCAACT5
CCCAATCCTCAAATTCGTGTTGGCA5
GGATTACCCAATGATCTACCAGAGT5
GTTCCAGGTTAGCATAGTCG0
GTGATGCCCGAGTATAGTTAGAGAT5
GCTAATGCCAATGATCTCTTCATCA5

DNA sequence

CAGTACATCACAAAGCCGCTTAGTTAGAACGTCTGCTTGCTGAAGGTGTGTCTACGACCCAGCAAGCAGACAGTGAGATTCACGAGGACCAGCTCCTTAA
CTTCCTCGTCAACTGCCTTGACGAGGAAGTTTCTCTCAACCTCGCCAACAACGCTGAAATCGGTGCAGAGGACATCTACGAGGTCCTCGTCGGCGCGACC
GCCGACGGGACCTCGATCTCGACGCTGTGCAACTCCAGTGAAGACTCCCCATCGGCGAACACGATTCTCTATCATCTACGGACGAAGTTCGAGCCGGAAC
GGCTCGAACGCGTCGCTAACACGCTTCTTCGCCGAGACATCGTCGAACTGCTCCCCGAGCAGGTGGAGGTCTGCGCAGACCTCCACCTGCGGCCCTACTA
CGGTGATGAAGACGACACGGAGAACCTCTATCACTCCGAGGCGAAGCGAGGAACCACCGCATTCCACGCCTACGCCACACTCTACGCGCGTGTGAAGAAC
AAACGCTACACGCTGGCGGTGCGCCGTCTCGAAGACGGCGACACCGCCAGCAGTGTCCTCGCTGAGTTCCTTGGTGTACTCGACGGCCTTGACACCGACG
TCAAGGCCGTCTATCTTGATCGCGGATTCTACGACAGCAAGTGTCTCACGCTGTTACAGACGCACAACTACGCCTACGTTGTCCCGATCATCCGGTGGGG
TGAAGCGATTCAGCAGGAACTCTCGGAAGGGTGGAGTCGCGTCATCCAACACGATCTGACGGGGAAACTCGACGGTCACAGCTGGACCGTCGAGTTTCCC
GTCTACATCGACTGTACGTACCTGAACGGACGGTACGACGAGCACGGCGTGGCGCGTCACGGCTACGCCGCTGACGCGCCGTTCATCGAGAATCCACGCG
ACGCTCGATACCACTACTCGAAACGGTTCGGTATCGAGTCGAGCTATCGGTTGTCTGAGCAAGCGATAGCGACGACAACGACGCGAGACTCCACGGTGAG
ACTGCTGTACGTCGTGGTGAGTCTGCTGTTGCAGAACACGTGGCGGTATCTGCACTACGAATACGTGGCGACGCCGCGCCGAGGCGGGCGTCGCCTCTGG
TGGTGGCCGTACAAGGAGTTCGTGAATATGGTTCGACGGGCAGCGTGGACGGCCCTCGCGGTGCGTCGGGCCGTCCCCGCGAACCGGCCACCAGACGACC
GGTTCCACCGGTAGTCACCCACCGAGTACGGCGTCTCCGCAAGTGGCAACGCTGTCGCGTCGGCGGCTGAGCGCCGCCGACAGCGACAGCTCCGCCTTCG
ATCAGCGTTGCTCAACCGTGATCGACGACTCACCACAACAGAACAGATGGCTCAAGTCGGATTAGCCGGCGATGCTTTGTGAGGTACTG
Protein section
ORF number : 1

 

ORF 1
LengthBeginEndStrandFusion ORF
1167 bp388 aa481214+No
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MSTTQQADSEIHEDQLLNFLVNCLDEEVSLNLANNAEIGAEDIYEVLVGATADGTSISTLCNSSEDSPSANTILYHLRTKFEPERLERVANTLLRRDIVE
LLPEQVEVCADLHLRPYYGDEDDTENLYHSEAKRGTTAFHAYATLYARVKNKRYTLAVRRLEDGDTASSVLAEFLGVLDGLDTDVKAVYLDRGFYDSKCL
TLLQTHNYAYVVPIIRWGEAIQQELSEGWSRVIQHDLTGKLDGHSWTVEFPVYIDCTYLNGRYDEHGVARHGYAADAPFIENPRDARYHYSKRFGIESSY
RLSEQAIATTTTRDSTVRLLYVVVSLLLQNTWRYLHYEYVATPRRGGRRLWWWPYKEFVNMVRRAAWTALAVRRAVPANRPPDDRFHR

 

Blast result :
Comments
Six copies are present in pNRC100 of Halobacterium sp. NRC-1 at coordinates 32042-33432 ; 101440-102830 ; 105569-106959 ; 143912-142522 ; 150875-152265 ; 191346-189957 (deletion of 1 bp on position 51; the first aa was different).
The differencies (aa) were present at coordinates : 206(A-->T)-282(T-->N)-33(V-->T)1 or 379(D-->N).
File updated: February 16 2010.
File updated: June 02 2010.
September 28 2012 : the files of ISH3A (accession number : L19296) and ISH40 were deleted : the sequence is mutated an probably inactive. The DNA is 97% identical to those of ISH3C.
Previous comments of ISH3A :
ISH3A has been isolated through its inactivation of the gvp operon (gas vesicle proteins, Vac-), in the gvpA promoter. ISH3A (Halladay et al., 1993) is a relative of ISH51, partially homologous to ISH6, and 98.5 % identical to ISH27-1. The DRs are 5 bp long (Pfeifer and Ghahraman, 1993), and not 3 as suggested by DasSarma et al. (1989); all coordinates have been changed accordingly.
Previous comments of ISH40 :
ISH40 old name was ISH4. ISH40 was found inserted into the gvp gene cluster of Halobacterium salinarum SD104 (Halladay et al., 1993). ISH40 is 98 % and 91 % identical to ISH27-2 and ISH27-3, respectively.
References
1] Ng W.V., Ciufo S.A., Smith T.M., Bumgarner R.E., Baskin D., Faust J., Hall B., Loretz C., Seto J., Slagel J., Hood L., and DasSarma S. (1998) Genome Res. 8, 1131-1141

2] Pfeiffer F., Schuster S.C., Broicher A., Falb M., Palm P., Rodewald K., Ruepp.A., Soppa J., Tittor J., Oesterhelt D. (2008) Genomics 91, 335-346

3] DasSarma, S., Halladay, J.T., Jones, J.G., Donovan, J.W., Giannasca, P.J., Tandeau de Marsac, N. (1988) Proc. Natl. Acad. Sci., USA, 85, 6861-6865.

4] Jones, J.G., Hackett, N.R., Halladay, J.T., Scothorn, D.J., Yang, C.-F., Ng, W.-L., and DasSarma, S. (1989) Nucl. Acids Res. 17, 7785-7793.

5] DasSarma, S. (1989) Can. J. Microbiol. 35, 65-72.

6] Ng, W.-L., Kothakota, S., and DasSarma, S. (1991) J. Bacteriol. 173, 1958-1964.

7] Ng, W.-L., and DasSarma, S. (1993) J. Bacteriol. 175, 4584-4596.

8] Pfeifer, F., and Ghahraman, P. (1993) Mol. Gen. Genet. 238, 193-200.

9] Halladay, J.T., Donovan, J.W., Jones, J.G., Young, D.C., and DasSarma, S. (1993) Unpublised results