ISPam3

  • Family IS3
  • Group IS407
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_010847 ND Paracoccus aminophilus
Paracoccus aminophilus plasmid pAMI2
DNA section
IS Length : 1197 bp

Ends


IR Length : 30/39

IRL : GGTAATCCTCCCGATGGTTAAGGGGATGCGGAAGTAGAATTTTCTCGGCA
IRR : GGTAATCCTCCCCGTTTTAACGGGGTGCGACCGTAGAACTCACGCGGCCA

Insertion site


Left flankDirect repeatRight flankDR Length
ATGGGCAGTGATACAGAAAAGTGA4
CAGAAGAGAAGGACGATCGGCGAG4

DNA sequence

GGTAATCCTCCCGATGGTTAAGGGGATGCGGAAGTAGAATTTTCTCGGCAGGATCGACGAGGAGATTCTGATGAAGAAGACGAGATTTACCGAGGCACAG
ATCATGCGCGTGCTGCGACAGGCCGAGGGCGGTATGCCCGTGGGCGAGTTGTGCCGCGAGCATGGGATCAGCAGCGCGACGTTCTATAAGTGGCGGGCGA
AGTATGGCGGCATGGACGTGTCAATGATGAGCCAGATGAAGGCGCTCGAAGACGAGAACCGGCGGCTGAAACGCATGTTCGCCGATCTGAGCATGCAGGC
CGACCTGCTTCGAGAGGCTCTTGGAAAAAAGTGACGCGGCCAGCTCGACGCCGGGAGTTGGCCGAGAAGGCGGTGGCGACGAAGGGTGTCAGCATCGCGC
TGGCGTGCCGCGCGTTCGGCGTCAGCGAGACCTGTTTCCGCTACAGTCCGAGGCGCGACGAAGAGAACGAGATGATCGCCGACCTGCTGGTGGGGCTGAC
CAATGTCCACAAGACGTGGGGGTTCGGGCTGTGCTTCCTCCACCTGCGGAACGTGAAGGGGCATGTCTGGAACCACAAGCGGGTTCACCGGATCTACTGC
GAACTGGAGCTGAACCTGCGCATCAAGCCGCGGCGACGGCTGAAGCGCGAGAAGCCCGAGGAACTGGCCGTGCCGGATGCCCCGAACCTGGTCTGGTCGA
TGGATTTCATGGCGGACCGCTTGGCCGACGGGCGGCAATTCCGGCTTCTGAACGTGCTAGACGACTTCAATCGCGAGGGCCTGGGGATCGAGGTCGACTT
CTCGCTGCCCGCCGAACGGGTCGTCCGCTCCCTGAACCAGATCATCGAATGGCGCGGAAAGCCCCTGGCGATCAGGGTCGACAACGGCCCCGAATACGTC
AGTTCCACGCTGATGACCTGGGCCGAGAAGCAGGGCATCGCCCTGACATACATCCAGCCCGGCAAGCCGCAGCAGAACGCCTATGTCGAGCGTTACAACC
GGACGGTCCGCCACGAATGGCTCGACCTCTACATCTTTGAAACCATCGAGGAGGTGCAGCAGATCGCCACCGAATGGCTATGGACCTACAACAACGAACG
CCCGAATATGGGCATCGGCGGCGTTACACCCGCCATGAAGCTGAAAATGGCCGCGTGAGTTCTACGGTCGCACCCCGTTAAAACGGGGAGGATTACC
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
264 bp87 aa71334+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MKKTRFTEAQIMRVLRQAEGGMPVGELCREHGISSATFYKWRAKYGGMDVSMMSQMKALEDENRRLKRMFADLSMQADLLREALGKK

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
969 bp322 aa1901158+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

VAGEVWRHGRVNDEPDEGARRREPAAETHVRRSEHAGRPASRGSWKKVTRPARRRELAEKAVATKGVSIALACRAFGVSETCFRYSPRRDEENEMIADLL
VGLTNVHKTWGFGLCFLHLRNVKGHVWNHKRVHRIYCELELNLRIKPRRRLKREKPEELAVPDAPNLVWSMDFMADRLADGRQFRLLNVLDDFNREGLGI
EVDFSLPAERVVRSLNQIIEWRGKPLAIRVDNGPEYVSSTLMTWAEKQGIALTYIQPGKPQQNAYVERYNRTVRHEWLDLYIFETIEEVQQIATEWLWTY
NNERPNMGIGGVTPAMKLKMAA

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1088 bp362 aa711158+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MKKTRFTEAQIMRVLRQAEGGMPVGELCREHGISSATFYKWRAKYGGMDVSMMSQMKALEDENRRLKRMFADLSMQADLLREALGKKVTRPARRRELAEK
AVATKGVSIALACRAFGVSETCFRYSPRRDEENEMIADLLVGLTNVHKTWGFGLCFLHLRNVKGHVWNHKRVHRIYCELELNLRIKPRRRLKREKPEELA
VPDAPNLVWSMDFMADRLADGRQFRLLNVLDDFNREGLGIEVDFSLPAERVVRSLNQIIEWRGKPLAIRVDNGPEYVSSTLMTWAEKQGIALTYIQPGKP
QQNAYVERYNRTVRHEWLDLYIFETIEEVQQIATEWLWTYNNERPNMGIGGVTPAMKLKMAA

 

Blast result :
Comments
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible -1 frameshift.
ISPam3 is 85% aa similar to ISSusp2.
This IS has atypic IRs: it begins with 'GG' instead of 'TG'.
ISPam3 has been identified by its transposition to the entrapment vectors pCM132TC (promoter-less tetA cassette). It is present in 1 copy in plasmid pAMI2. ISPam3 carries a sequence 5’-GCTGGTGG-3’ (position 486) identical to the Chi sites, which specify the place of action for RecBCD nuclease. At position 325, ISPam3 harbours the sequence 5'-AAAAAAG-3' that might function as a -1 translational frameshifting site. As judged from DNA hybridization analysis ISPam3 is present in P. aestuarii DSM 19484, P. alcaliphilus JCM 7364, P. halophilus JCM 14014, P. marcusii OS22, P. pantotrophus DSM 11073 and P. versutus UW1.
References
1] Dziewit,L., Jazurek,M., Drewniak,L., Baj,J. and Bartosik,D. (2007) J. Bacteriol. 189 (5), 1983-1997
2] Dziewit, L., Dmowski, M., Baj, J., and Bartosik, D. (2010) Appl. Environ. Microbiol. 76, 1861-1869.
3] Dziewit, L., Baj, J., Szuplewska, M., Maj A., Tabin, M., Czyzkowska, A., Skrzypczyk, G., Adamczuk, M., Sitarek, T., Stawinski, P., Tudek, A., Wanasz, K., Wardal, E., Piechucka, E., Bartosik, D. (2012) PLoS ONE 7: e32277