ISBlo10
- Family IS3
- Group
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| NC_004307 | ND | Bifidobacterium longum | Bifidobacterium longum NCC2705 |
DNA section
IS Length : 1339 bp
Ends
IR Length : 23/25
IRL : TGATATGAACTGATTTTTGTTCCGCATTTCCCCTAACTCGATGGGAGATG
IRR : TGATATGGCCTGATTTTTGTTCCGCCCTTATAGTGGGGCGGCTTGCGCCG
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|
DNA sequence
TGATATGAACTGATTTTTGTTCCGCATTTCCCCTAACTCGATGGGAGATGATGGAACCATGGCAAAAGGAACGAGATACACGCCGGAGTTCAAGGCGAAG
GCCGTCAGGCTGTTGACCGAGTCGCGCGGCTCGTATTCGTCGGAGACCAAGGCGATCGAACAGGTCGCCAAGGATCCGGGGGTCGCGCCGGAGACGCTGC
GCCGTTGGCGCAACAAGACGGACGCCACGGTCGCGGCGGAGACCAAGCGGTCGGCCGAAGACGCGATGGCGGAGTTGAAGAGTTTGCGGGCCGAGGTCGC
GCGATTGAGGCGGGCGAACGAGATATTGACGACGGCGTCGGCTTTTTTCGCGGCACGGCTCGACCCGACACGGCGTTGATGGTCGCTTACATCGACGAAT
TCAAGGACCGTTTCAGGGTCGGGCCGATCTGCAGGGTGCTGGCCGCTTCGCTGGACTGCGGGTCCGTCACGCCGCGCGGCTACCGCATGTTCAGATCCAG
GCCCGTCAGCCGCATGGCCGCCAGGCACGAGGCACTGGCCCGCGACATCCTCGAGATCCATGCCGATTTCTTCATGGCCGTGTACGGGTACCGCAAGACG
CGCGCCCAGTTGTTGGCGCGGGGCTGGGATCCGGCCGAGATCGGCCGCGACCAGGTGATGAACGTCATGCGGGAATCGGGAATCCGCGGCGTGCGCCGCG
GCAGGACGCCCGTCACCACCAAACCGGCGAAGGGCACGGGCGGCAGGCCCGACCTCGTGGAACGCGGGTTCGAGGCGGAGGCACCGAACCGGCTGCACGT
GGCCGACATCACCTACGTGCGCATGGCCAACGGCTCGTTCGGCTACACGGCGTTCGCCGCCGACGTGTTCGCCCGCAGGATCGTCGGATGGGCGTGCGCC
ACCACCATGGACACCAGGGAGCTGCCGTTGCAGGCGCTGGAACAGGCGATATCATGGGCCGCCTCGCATGGCGGCGCGGACGGTCTCGTGCACCATTCCG
ACCATGGCGCGCAGTACATCAGCCTCGTGTACACCACCAGGGTCGGGGAATTCGGCATGCTTCCCTCGACCGGCACGGTCGGCGACTCGTACGACAACGC
CATGGCCGAGAGCGCCGACGGCGCGTACAGGACCGAGCTCGTCTGGCGACGCAAGCCCTTCCAGGATTTGAGGGACCTGGAATTGGCGACGTTCCGGTGG
GTCTCGTGGCGGGGACTCGAAGCGTCTGCACCAGTCCTTGGGCTACAGGACACCGGAACGGACCGAAACCGAGTATTATGCAAACCAAGCGGCGCAAGCC
GCCCCACTATAAGGGCGGAACAAAAATCAGGCCATATCA
GCCGTCAGGCTGTTGACCGAGTCGCGCGGCTCGTATTCGTCGGAGACCAAGGCGATCGAACAGGTCGCCAAGGATCCGGGGGTCGCGCCGGAGACGCTGC
GCCGTTGGCGCAACAAGACGGACGCCACGGTCGCGGCGGAGACCAAGCGGTCGGCCGAAGACGCGATGGCGGAGTTGAAGAGTTTGCGGGCCGAGGTCGC
GCGATTGAGGCGGGCGAACGAGATATTGACGACGGCGTCGGCTTTTTTCGCGGCACGGCTCGACCCGACACGGCGTTGATGGTCGCTTACATCGACGAAT
TCAAGGACCGTTTCAGGGTCGGGCCGATCTGCAGGGTGCTGGCCGCTTCGCTGGACTGCGGGTCCGTCACGCCGCGCGGCTACCGCATGTTCAGATCCAG
