ISBj1
- Family IS1380
- Group
Isoform Synonym(s) HRS1, HRS1a, ISB20, HRS1, HRS1a, ISB20,
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| L09226 | ND | Bradyrhizobium japonicum | Bradyrhizobium japonicum serocluster 123 USDA438 Bradyrhizobium japonicum serocluster 123 USDA424 Bradyrhizobium japonicum serocluster 123 IA44 Bradyrhizobium japonicum serocluster 123 IN64 |
DNA section
IS Length : 2071 bp
Ends
IR Length : 6/7
IRL : CCCGTCTTATTCGCGAGAGGGCGCCTGAGAGGCTGGCGAGCGTCGTGTAA
IRR : CCGTCTATTCGTGAGAGTGCGGCTTTTGGGCCCGATTGATGCGGCCGCAC
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| CGCACTGAAG | CTAG | GCGTTTACGT | 4 |
DNA sequence
CCCGTCTTATTCGCGAGAGGGCGCCTGAGAGGCTGGCGAGCGTCGTGTAAAGCGCTGATGCGGTCGTAGGATTCGGTTGCGAAGCCACCCCATCACCTTC
AACCGCGAACGCCACGCCCGCCATGACCGATGATACGATTTCAGACCACTATCGAGAAGCAAGAATTCAACACAAATAAAACCTCTGCCTCGCGCTCGAT
CTCTTCATGCTTGATAGTCTCGTTTCGGAGGCTGATCACCTACCGCGTCTAATAGGCCGCTCGCGACCCGGTTTCTTTGGACGCGGCACGACGCACGCTC
CACGTTTCGGCACAGAAATGATCGGGAGTCACTCAATCTTTCTTCAACTTAACCCGTCTTATTCGTAAGAGTGCGCCTGAGGGGTAAAGCGCTGATGCGC
GTAGGATTCGGTTGCGAACGCAACCCCATCACCTCCAACCGCGAACGCCACGCCCGCCATGACCGACGATACGATTCCGCCCTTCTCGTTTCCAGCCGTT
CACGCCAAGAAAGTCACAGCTGCCTTCGATGGTGGGCTCCTAACCTCGAACGGGGGCGTGATGCTTCTGGCGATGGCCGGCGGCGGGACGGTCTCGGTTT
GGCCAACAATCTGGCCCGGGTGTTCCCGGATCGGCGCGATCCGACGCGGGTCATGCACAGCCTGGTCGATATGTTCCGCGCTCGCATGTTCGCGATCTGC
TGCGGCTACGAGGACGCCGACGACCTCGATCATCTGAGGTCCGATCCGGCATTCAAACTGGCTGCGGACGGCGTCCGGACACGGGCCGGGATTTGTGTTC
CCAGCCGAGCTGTCGCGGCTGGAGAATGCTCGCGCCTGCGCGACGTGATCCGGCTGACCTACATTTTGGTCGACGCATGGATGGATAGCTACCCGCGCGA
CGCGGCATCCGTCACGCTCGACATCGATGATACCTGCGACGTCGTCCACGGCCATCAGCAGCTCTCGCTGTTCAACGCTCATTATGACGAACGCTGCTTC
CTGCCGATCCACGTCTACGACACGGAGAAGAGCCGGCCCGTGCTGCGTGCTGCGGCCCGGCAAGACGCGCGCGTCGAGGTGCGTGCCCATCTGCGCCGCC
TGGTACGGCATATCCGGACGCGATGGCACAACACGCAAATTACGTTCCGTGGCGAGCGCACTATGCCCGCGGAGGCCATGGCGTGGTGCGAGACCAACGG
CATCGACTACATCTTCGGTCTGTCGGCACCAAGCCTCTCGCGCAGAAAAGTCGACGAGGTCGCCGACGACATCCGCACGCGACGCGCCCATCGAGAACCT
GCCGGTTCTGCGTGGCTATACCGAGACGACGCCACAAGGCAAAGTCCTGGGATCGCGAACGGGCCACTGTCGCCGTATTGAGGCGACGATGCTCGGCCTC
GACATCCGCTTCGTCGTCACCAGCCTCGATGTCGGCTCGGACCGAGTGGATCTACGACAGCCTGTATTGCGCGACGAGCCAAGCCGAGAATCTGATCAAG
