ISH3C
- Family ISH3
- Group
Isoform ISH27-2Synonym(s) ISH3A, ISH3D, ISH3E, ISH40
Accession number | Transposition | Origin | Host |
---|---|---|---|
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 flank | Direct repeat | Right flank | DR Length |
---|---|---|---|
AGCGTATCCC | AATCT | TCGTCGAAGA | 5 |
AGAGTTCTGG | AATCT | CATCTTCCCT | 5 |
ATATGATTCC | AGTTT | AGAACATAGT | 5 |
CTCAGAGACG | AGGAT | AAGAGCGCAT | 5 |
GCTAATGCCA | ATGAT | CTCTTCATCA | 5 |
GTGATGCCCG | AGTAT | AGTTAGAGAT | 5 |
TGGATTTCAC | AGTAT | GGACAATCCG | 5 |
ATGGAGAAAA | AGTAT | GGTGAGTTCG | 5 |
CAGCAGCAAC | AGATT | ACGGTCTCCG | 5 |
AACACCGACG | AGTCT | CCCTACCAGT | 5 |
ACCGAGACGT | ACACT | GGGTACTCGA | 5 |
TGCTGATCTG | AATAT | CGTTGGGACT | 5 |
AGGTGAGTCT | ATAAT | GAGTCGGATA | 5 |
GGATTACCCA | ATGAT | CTACCAGAGT | 5 |
GCAAAAACGA | ATGGT | GGGACCAACT | 5 |
CCCAATCCTC | AAATT | CGTGTTGGCA | 5 |
GGATTACCCA | ATGAT | CTACCAGAGT | 5 |
GTTCCAGGTT | AGCATAGTCG | 0 | |
GTGATGCCCG | AGTAT | AGTTAGAGAT | 5 |
GCTAATGCCA | ATGAT | CTCTTCATCA | 5 |
DNA sequence
CAGTACATCACAAAGCCGCTTAGTTAGAACGTCTGCTTGCTGAAGGTGTGTCTACGACCCAGCAAGCAGACAGTGAGATTCACGAGGACCAGCTCCTTAA
CTTCCTCGTCAACTGCCTTGACGAGGAAGTTTCTCTCAACCTCGCCAACAACGCTGAAATCGGTGCAGAGGACATCTACGAGGTCCTCGTCGGCGCGACC
GCCGACGGGACCTCGATCTCGACGCTGTGCAACTCCAGTGAAGACTCCCCATCGGCGAACACGATTCTCTATCATCTACGGACGAAGTTCGAGCCGGAAC
GGCTCGAACGCGTCGCTAACACGCTTCTTCGCCGAGACATCGTCGAACTGCTCCCCGAGCAGGTGGAGGTCTGCGCAGACCTCCACCTGCGGCCCTACTA
CGGTGATGAAGACGACACGGAGAACCTCTATCACTCCGAGGCGAAGCGAGGAACCACCGCATTCCACGCCTACGCCACACTCTACGCGCGTGTGAAGAAC
AAACGCTACACGCTGGCGGTGCGCCGTCTCGAAGACGGCGACACCGCCAGCAGTGTCCTCGCTGAGTTCCTTGGTGTACTCGACGGCCTTGACACCGACG
TCAAGGCCGTCTATCTTGATCGCGGATTCTACGACAGCAAGTGTCTCACGCTGTTACAGACGCACAACTACGCCTACGTTGTCCCGATCATCCGGTGGGG
TGAAGCGATTCAGCAGGAACTCTCGGAAGGGTGGAGTCGCGTCATCCAACACGATCTGACGGGGAAACTCGACGGTCACAGCTGGACCGTCGAGTTTCCC
GTCTACATCGACTGTACGTACCTGAACGGACGGTACGACGAGCACGGCGTGGCGCGTCACGGCTACGCCGCTGACGCGCCGTTCATCGAGAATCCACGCG
ACGCTCGATACCACTACTCGAAACGGTTCGGTATCGAGTCGAGCTATCGGTTGTCTGAGCAAGCGATAGCGACGACAACGACGCGAGACTCCACGGTGAG
ACTGCTGTACGTCGTGGTGAGTCTGCTGTTGCAGAACACGTGGCGGTATCTGCACTACGAATACGTGGCGACGCCGCGCCGAGGCGGGCGTCGCCTCTGG
TGGTGGCCGTACAAGGAGTTCGTGAATATGGTTCGACGGGCAGCGTGGACGGCCCTCGCGGTGCGTCGGGCCGTCCCCGCGAACCGGCCACCAGACGACC