GCCCGTCAGCCGCATGGCCGCCAGGCACGAGGCACTGGCCCGCGACATCCTCGAGATCCATGCCGATTTCTTCATGGCCGTGTACGGGTACCGCAAGACG
CGCGCCCAGTTGTTGGCGCGGGGCTGGGATCCGGCCGAGATCGGCCGCGACCAGGTGATGAACGTCATGCGGGAATCGGGAATCCGCGGCGTGCGCCGCG
GCAGGACGCCCGTCACCACCAAACCGGCGAAGGGCACGGGCGGCAGGCCCGACCTCGTGGAACGCGGGTTCGAGGCGGAGGCACCGAACCGGCTGCACGT
GGCCGACATCACCTACGTGCGCATGGCCAACGGCTCGTTCGGCTACACGGCGTTCGCCGCCGACGTGTTCGCCCGCAGGATCGTCGGATGGGCGTGCGCC
ACCACCATGGACACCAGGGAGCTGCCGTTGCAGGCGCTGGAACAGGCGATATCATGGGCCGCCTCGCATGGCGGCGCGGACGGTCTCGTGCACCATTCCG
ACCATGGCGCGCAGTACATCAGCCTCGTGTACACCACCAGGGTCGGGGAATTCGGCATGCTTCCCTCGACCGGCACGGTCGGCGACTCGTACGACAACGC
CATGGCCGAGAGCGCCGACGGCGCGTACAGGACCGAGCTCGTCTGGCGACGCAAGCCCTTCCAGGATTTGAGGGACCTGGAATTGGCGACGTTCCGGTGG
GTCTCGTGGCGGGGACTCGAAGCGTCTGCACCAGTCCTTGGGCTACAGGACACCGGAACGGACCGAAACCGAGTATTATGCAAACCAAGCGGCGCAAGCC
GCCCCACTATAAGGGCGGAACAAAAATCAGGCCATATCA
Recoding section
- Recoding by frameshift
- Frame
- Type
- Experimentally demonstrated
Stimulators :
- Shine-Dalgarno sequence :
- Secondary structure :
Recoding motif :
Protein section
ORF number : 3
ORF 1
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 321 bp | 106 aa | 59 | 379 | + | No |
Description : First part of the transposase
ORF sequence :
MAKGTRYTPEFKAKAVRLLTESRGSYSSETKAIEQVAKDPGVAPETLRRWRNKTDATVAAETKRSAEDAMAELKSLRAEVARLRRANEILTTASAFFAAR
LDPTRR
LDPTRR
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1288 bp | 428 aa | 52 | 1339 | + | No |
Description : Second part of the transposase
ORF sequence :
WNHGKRNEIHAGVQGEGRQAVDRVARLVFVGDQGDRTGRQGSGGRAGDAAPLAQQDGRHGRGGDQAVGRRRDGGVEEFAGRGAIEAGERDIDDGVGFFRG
TARPDTALMVAYIDEFKDRFRVGPICRVLAASLDCGSVTPRGYRMFRSRPVSRMAARHEALARDILEIHADFFMAVYGYRKTRAQLLARGWDPAEIGRDQ
VMNVMRESGIRGVRRGRTPVTTKPAKGTGGRPDLVERGFEAEAPNRLHVADITYVRMANGSFGYTAFAADVFARRIVGWACATTMDTRELPLQALEQAIS
WAASHGGADGLVHHSDHGAQYISLVYTTRVGEFGMLPSTGTVGDSYDNAMAESADGAYRTELVWRRKPFQDLRDLELATFRWVSWRGLEASAPVLGLQDT
GTDRNRVLCKPSGASRPTIRAEQKSGHI
TARPDTALMVAYIDEFKDRFRVGPICRVLAASLDCGSVTPRGYRMFRSRPVSRMAARHEALARDILEIHADFFMAVYGYRKTRAQLLARGWDPAEIGRDQ
VMNVMRESGIRGVRRGRTPVTTKPAKGTGGRPDLVERGFEAEAPNRLHVADITYVRMANGSFGYTAFAADVFARRIVGWACATTMDTRELPLQALEQAIS
