ISRj2

  • Family IS3
  • Group IS150
MGE type ISRelated element(s) :
Isoform Synonym(s) RSbeta, RSRj-beta
Accession numberTranspositionOriginHost
NC_004463 ND Bradyrhizobium japonicum
Bradyrhizobium japonicum USDA110
DNA section
IS Length : 1364 bp

Ends


IR Length : 21/26

IRL : AGAGCTGGCCCCGCAAATTCGGACAGTAGCTTGAGTGGATTTTCTGCCTG
IRR : AGAGCTGGCCCCGGTTGTTTGGACAGCGCCCCGCTGGATTTAAGTGGATT

Insertion site


Left flankDirect repeatRight flankDR Length
CCTTTGATTCGTTCCTCGTTCAT3

DNA sequence

AGAGCTGGCCCCGCAAATTCGGACAGTAGCTTGAGTGGATTTTCTGCCTGACAGCGGCGAGGATTCTTGCTGCGAATCAGGAGCGAAGATGACGAAGAAG
AGCCGCCGGACGCATTCTCCGGCATTCAAGGCGAAGGTTGCTTTGGCTGCGGTCAAAGGAGACAAGACACTGGCGGAGCTGGCGCAACTGTTTGATGTTC
ATCCGAACCAGATCACGATCTGGAAAAACCAGCTCCTGGAAGGCGCCGCCGGCGTGTTTGGGCATGACAAGACATCGGCCGAGACGCCGGTCGATTTGAA
GGCGTTGCATGCCAAGATCGGCGAGCTGGCGTTGGAAAACGATTTTTTGTCCGGCGCGCTCACCAAGGCGGGCCTGCTGAGCGCAAAGCGATGATCGACC
GCGGTCATGATCTTTCTATCGTGCGCCAGGCGAAGGTCCTGAAGCTGGCTCGCAGCACGGTCTACTATGAACCTCGGCCAGTTTCGGCCGAGGACCTTGC
CTTGATGCGTCGGCTCGATGAGCTGCATCTCGATTATCCCTTCGCGGGAGCGCGTATGCTGCGATCGTTGCTGCGGCGGGAGGGGGTATACGCCGGTCGC
CGCCACATCGCGACGCTGATGAAGCGCATGGGGATCGAGGCGGTCTATCGTCGCCCGAACACGAGCAAGCCGGCTCCGGGTCACAAGATCTACCCGTACC
TGTTGCGCGGATTGAAGATCGAGCGGCCCGACCATGCGTGGGCAATGGACATCACCTACATTCCGATGCGGCGTGGCTTCGTCTATCTCGCGGCGGTCGT
CGATGTGTTCAGCCGACGGGTCCTGGCCCATCGCGTCTCGATCACAATGGAGGCGGCCTTCTGCGTCCAAGCGGTCCAGGAGGCGTTGGCGAAGCACGGC
AGACCCGAGATTTTCAACACGGATCAGGGCAGCCAGTTCACCAGCCTCGAGTTCACCGATGTGCTGCTGGACGCGAAGATCGCCATCAGCATGGACGGCA
AGGGCGCCTGGCGCGACAACGTGTTTGTCGAGCGGCTCTGGCGCACGGTCAAATACGAAGAAGTTTATCTCCGCGCCTACGACAGCGTGTCCGAGGCGCG
AGCGTCAATTGCCAAGTATCTGGCCTTCTACAATCAGGGACGCCCTCACTCGAGCCTTGACGGGCGCACGCCCGACGAGGCTTACTTCGGCACGCAAGCT
ATGGTGATGGCCGCATGACCGTCGCCGACGATTTTGTCGTCGCTCTGGTCGGGCTACGCCCTCCCGACGCAACGACAAAATCGTAAAGCCCCGCGTTCAG
CATAACCCGGCAGGAATCCACTTAAATCCAGCGGGGCGCTGTCCAAACAACCGGGGCCAGCTCT
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
306 bp119 aa89394+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MTKKSRRTHSPAFKAKVALAAVKGDKTLAELAQLFDVHPNQITIWKNQLLEGAAGVFGHDKTSAETPVDLKALHAKIGELALENDFLSGALTKAGLLSAK
R

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
951 bp316 aa2681218+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

QDIGRDAGRFEGVACQDRRAGVGKRFFVRRAHQGGPAERKAMIDRGHDLSIVRQAKVLKLARSTVYYEPRPVSAEDLALMRRLDELHLDYPFAGARMLRS
LLRREGVYAGRRHIATLMKRMGIEAVYRRPNTSKPAPGHKIYPYLLRGLKIERPDHAWAMDITYIPMRRGFVYLAAVVDVFSRRVLAHRVSITMEAAFCV
QAVQEALAKHGRPEIFNTDQGSQFTSLEFTDVLLDAKIAISMDGKGAWRDNVFVERLWRTVKYEEVYLRAYDSVSEARASIAKYLAFYNQGRPHSSLDGR
TPDEAYFGTQAMVMAA

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1130 bp376 aa891218+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MTKKSRRTHSPAFKAKVALAAVKGDKTLAELAQLFDVHPNQITIWKNQLLEGAAGVFGHDKTSAETPVDLKALHAKIGELALENDFFVRRAHQGGPAERK
AMIDRGHDLSIVRQAKVLKLARSTVYYEPRPVSAEDLALMRRLDELHLDYPFAGARMLRSLLRREGVYAGRRHIATLMKRMGIEAVYRRPNTSKPAPGHK
IYPYLLRGLKIERPDHAWAMDITYIPMRRGFVYLAAVVDVFSRRVLAHRVSITMEAAFCVQAVQEALAKHGRPEIFNTDQGSQFTSLEFTDVLLDAKIAI
SMDGKGAWRDNVFVERLWRTVKYEEVYLRAYDSVSEARASIAKYLAFYNQGRPHSSLDGRTPDEAYFGTQAMVMAA

 

Blast result :
Comments
There are at least six ISRj2 copies in Bradyrhizobium japonicum USDA110, three being located in the nifDK-nifH region (Kaluza et al., 1985).
ISRj2 is 82% aa similar to ISKpn11.
The third ORF is the putative ORFAB transposase reconstructed in silico by possible -1 frameshift.
References
1] Kaluza, K., Hahn, M., and Hennecke, H. (1985) J. Bacteriol. 162, 535-542.
2] Hahn, M., and Hennecke, H. (1987) Appl. Environ. Microbiol. 53, 2247-2252.