CTGCATAAGACGCAGCTCGCCTCCGATCGCACCAGCTGCCGTTCGGCGCTCGCCAACCAGGTCCGTCTCGTGCTCCATACGGCCGCTTATTGGCTGATGC
TGACCGTGCGCGACGCCATTCCCAAAGCCCGGGAATTGGCCGCTGCCGAGTTCGCGACGCTGCGTCTTCGGCTCTTGAAAATCGCCGCCCGTGTCGTCGA
GACCACGAGCCGCGCATTCGCCTTGCGTTTGCCGCGGCATGTCCCGAAGCCGACCTGATCTGCGGCTTGCCCGGCGCGCTGCTGCCGCTCGGTCCTTGAC
GGCGCGTCCGCCCCCGTTCGCCCAACCCTTCGCCTTGCGTTTGCCGCGGCATGTCCCGAAGCCGACCTGATCTGCGGCTTGCCCGGCGCGCTGCTGCCGC
TCGGTCCTTGACGGCGCGTCCGCCCCCGTTCGCCCAACCCATCCCTCAAGCGCGTTGCAAAGTACCGGTCGTCAGGCGGCGAAAAGCCGAAGGCAATCCT
GTGCGCCTCGTCAGACAAGATGTGCGGCCGCATCAATCGGGCCCAAAAGCCGCACTCTCACGAATAGACGG
AACCGCGAACGCCACGCCCGCCATGACCGATGATACGATTTCAGACCACTATCGAGAAGCAAGAATTCAACACAAATAAAACCTCTGCCTCGCGCTCGAT
CTCTTCATGCTTGATAGTCTCGTTTCGGAGGCTGATCACCTACCGCGTCTAATAGGCCGCTCGCGACCCGGTTTCTTTGGACGCGGCACGACGCACGCTC
CACGTTTCGGCACAGAAATGATCGGGAGTCACTCAATCTTTCTTCAACTTAACCCGTCTTATTCGTAAGAGTGCGCCTGAGGGGTAAAGCGCTGATGCGC
GTAGGATTCGGTTGCGAACGCAACCCCATCACCTCCAACCGCGAACGCCACGCCCGCCATGACCGACGATACGATTCCGCCCTTCTCGTTTCCAGCCGTT
CACGCCAAGAAAGTCACAGCTGCCTTCGATGGTGGGCTCCTAACCTCGAACGGGGGCGTGATGCTTCTGGCGATGGCCGGCGGCGGGACGGTCTCGGTTT
GGCCAACAATCTGGCCCGGGTGTTCCCGGATCGGCGCGATCCGACGCGGGTCATGCACAGCCTGGTCGATATGTTCCGCGCTCGCATGTTCGCGATCTGC
TGCGGCTACGAGGACGCCGACGACCTCGATCATCTGAGGTCCGATCCGGCATTCAAACTGGCTGCGGACGGCGTCCGGACACGGGCCGGGATTTGTGTTC
CCAGCCGAGCTGTCGCGGCTGGAGAATGCTCGCGCCTGCGCGACGTGATCCGGCTGACCTACATTTTGGTCGACGCATGGATGGATAGCTACCCGCGCGA
CGCGGCATCCGTCACGCTCGACATCGATGATACCTGCGACGTCGTCCACGGCCATCAGCAGCTCTCGCTGTTCAACGCTCATTATGACGAACGCTGCTTC
CTGCCGATCCACGTCTACGACACGGAGAAGAGCCGGCCCGTGCTGCGTGCTGCGGCCCGGCAAGACGCGCGCGTCGAGGTGCGTGCCCATCTGCGCCGCC
TGGTACGGCATATCCGGACGCGATGGCACAACACGCAAATTACGTTCCGTGGCGAGCGCACTATGCCCGCGGAGGCCATGGCGTGGTGCGAGACCAACGG
CATCGACTACATCTTCGGTCTGTCGGCACCAAGCCTCTCGCGCAGAAAAGTCGACGAGGTCGCCGACGACATCCGCACGCGACGCGCCCATCGAGAACCT
GCCGGTTCTGCGTGGCTATACCGAGACGACGCCACAAGGCAAAGTCCTGGGATCGCGAACGGGCCACTGTCGCCGTATTGAGGCGACGATGCTCGGCCTC
GACATCCGCTTCGTCGTCACCAGCCTCGATGTCGGCTCGGACCGAGTGGATCTACGACAGCCTGTATTGCGCGACGAGCCAAGCCGAGAATCTGATCAAG
CTGCATAAGACGCAGCTCGCCTCCGATCGCACCAGCTGCCGTTCGGCGCTCGCCAACCAGGTCCGTCTCGTGCTCCATACGGCCGCTTATTGGCTGATGC
TGACCGTGCGCGACGCCATTCCCAAAGCCCGGGAATTGGCCGCTGCCGAGTTCGCGACGCTGCGTCTTCGGCTCTTGAAAATCGCCGCCCGTGTCGTCGA