WAASHGGADGLVHHSDHGAQYISLVYTTRVGEFGMLPSTGTVGDSYDNAMAESADGAYRTELVWRRKPFQDLRDLELATFRWVSWRGLEASAPVLGLQDT
GTDRNRVLCKPSGASRPTIRAEQKSGHI
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1281 bp | 427 aa | 59 | 1339 | + | Yes |
Chemistry : DDE
ORF sequence :
MAKGTRYTPEFKAKAVRLLTESRGSYSSETKAIEQVAKDPGVAPETLRRWRNKTDATVAAETKRSAEDAMAELKSLRAEVARLRRANEILTTASAFFRGT
ARPDTALMVAYIDEFKDRFRVGPICRVLAASLDCGSVTPRGYRMFRSRPVSRMAARHEALARDILEIHADFFMAVYGYRKTRAQLLARGWDPAEIGRDQV
MNVMRESGIRGVRRGRTPVTTKPAKGTGGRPDLVERGFEAEAPNRLHVADITYVRMANGSFGYTAFAADVFARRIVGWACATTMDTRELPLQALEQAISW
AASHGGADGLVHHSDHGAQYISLVYTTRVGEFGMLPSTGTVGDSYDNAMAESADGAYRTELVWRRKPFQDLRDLELATFRWVSWRGLEASAPVLGLQDTG
TDRNRVLCKPSGASRPTIRAEQKSGHI
ARPDTALMVAYIDEFKDRFRVGPICRVLAASLDCGSVTPRGYRMFRSRPVSRMAARHEALARDILEIHADFFMAVYGYRKTRAQLLARGWDPAEIGRDQV
MNVMRESGIRGVRRGRTPVTTKPAKGTGGRPDLVERGFEAEAPNRLHVADITYVRMANGSFGYTAFAADVFARRIVGWACATTMDTRELPLQALEQAISW
AASHGGADGLVHHSDHGAQYISLVYTTRVGEFGMLPSTGTVGDSYDNAMAESADGAYRTELVWRRKPFQDLRDLELATFRWVSWRGLEASAPVLGLQDTG
TDRNRVLCKPSGASRPTIRAEQKSGHI
Blast result :
Comments
The genome of NCC2705 have two copies of ISBlo10, both truncated by insertion of a mobile element of a new type (see ref). As ISBlo10b is only about 80% identical to ISBlo10a, it is debatable whether this is really the same element, but this is not fundamental since ISBlo10b is only partial.
The second ORF has no stop codon. An alignement with the transposase of IS3501 revealed a probable frameshift (379-1212)join(1211-1312) (PEP3).
Coordinates:
ISBlo10a (complement(320779..321776))join(complement(316965..317305))
ISBlo10b (complement(325435..326433))join(complement(321777..321958))
The second ORF has no stop codon. An alignement with the transposase of IS3501 revealed a probable frameshift (379-1212)join(1211-1312) (PEP3).
Coordinates:
ISBlo10a (complement(320779..321776))join(complement(316965..317305))
ISBlo10b (complement(325435..326433))join(complement(321777..321958))
References
1] Schell,M.A., Karmirantzou,M., Snel,B., Vilanova,D., Berger,B., Pessi,G., Zwahlen,M.-C., Desiere,F., Bork,P., Delley,M., Pridmore,D. and Arigoni,F. (2002) Proc. Natl. Acad. Sci. U.S.A. 99 (22), 14422-14427