ISPpu4
- Family IS3
- Group IS3
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| AJ233397 | ND | Pseudomonas putida | Pseudomonas putida P1 Pseudomonas migulae D2RT plasmid pD2RT |
DNA section
IS Length : 1663 bp
Ends
IR Length : 23/33
IRL : CCCCCGGTGTCAGGCTAGTTGTCGCCTGAGCTGATTTATCAAAACGATAG
IRR : GGCGTTTTGCAAGGTAGTTGTCGCGTCAGCTGTGTTTTTATGCGGCTATT
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| CACAGATTTC | GCGTACGGCA | 0 | |
| ACCATCCGTA | GACCCCCGGC | 0 |
DNA sequence
CCCCCGGTGTCAGGCTAGTTGTCGCCTGAGCTGATTTATCAAAACGATAGATCGGGGGCGCCAAAGAGAGCTGTAATGTCGAGCTATTCACCTGAGCGTA
AAGTGGCCCTTATCAACAAATTGCTGCCGCCTCAAAACATGTCCGTGGCCGAGTTGTCGCGTCAAGAAGGCATCTCTCAAGCCACCCTGTATGCTTGGCG
AACCAAGCTCAAAGCAGGAGGCGCAGTGGTGCCCGGAGATAAAAGCAGTGCCGATAACTGGTCGGCTGAAGCCAAGTTCGCAGCGGTGTTGCACACGGCC
ACGTTGAGCGAGATCGAGCTTAGCGAATACTGTCGCAGCAAGGGTTTGTACCCCGAGCAAATTGGCGCTTGGCGACAGGCCTGCATCAGTGGCCAGCTAA
CAGCCCAGGCACAGCGCCAGGCCGAGCGAGAACAGGCGCGCGCCGACAAAAAACGCATCGCCGAGTTGGAGCGTGAACTGCGGCGCAAGGACAAGGCGCT
CGCAGAAACCACCGCGATTCTGGTGCTGCGAAAAAGATGAATGCCTTCTGGGGAAACGACAGCGAGGACGTCTGACCTCGCTGCCAGAACGGCAACAACT
CGTTGAACGTTTTAACCAAGCCGTTGCTTCTGGTGCACGCAAAACTATTGCCAGCGCGGAGATCGGGCTGTCGCTGCGCAGCCTGCAACGCTGGGCGCTG
ACGCCTGTGATGCAGGCCGACGTGCGCACCACCACGTCACGTCCGCGACCACTTAATGCCCTGAGTGAACAGGAGCGTTGCGCTATTTTAGAGGTCTGCA
ACAGTCCGCCATTCGTCAGCCTGCCGCCCAGCCAGATCGTCCCGATACTGGCCGATCAAGGCCGTTATCTGGCCTCAGAGGCAACCTTTTACCGCGTCCT
GAAGGAAGCTGATCAGCAGCACCGACGTGGCCGCAGCCATGCACCGCACAAGCATGCTGCGCCGACAACTCACAGCGCAACCACAGCCAATAAGGTCTGG
TCTTGGGACATCACCTACTTGCCATCGCCAGTGCGTGGGAAGTACTACTATCTGTATTTGATCGAGGACATCTACAGCCGAAAGGCCGTGGGCTGGGAAG
TTTACGAGCAAGAAAGTGGCGAGCTGGCGGCCGAACTGATGCAGCGCACCGTGCTCACCGAACGCTGCGCCGGACGGCCCTTAGTGCTGCACTCGGACAA
CGGTGCACCGATGAAATCGGTGACGTTGCTGAGCAAACTGTACGAACTCGGCATCACCCCGTCACGCGGACGACCACGGGTGAGTAACGATAATCCCTAC
TCAGAATCGCTGTTTAGAACCCTGAAATATTGCCCGCAATGGCCTCCTGGTGGTTTTGCAGATTTGGACGCGGCACGCAGCTGGGTGCGCGATTTTATCC
GCTGGTACAACCACCACACCGCCACAGCCGCATCCGCTTCGTGACCCCGGCACAGCGTCATCGAGGCGAGGATCAAGAGATCTTAGCCAAGCGTCATGCG
CTGTATCAGCAAGCCCGCAATCAGCATCCACACCGCTGGTCGGGTGCGACACGCAATTGGCAGCCCATCGGTGCTGTCACACTCAATCCGGAAAGGGACT
TACCGACACTGAAAATAGCCGCATAAAAACACAGCTGACGCGACAACTACCTTGCAAAACGCC
AAGTGGCCCTTATCAACAAATTGCTGCCGCCTCAAAACATGTCCGTGGCCGAGTTGTCGCGTCAAGAAGGCATCTCTCAAGCCACCCTGTATGCTTGGCG
AACCAAGCTCAAAGCAGGAGGCGCAGTGGTGCCCGGAGATAAAAGCAGTGCCGATAACTGGTCGGCTGAAGCCAAGTTCGCAGCGGTGTTGCACACGGCC
