ISPst4
- Family IS3
- Group IS51
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| AY894751 | Y | Pseudomonas stutzeri | Pseudomonas stutzeri Q |
DNA section
IS Length : 1312 bp
Ends
IR Length : 27
IRL : TGAATCACCCCGGGTTTCGTGGAGGCCTCAACTCTTGAGAAGATGAGGCC
IRR : TGAATCGCCCCGGGTTTTGTGGAGGCCGTTTCGTTTAAGTCAGGCCGCCA
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| GATAATCTCA | TGA | CCAAAATCCC | 3 |
| TCCACTGAGC | GTC | AGACCCCGTA | 3 |
| CTACAAGCCA | TCC | GTCGACTTGC | 3 |
DNA sequence
TGAATCACCCCGGGTTTCGTGGAGGCCTCAACTCTTGAGAAGATGAGGCCATGAGAAAGACTACTACCTACTCCCCTGAAGTCCGTGAGCGTGCTGTGCG
CATGGTTCTGGAACACCTGAACGACTATCCGTCCGAGTGGGCAGCCATTGAGGCCATCGCTCCGAAGATTGGCTGTGCCGCGCAAACCCTGCATGGCTGG
ATTCGTCGCCAGCAGACCGATGCGGGGCAGCGCCCCGGTCAGACCAGTGAAGAGCGCGAGCGCATCAGAGCCCTAGAGCGCGAAAACCGCGAACTGCGTA
AGGCAAACGAGATATTGCGCCTGGCCAGTGCGTATTTTGCCCAGGCGGAGCTCGACCGCCGCACCAAGTCCTGAGGGCGTTTGTCGATCAGCATCGTGAC
CGTCTCGGGGTCGAGTCGATCTGCCGCGTGTTGCAGATCGCCCCGTCCGGTTACCGCAGGCACGTGGCTCAACAGCGCAACCCGGCACTGCGCTGTTGTC
GTGCTCAGCGCGATGACGCATTGACCCTGGAAATCCAGCGAGTGTGGGATGCCAATATGCAGTGCTATGGCGCGGTGAAGGTCTGGAAGCAGCTGCGGCG
AGAAGGCATCGAGGTCGCCAGATGCACGGTGGAGCGGTTAATGCGTCGGGCCGGATTGCAGGGCATTAGACGTGGCCAGATCGTGCAGACAACGGTGGCC
GGCGACAAGGCCCTTTGCCCGCTGGATCGTGTCCAACGCCAGTTCCATGCCGACCGCCCGAACCAGTTGTGGGTGTCGGACTTCACCTATGTATCGACCT
GGCAGGGCTGGCTGTACGTGGCGTTCGTGATCGACGTCTTTGCACGGCGGATCGTCGGCTGGCGAGTCAGTACCAGCATGAAGACAGACTTCGTACTGGA
TGCCCTAGAGCAAGCCTTGTATGCCCGTCAGCCGCATTGCTCGGGTGGTCTGATCCATCACAGCGACCGTGGAAGCCAGTACGTCTCGATCCGCTATACC
GAACGGCTGGCAGAGGCCGGCATTGAGCCTTCGGTTGGCAGCAAGGGAGACAGCTACGACAACGCCTTGGCCGAAACCATCAACGGGTTGTACAAGGCCG
AGCTGATTTACCGTCAGTCATGGAAGAGCCGCGAAGCCGTCGAAATGGCGACTTTGAAATGGGTGCACTGGTACAACCACCAACGCCTGCTGAGCTCAAT
CGGATATATCCCGCCTGCGGAGGCTGAGGCAAACTTCCACCAGCAACAAGCAGGTCAGGCCATGGCGGCCTGACTTAAACGAAACGGCCTCCACAAAACC
CGGGGCGATTCA
CATGGTTCTGGAACACCTGAACGACTATCCGTCCGAGTGGGCAGCCATTGAGGCCATCGCTCCGAAGATTGGCTGTGCCGCGCAAACCCTGCATGGCTGG
ATTCGTCGCCAGCAGACCGATGCGGGGCAGCGCCCCGGTCAGACCAGTGAAGAGCGCGAGCGCATCAGAGCCCTAGAGCGCGAAAACCGCGAACTGCGTA
AGGCAAACGAGATATTGCGCCTGGCCAGTGCGTATTTTGCCCAGGCGGAGCTCGACCGCCGCACCAAGTCCTGAGGGCGTTTGTCGATCAGCATCGTGAC
CGTCTCGGGGTCGAGTCGATCTGCCGCGTGTTGCAGATCGCCCCGTCCGGTTACCGCAGGCACGTGGCTCAACAGCGCAACCCGGCACTGCGCTGTTGTC
GTGCTCAGCGCGATGACGCATTGACCCTGGAAATCCAGCGAGTGTGGGATGCCAATATGCAGTGCTATGGCGCGGTGAAGGTCTGGAAGCAGCTGCGGCG
AGAAGGCATCGAGGTCGCCAGATGCACGGTGGAGCGGTTAATGCGTCGGGCCGGATTGCAGGGCATTAGACGTGGCCAGATCGTGCAGACAACGGTGGCC
GGCGACAAGGCCCTTTGCCCGCTGGATCGTGTCCAACGCCAGTTCCATGCCGACCGCCCGAACCAGTTGTGGGTGTCGGACTTCACCTATGTATCGACCT
GGCAGGGCTGGCTGTACGTGGCGTTCGTGATCGACGTCTTTGCACGGCGGATCGTCGGCTGGCGAGTCAGTACCAGCATGAAGACAGACTTCGTACTGGA
TGCCCTAGAGCAAGCCTTGTATGCCCGTCAGCCGCATTGCTCGGGTGGTCTGATCCATCACAGCGACCGTGGAAGCCAGTACGTCTCGATCCGCTATACC