GGTTCCACCGGTAGTCACCCACCGAGTACGGCGTCTCCGCAAGTGGCAACGCTGTCGCGTCGGCGGCTGAGCGCCGCCGACAGCGACAGCTCCGCCTTCG
ATCAGCGTTGCTCAACCGTGATCGACGACTCACCACAACAGAACAGATGGCTCAAGTCGGATTAGCCGGCGATGCTTTGTGAGGTACTG
CTTCCTCGTCAACTGCCTTGACGAGGAAGTTTCTCTCAACCTCGCCAACAACGCTGAAATCGGTGCAGAGGACATCTACGAGGTCCTCGTCGGCGCGACC
GCCGACGGGACCTCGATCTCGACGCTGTGCAACTCCAGTGAAGACTCCCCATCGGCGAACACGATTCTCTATCATCTACGGACGAAGTTCGAGCCGGAAC
GGCTCGAACGCGTCGCTAACACGCTTCTTCGCCGAGACATCGTCGAACTGCTCCCCGAGCAGGTGGAGGTCTGCGCAGACCTCCACCTGCGGCCCTACTA
CGGTGATGAAGACGACACGGAGAACCTCTATCACTCCGAGGCGAAGCGAGGAACCACCGCATTCCACGCCTACGCCACACTCTACGCGCGTGTGAAGAAC
AAACGCTACACGCTGGCGGTGCGCCGTCTCGAAGACGGCGACACCGCCAGCAGTGTCCTCGCTGAGTTCCTTGGTGTACTCGACGGCCTTGACACCGACG
TCAAGGCCGTCTATCTTGATCGCGGATTCTACGACAGCAAGTGTCTCACGCTGTTACAGACGCACAACTACGCCTACGTTGTCCCGATCATCCGGTGGGG
TGAAGCGATTCAGCAGGAACTCTCGGAAGGGTGGAGTCGCGTCATCCAACACGATCTGACGGGGAAACTCGACGGTCACAGCTGGACCGTCGAGTTTCCC
GTCTACATCGACTGTACGTACCTGAACGGACGGTACGACGAGCACGGCGTGGCGCGTCACGGCTACGCCGCTGACGCGCCGTTCATCGAGAATCCACGCG
ACGCTCGATACCACTACTCGAAACGGTTCGGTATCGAGTCGAGCTATCGGTTGTCTGAGCAAGCGATAGCGACGACAACGACGCGAGACTCCACGGTGAG
ACTGCTGTACGTCGTGGTGAGTCTGCTGTTGCAGAACACGTGGCGGTATCTGCACTACGAATACGTGGCGACGCCGCGCCGAGGCGGGCGTCGCCTCTGG
TGGTGGCCGTACAAGGAGTTCGTGAATATGGTTCGACGGGCAGCGTGGACGGCCCTCGCGGTGCGTCGGGCCGTCCCCGCGAACCGGCCACCAGACGACC
GGTTCCACCGGTAGTCACCCACCGAGTACGGCGTCTCCGCAAGTGGCAACGCTGTCGCGTCGGCGGCTGAGCGCCGCCGACAGCGACAGCTCCGCCTTCG
ATCAGCGTTGCTCAACCGTGATCGACGACTCACCACAACAGAACAGATGGCTCAAGTCGGATTAGCCGGCGATGCTTTGTGAGGTACTG
Protein section
ORF number : 1
ORF 1
Length | Begin | End | Strand | Fusion ORF | |
---|---|---|---|---|---|
1167 bp | 388 aa | 48 | 1214 | + | No |
Chemistry : DDE
ORF sequence :
MSTTQQADSEIHEDQLLNFLVNCLDEEVSLNLANNAEIGAEDIYEVLVGATADGTSISTLCNSSEDSPSANTILYHLRTKFEPERLERVANTLLRRDIVE
LLPEQVEVCADLHLRPYYGDEDDTENLYHSEAKRGTTAFHAYATLYARVKNKRYTLAVRRLEDGDTASSVLAEFLGVLDGLDTDVKAVYLDRGFYDSKCL
TLLQTHNYAYVVPIIRWGEAIQQELSEGWSRVIQHDLTGKLDGHSWTVEFPVYIDCTYLNGRYDEHGVARHGYAADAPFIENPRDARYHYSKRFGIESSY
RLSEQAIATTTTRDSTVRLLYVVVSLLLQNTWRYLHYEYVATPRRGGRRLWWWPYKEFVNMVRRAAWTALAVRRAVPANRPPDDRFHR
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.
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
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