ACGTTGAGCGAGATCGAGCTTAGCGAATACTGTCGCAGCAAGGGTTTGTACCCCGAGCAAATTGGCGCTTGGCGACAGGCCTGCATCAGTGGCCAGCTAA
CAGCCCAGGCACAGCGCCAGGCCGAGCGAGAACAGGCGCGCGCCGACAAAAAACGCATCGCCGAGTTGGAGCGTGAACTGCGGCGCAAGGACAAGGCGCT
CGCAGAAACCACCGCGATTCTGGTGCTGCGAAAAAGATGAATGCCTTCTGGGGAAACGACAGCGAGGACGTCTGACCTCGCTGCCAGAACGGCAACAACT
CGTTGAACGTTTTAACCAAGCCGTTGCTTCTGGTGCACGCAAAACTATTGCCAGCGCGGAGATCGGGCTGTCGCTGCGCAGCCTGCAACGCTGGGCGCTG
ACGCCTGTGATGCAGGCCGACGTGCGCACCACCACGTCACGTCCGCGACCACTTAATGCCCTGAGTGAACAGGAGCGTTGCGCTATTTTAGAGGTCTGCA
ACAGTCCGCCATTCGTCAGCCTGCCGCCCAGCCAGATCGTCCCGATACTGGCCGATCAAGGCCGTTATCTGGCCTCAGAGGCAACCTTTTACCGCGTCCT
GAAGGAAGCTGATCAGCAGCACCGACGTGGCCGCAGCCATGCACCGCACAAGCATGCTGCGCCGACAACTCACAGCGCAACCACAGCCAATAAGGTCTGG
TCTTGGGACATCACCTACTTGCCATCGCCAGTGCGTGGGAAGTACTACTATCTGTATTTGATCGAGGACATCTACAGCCGAAAGGCCGTGGGCTGGGAAG
TTTACGAGCAAGAAAGTGGCGAGCTGGCGGCCGAACTGATGCAGCGCACCGTGCTCACCGAACGCTGCGCCGGACGGCCCTTAGTGCTGCACTCGGACAA
CGGTGCACCGATGAAATCGGTGACGTTGCTGAGCAAACTGTACGAACTCGGCATCACCCCGTCACGCGGACGACCACGGGTGAGTAACGATAATCCCTAC
TCAGAATCGCTGTTTAGAACCCTGAAATATTGCCCGCAATGGCCTCCTGGTGGTTTTGCAGATTTGGACGCGGCACGCAGCTGGGTGCGCGATTTTATCC
GCTGGTACAACCACCACACCGCCACAGCCGCATCCGCTTCGTGACCCCGGCACAGCGTCATCGAGGCGAGGATCAAGAGATCTTAGCCAAGCGTCATGCG
CTGTATCAGCAAGCCCGCAATCAGCATCCACACCGCTGGTCGGGTGCGACACGCAATTGGCAGCCCATCGGTGCTGTCACACTCAATCCGGAAAGGGACT
TACCGACACTGAAAATAGCCGCATAAAAACACAGCTGACGCGACAACTACCTTGCAAAACGCC
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 | |
|---|---|---|---|---|---|
| 465 bp | 154 aa | 76 | 540 | + | No |
Description : First part of the transposase
ORF sequence :
MSSYSPERKVALINKLLPPQNMSVAELSRQEGISQATLYAWRTKLKAGGAVVPGDKSSADNWSAEAKFAAVLHTATLSEIELSEYCRSKGLYPEQIGAWR
QACISGQLTAQAQRQAEREQARADKKRIAELERELRRKDKALAETTAILVLRKR
QACISGQLTAQAQRQAEREQARADKKRIAELERELRRKDKALAETTAILVLRKR
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1223 bp | 414 aa | 401 | 1623 | + | No |
Description : Second part of the transposase
ORF sequence :
QPRHSARPSENRRAPTKNASPSWSVNCGARTRRSQKPPRFWCCEKDECLLGKRQRGRLTSLPERQQLVERFNQAVASGARKTIASAEIGLSLRSLQRWAL
TPVMQADVRTTTSRPRPLNALSEQERCAILEVCNSPPFVSLPPSQIVPILADQGRYLASEATFYRVLKEADQQHRRGRSHAPHDAKHAAPTTHSATTANK
VWSWDITYLPSPVRGKYYYLYLIEDIYSRKAVGWEVYEQESGELAAELMQRTVLTERCAGRPLVLDAHSDNGAPMKSVTLLSKLYELGITPSRGRPRVSN
DNPYSESLFRTLKYCPQWPPGGFADLDAARSWVRDFIRWYNHHHRHSDARIRFVTPAQRHRGEDQEILAKRHALYQQARNQHPHRWSGATRNWQPIGAVT
LNPERDLPTLKIAA
TPVMQADVRTTTSRPRPLNALSEQERCAILEVCNSPPFVSLPPSQIVPILADQGRYLASEATFYRVLKEADQQHRRGRSHAPHDAKHAAPTTHSATTANK