GAACGGCTGGCAGAGGCCGGCATTGAGCCTTCGGTTGGCAGCAAGGGAGACAGCTACGACAACGCCTTGGCCGAAACCATCAACGGGTTGTACAAGGCCG
AGCTGATTTACCGTCAGTCATGGAAGAGCCGCGAAGCCGTCGAAATGGCGACTTTGAAATGGGTGCACTGGTACAACCACCAACGCCTGCTGAGCTCAAT
CGGATATATCCCGCCTGCGGAGGCTGAGGCAAACTTCCACCAGCAACAAGCAGGTCAGGCCATGGCGGCCTGACTTAAACGAAACGGCCTCCACAAAACC
CGGGGCGATTCA
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 | |
|---|---|---|---|---|---|
| 322 bp | 107 aa | 53 | 374 | + | No |
Description : First part of the transposase
ORF sequence :
MRKTTTYSPEVRERAVRMVLEHLNDYPSEWAAIEAIAPKIGCAAQTLHGWIRRQQTDAGQRPGQTSEERERIRALERENRELRKANEILRLASAYFAQAE
LDRRTKS
LDRRTKS
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 972 bp | 323 aa | 302 | 1273 | + | No |
Description : Second part of the transposase
ORF sequence :
GKRDIAPGQCVFCPGGARPPHQVLRAFVDQHRDRLGVESICRVLQIAPSGYRRHVAQQRNPALRCCRAQRDDALTLEIQRVWDANMQCYGAVKVWKQLRR
EGIEVARCTVERLMRRAGLQGIRRGQIVQTTVAGDKALCPLDRVQRQFHADRPNQLWVSDFTYVSTWQGWLYVAFVIDVFARRIVGWRVSTSMKTDFVLD
ALEQALYARQPHCSGGLIHHSDRGSQYVSIRYTERLAEAGIEPSVGSKGDSYDNALAETINGLYKAELIYRQSWKSREAVEMATLKWVHWYNHQRLLSSI
GYIPPAEAEANFHQQQAGQAMAA
EGIEVARCTVERLMRRAGLQGIRRGQIVQTTVAGDKALCPLDRVQRQFHADRPNQLWVSDFTYVSTWQGWLYVAFVIDVFARRIVGWRVSTSMKTDFVLD
ALEQALYARQPHCSGGLIHHSDRGSQYVSIRYTERLAEAGIEPSVGSKGDSYDNALAETINGLYKAELIYRQSWKSREAVEMATLKWVHWYNHQRLLSSI
GYIPPAEAEANFHQQQAGQAMAA
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1221 bp | 407 aa | 53 | 1273 | + | Yes |
Chemistry : DDE
ORF sequence :
MRKTTTYSPEVRERAVRMVLEHLNDYPSEWAAIEAIAPKIGCAAQTLHGWIRRQQTDAGQRPGQTSEERERIRALERENRELRKANEILRLASAYFCPGG
ARPPHQVLRAFVDQHRDRLGVESICRVLQIAPSGYRRHVAQQRNPALRCCRAQRDDALTLEIQRVWDANMQCYGAVKVWKQLRREGIEVARCTVERLMRR
AGLQGIRRGQIVQTTVAGDKALCPLDRVQRQFHADRPNQLWVSDFTYVSTWQGWLYVAFVIDVFARRIVGWRVSTSMKTDFVLDALEQALYARQPHCSGG
LIHHSDRGSQYVSIRYTERLAEAGIEPSVGSKGDSYDNALAETINGLYKAELIYRQSWKSREAVEMATLKWVHWYNHQRLLSSIGYIPPAEAEANFHQQQ
AGQAMAA
ARPPHQVLRAFVDQHRDRLGVESICRVLQIAPSGYRRHVAQQRNPALRCCRAQRDDALTLEIQRVWDANMQCYGAVKVWKQLRREGIEVARCTVERLMRR
AGLQGIRRGQIVQTTVAGDKALCPLDRVQRQFHADRPNQLWVSDFTYVSTWQGWLYVAFVIDVFARRIVGWRVSTSMKTDFVLDALEQALYARQPHCSGG
LIHHSDRGSQYVSIRYTERLAEAGIEPSVGSKGDSYDNALAETINGLYKAELIYRQSWKSREAVEMATLKWVHWYNHQRLLSSIGYIPPAEAEANFHQQQ
AGQAMAA
Blast result :
Comments
ISPst4 was detected after transposition into a pUC-based plasmid which replicates (albeit poorly) in P.stutzeri strain Q. In two of three cases, ISPst4 transposed immediately upstream of the pUC origin of replication in the construct, leading us to believe that the IS activates this origin and stabilises the plasmid in P.stutzeri.
ISPst4 is 83% (ORF1) and 87% (ORF 2) aa simialr to IS401
ISPst4 is 83% (ORF1) and 87% (ORF 2) aa simialr to IS401
References
1] Nick Coleman (2005) Direct submission