GACCACGAGCCGCGCATTCGCCTTGCGTTTGCCGCGGCATGTCCCGAAGCCGACCTGATCTGCGGCTTGCCCGGCGCGCTGCTGCCGCTCGGTCCTTGAC
GGCGCGTCCGCCCCCGTTCGCCCAACCCTTCGCCTTGCGTTTGCCGCGGCATGTCCCGAAGCCGACCTGATCTGCGGCTTGCCCGGCGCGCTGCTGCCGC
TCGGTCCTTGACGGCGCGTCCGCCCCCGTTCGCCCAACCCATCCCTCAAGCGCGTTGCAAAGTACCGGTCGTCAGGCGGCGAAAAGCCGAAGGCAATCCT
GTGCGCCTCGTCAGACAAGATGTGCGGCCGCATCAATCGGGCCCAAAAGCCGCACTCTCACGAATAGACGG
Recoding section
- Recoding by frameshift
- Frame
- Type
- Experimentally demonstrated
Stimulators :
- Shine-Dalgarno sequence :
- Secondary structure :
Recoding motif :
Protein section
ORF number : 1
ORF 1
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1364 bp | 454 aa | 458 | 1821 | + | Yes |
Chemistry : DDE
ORF sequence :
MRVGFGCERNPITSNRERHARHDRRYDSALLVSSRSRQESHSCLRWWAPNLERGRDASGDGRRRDGLGLANNLARVFPDRRDPTRVMHSLVDMFRARMFA
ICCGYEDADDLDHLRSDPAFKLAADGVRTRAGICVPSRAVAAGECSRLRDVIRLTYILVDAWMDSYPRDAASVTLDIDDTCDVVHGHQQLSLFNAHYDER
CFLPIHVYDTEKSRPVLRAAARQDARVEVRAHLRRLVRHIRTRWHNTQITFRGERTMPAEAMAWCETNGIDYIFGLSAPSLSRRKVDEVADDIRTRRAHR
EPCRFCVAIPRRRHKAKSWDRERATVAVLRRRCSASTSASSSPASMSARTEWIYDSLYCATSQAENLIKLHKTQLASDRTSCRSALANQVRLVLHTAAYW
LMLTVRDAIPKARELAAAEFATLRLRLLKIAARVVETTSRAFALRLPRHVPKPT
ICCGYEDADDLDHLRSDPAFKLAADGVRTRAGICVPSRAVAAGECSRLRDVIRLTYILVDAWMDSYPRDAASVTLDIDDTCDVVHGHQQLSLFNAHYDER
CFLPIHVYDTEKSRPVLRAAARQDARVEVRAHLRRLVRHIRTRWHNTQITFRGERTMPAEAMAWCETNGIDYIFGLSAPSLSRRKVDEVADDIRTRRAHR
EPCRFCVAIPRRRHKAKSWDRERATVAVLRRRCSASTSASSSPASMSARTEWIYDSLYCATSQAENLIKLHKTQLASDRTSCRSALANQVRLVLHTAAYW
LMLTVRDAIPKARELAAAEFATLRLRLLKIAARVVETTSRAFALRLPRHVPKPT
Blast result :
Comments
ORF1 is 31% identical to that of IS1380. By analogy to IS1380, the limits of ISBj1 (1 bp deletion) and its DRs (4 and not 5 bp) have been reconsidered. ISBj1 is apparently associated with a restricted nodulation phenotype (nodD2, nolA). One copy is located next to the fixR-nifA locus in Bradyrhizobium japonicum USDA424. Note that there is most probably a sequencing error around position 1365. The ORF considered here is the "fusion" between the 302-aa ORF1 (458-1363) and the 152-aa ORF2 (1363-1821). Also, there is a 112-bp duplication at the end of the element: 1780-1891 = 1892-2003 !
References