VWSWDITYLPSPVRGKYYYLYLIEDIYSRKAVGWEVYEQESGELAAELMQRTVLTERCAGRPLVLDAHSDNGAPMKSVTLLSKLYELGITPSRGRPRVSN
DNPYSESLFRTLKYCPQWPPGGFADLDAARSWVRDFIRWYNHHHRHSDARIRFVTPAQRHRGEDQEILAKRHALYQQARNQHPHRWSGATRNWQPIGAVT
LNPERDLPTLKIAA
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1548 bp | 523 aa | 76 | 1623 | + | Yes |
Chemistry : DDE
ORF sequence :
MSSYSPERKVALINKLLPPQNMSVAELSRQEGISQATLYAWRTKLKAGGAVVPGDKSSADNWSAEAKFAAVLHTATLSEIELSEYCRSKGLYPEQIGAWR
QACISGQLTAQAQRQAEREQARADKKNASPSWSVNCGARTRRSQKPPRFWCCEKDECLLGKRQRGRLTSLPERQQLVERFNQAVASGARKTIASAEIGLS
LRSLQRWALTPVMQADVRTTTSRPRPLNALSEQERCAILEVCNSPPFVSLPPSQIVPILADQGRYLASEATFYRVLKEADQQHRRGRSHAPHDAKHAAPT
THSATTANKVWSWDITYLPSPVRGKYYYLYLIEDIYSRKAVGWEVYEQESGELAAELMQRTVLTERCAGRPLVLDAHSDNGAPMKSVTLLSKLYELGITP
SRGRPRVSNDNPYSESLFRTLKYCPQWPPGGFADLDAARSWVRDFIRWYNHHHRHSDARIRFVTPAQRHRGEDQEILAKRHALYQQARNQHPHRWSGATR
NWQPIGAVTLNPERDLPTLKIAA
QACISGQLTAQAQRQAEREQARADKKNASPSWSVNCGARTRRSQKPPRFWCCEKDECLLGKRQRGRLTSLPERQQLVERFNQAVASGARKTIASAEIGLS
LRSLQRWALTPVMQADVRTTTSRPRPLNALSEQERCAILEVCNSPPFVSLPPSQIVPILADQGRYLASEATFYRVLKEADQQHRRGRSHAPHDAKHAAPT
THSATTANKVWSWDITYLPSPVRGKYYYLYLIEDIYSRKAVGWEVYEQESGELAAELMQRTVLTERCAGRPLVLDAHSDNGAPMKSVTLLSKLYELGITP
SRGRPRVSNDNPYSESLFRTLKYCPQWPPGGFADLDAARSWVRDFIRWYNHHHRHSDARIRFVTPAQRHRGEDQEILAKRHALYQQARNQHPHRWSGATR
NWQPIGAVTLNPERDLPTLKIAA
Blast result :
Comments
Two copies of ISPpu4 flank the alk gene clusters of Pseudomonas putida P1. The ends of the insertion sequence could not be identified unambiguously, as the homology between ISPpu4 and IS1240 extends several bases beyond the inverted repeats, and direct repeats could not be identified. Southern blots indicate that other copies are present as well. ORF2 has a frameshift in a series of histidine codons. The sequence at the likely location of the frameshift is repetitive (CAACCACCACACC), and a shift to the -1 phase in this sequence would allow the synthesis of the full length protein.
ISPpu4 (ORF B) is 81% aa similar to IS1240 and 54% to IS1141.
File updated: September 19 2013. Extremities were modified, the proposed ends for this sequence are based on the similarities with closely relative elements.
ISPpu4 (ORF B) is 81% aa similar to IS1240 and 54% to IS1141.
File updated: September 19 2013. Extremities were modified, the proposed ends for this sequence are based on the similarities with closely relative elements.
References