ISPlu22

  • Family ISNCY
  • Group ISPlu15
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
BX470251 ND Photorhabdus luminescens
Photorhabdus luminescens
DNA section
IS Length : 1547 bp

Ends


IR Length : none

IRL : CAAAATCCATTGTAAATTTTTCTTCTAATGAGAGTGGCAATTATTATGTG
IRR : ACGAACTCTGTTCGGATGCCAAAATCAGTAATAAAAGGTCACATCAGGCA

Insertion site


Left flankDirect repeatRight flankDR Length
GTAGGGTTTTAGGAACCCCTTTGT0
GTAGGGTTTTAGGACACCCTTTAT0
TTTTGTTGCTGCAAAAAAGCAAAC0
GTCTCGTACCATTATAACTTTTAA0

DNA sequence

CAAAATCCATTGTAAATTTTTCTTCTAATGAGAGTGGCAATTATTATGTGAGTCCAAGATTAACAGAAATATAAATAATCGATATTTTGATAACGGGATT
ATTATTATTCGAATACAAGTTAAAAACTCATTTAAATAAATGGCTTTCATTGAATGGTTGTTGTAAATATAATGTTTTCTCTTTTTTTCTTTTCTGATAT
TTGGTTCTTTAGGCTCTTCTATTAATGCATTCGGTAAAGATTTGCCTGAGAAAATATGGGAAGATGTTTTTTGTAGCTTGGTAGAAATACTATAAATGGT
AATGACTAACTAATAATACAGAGAAACAGATTGTGGCAAAGAAAGAAAAACGGCCTCACCATGACGGATTATTTAAATATTTTTTAACGCAGCCTGAAAC
GGCCAGAGAGTTTCTATCCCTTTATTTGCCCGAAGAAATCCAGTTGTTGTGTGATTTAGCCACATTGAAACTGGAGCCCGGCAGTTTTGTGGATGAGCAT
TTACGTCAACTGCACAGTGATGTGTTGTACTCGGTCGAAACGGCCCGGGGACAGGGCTATATCTATTGCCTGATTGAACATCAGTCCACCCCTGACCCGT
TAATGGCCTGGCGGCTGATGTATTATGCCATGTTAGCCATGGCGGCTCACCTGAAAAAAGGCCATACTGAACTCCCGTTGGTGGCACCTCTGCTGTTTTA
TCATGGTGAGATTCGGCCGTATCCTTACTCAAACCGGTGGCTGGATTGTTTCACGCTCCCCGAACAGGCGGCTCGCTTATACCGTCAGGCGTTTCCGTTG
GTGGACGTCAGTGTGCTCAGCGATGAAGAGATCCTGACGCATAAAGGGGTTGCCCTGATGGAGCTGGTGCAAAAACATATTCGCTGTCGGGATATGCAGG
AATGGCTCCTCCAATTGGTGGAACTCTTGAATGCAGGGTATAATACAACCGAGCAGCTCAATGTGGTGTTACTCTATATTTTACTGAATGGACATACGCT
GGATCTCTCACATTTTGTCCATCAACTGATTGAACAATCTCCGGAGCATGAAACGATGTTGATGACTATTGCAGAACAGCTTGAACAAAAAGGGCTTGAG
CGAGGTATCAAGCAAGGTATTGAGCTAGGTCGAGAGGAAGGTCGAGAAGAAGGCCGAGAGGAAGGTAAACTGGAAACGGCTTGTGCCTTATTACGGCATG
GCGTGAGTTTGGACATTATTGTCACCAGTACCGGCCTGAGCCGGGATAAAATCGAAGCGTTAAAGCATTAAATTAATCTCCTCTTTCACAGCAAAATGCC
GATATTCAAGTTCGGCATTTTTGTTCTTATTCAGGATGATGGTTATACAAGGGATTTTTACGTTTGCCCGGCGAAGCTGAAACCTATCAGACGGAAGCAG
CTTTATAGGGGCCATAAGAGCATGGGGAACGCGATTAAGTGAGTTGTTTGCGGAAACAAATAACTCGTTCTGTTTCGTCAAAACCTCAATGTTCATGTGC
CTGATGTGACCTTTTATTACTGATTTTGGCATCCGAACAGAGTTCGT
Protein section
ORF number : 1

 

ORF 1
LengthBeginEndStrandFusion ORF
939 bp312 aa3331271+No
ORF function : Transposase
Description :

ORF sequence :

MAKKEKRPHHDGLFKYFLTQPETAREFLSLYLPEEIQLLCDLATLKLEPGSFVDEHLRQLHSDVLYSVETARGQGYIYCLIEHQSTPDPLMAWRLMYYAM
LAMAAHLKKGHTELPLVAPLLFYHGEIRPYPYSNRWLDCFTLPEQAARLYRQAFPLVDVSVLSDEEILTHKGVALMELVQKHIRCRDMQEWLLQLVELLN
AGYNTTEQLNVVLLYILLNGHTLDLSHFVHQLIEQSPEHETMLMTIAEQLEQKGLERGIKQGIELGREEGREEGREEGKLETACALLRHGVSLDIIVTST
GLSRDKIEALKH

 

Blast result :
Comments
The transposase is plu1611.
There are 6 copies of this element in the genome, of which 4 are complete.
In several copies, the region between the stop codon and the 3pr end contains a region with high similarity to the C-term coding region of the transposase, which, however it truncated at the N-terminus (pseudocoding region)

note to ISFinder staff:
- there are 6 copies of this element in the genome, which allowed to identify
meaningful termini by homology consideration
- I want to confirm that two copies have an identical left flanking sequence
- in addition to the 6 copies, there is a 7th element which is closely
related ca 90% seq_id) but also incomplete at the 3pr end
- the transposases encoded in this element show ca 50% seq_id to the
transposase of ISPlu15
- as mentioned in my feedback from 5-JUL-2016, ISPlu15 is INCOMPLETE
in ISFinder! The element covers only the N-term (highly conserved)
part of the transposase; the well-conserved but short C-term part and
the rather variable linker region are missing from ISPlu15
- for ISPlu15 you mention three complete elements; there are ISPlu15 itself
plus a "complete" close homolog plus another close homolog with certainly
is incomplete at the 3pr end
- in the comment above it is mentioned that many copies of this element
contain a pseudocoding region which is a highly conserved duplication of
the C-terminal coding region but being truncated at the N-terminus.
also, ISPlu15 contains such a pseudocoding region
- ISPlu15 and its "complete" close homolog do not show extended similarity
beyond the stop codon of the pseudocoding region. Thus, the 3pr end
of these elements cannot be delineated. Thus, the stop codon of the
pseudocoding region has currently to be considered the end of the
element. Up to that position, ISPlu15 is 1410 bp long.
- at the 5pr end, the two related elements show similarity for ca 100 bp
upstream of the element start defined in ISFinder for ISPlu15. Thus,
the 5pr terminus has to be considered questionable. Unfortunately, I was
not able to define the 5pr end
- the termini of ISPlu22 seem unrelated to those of ISPlu15
References
1] Pfeiffer F. (2017) Direct submission to ISfinder
1] Duchaud,E., Rusniok,C., Frangeul,L., Buchrieser,C., Taourit,S., Bocs,S., Boursaux-Eude,C., Chandler,M., Dassa,E., Derose,R., Derzelle,S., Freyssinet,G., Gaudriault,S., Givaudan,A., Glaser,P., Medigue,C., Lanois,A., Powell,K., Siguier,P., Wingate,V., Zouine,M., Boemare,N., Danchin,A. and Kunst,F. (2003) Nat. Biotechnol. 11: 1307-1313