ISfinder Mirror Site

ISPsy4

Family IS21
Group

MGE type ISRelated element(s) :
Isoform Synonym(s)

Accession number	Transposition	Origin	Host
AE016853	ND	Pseudomonas syringae	Pseudomonas syringae DC3000

DNA section

IS Length : 1962 bp

Ends

IR Length : 23/29

IRL : TGTCACCGCCACTGTAAAAATGACCCCCTAACGCCAACCTAGAATTGACC
IRR : TGTCAACGCCAACTAAAAAGTGACCCCCTTCCGTGCTAAATCGCCAACTT

Insertion site

Left flank	Direct repeat	Right flank	DR Length
GGTGAGCGCC	ATTGGT	TGCCTTATCA	6
AGTACCGTCA	GCCAAG	GCCAGCTTGC	6
GGCCTGAGGG	GTTAGC	TGAAGCCATC	6
CCAGGATGGA	TATGGG	TTTCGACTTG	6
CACACTCGGC	CCTACG	TCATACAACA	6
ACCTTGCTAA	ATAAAT	ATTATTATTT	6
CAAGACAGTA	CGTAGT	GGGACAGACG	6
GACACTAACT	CATGGT	GCATATAAGG	6
GCCGATGTCT	CGGAGT	AGAGCTAATG	6
CTTGCAGGGC	AAGTGG	TTCAGAAAAG	6
TGTCCTGTTT	GTTGGG	GCGCATTTCA	6
TAAATCCGTC	TGAAAG	GCGGGACTGG	6
TGTCCGGCCT	CATAGA	TAAAGTCTTT	6
CAATCTCTCC	CCTGAG	CAACGAAGCG	6
ATCAGAATGG	CATAGC	TACGCTTACC	6
ACCTGGCCTG	TCTACG	CCATGACGTT	6
CGTTATCACC	AATAAT	TGGCCTACCA	6
GGTGGCATCG	ACGATG	GTGCCCTGGC	6
ACGCGGGGCT	GGTAGG	TAGCTGTTTG	6
ACTGTTCGAG	CCTACC	CAGTTTTTGG	6
ATATTCACAT	CCTGAG	ACGTACATTA	6
TGCCGCGACG	AATCAC	TAGCACGCCA	6

DNA sequence

TGTCACCGCCACTGTAAAAATGACCCCCTAACGCCAACCTAGAATTGACCCCCCTGGGTAAAACTGGCGGCTTTGAGCTGCCAATATGTTGACCCAGGAG
CAGTCTGTGGAAATTAAAGTGTTGGCCCGTCAGGGCCATGGCATCAAATTCATCGCCCGTGAGCTGGGTATTTCGCGTAACACCGTGCGCAAGTACCTGC
GAAAGGCCCGGTCGCTACCCAGTGACAAGGTGAGACCCGCACGTCCGTGCAAAATCGACCCCTTCAAGGACTACCTGCACGAGCGTATTGAGGCGGCGCG
CCCACACTGGATTCCGGCGACCGTCCTGCTGCGTGAGATCACGGCATTGGGGTACAGCGGCGGCGTCAGTCGTCTGAAGGCTTATATTCGCCCCTTCAAA
CGTAAGGCAGAAGAGCCGGTGGTACGTTTCGAGACACTGCCCGGCAAGCAGATACAGGTGGACTTCACCACCATTCGACGAGGCCGTCAGCCGCTTAAGG
CGTTCGTGGCGACACTTGGTTTTAGTCGAGCAAGCTTTGTCCGTTTCTCCGAGCGAGAGGACAGCGAAGCCTGGCTGACAGGGCTTCGGGAGGCGTTCGC
TTACTTTGGCGGCGTGCCCGAGCAGGCATTGTTTGATAACGCCGGAACCATCATCACCGAGCGAGATGCTTTTGGGGAGGGCCAGCACCGTTGGCATCCC
CGATTGGCTGCGCTGGCCGATGAGTTTGGTTTTATTCCCAAGGTCTGCCGCCCTTACCGTGCCCAGACCAAGGGCAAGGTTGAGCGCTTCAACGGGTATC
TGAAGGGCAGTTTCATTACCCCGTTGGCCGCTACGCTCAAGAGTGCGGGTCTGACGCTGGATGTGGTGACGGCCAACGCACATATCGGCCAATGGCTCGA
CGAAGTCGCTCATCAGCGGATTCACGGCACGACGGGTGTTCAACCGGCGGTACGTCTGGCCCAAGAGCAGCAGGTACTATTACCACTGCCAACACAGAGC
CTGCGCCCACAACCCGCCCAAGGCCTACGCCTGGGACGGGTCCTGCCGTACGAGAGCTTGCAGCATCCGCTGTCGGTTTATGAGCAACTGCTGGAGGTGA
GAGCATGAACCTTCAACATGCTCGCCTGACAGAACTATGCAAGGGGCTAAAGCTTGAGCGCGTCGGGGTGGACTGGCCGCACCTGGCCCAACAAGCAGCA
AGCGGCGAAGACAGCTTTGCCGACTTCCTCGAAAAGCTGCTGGCTGCCGAGACCGATGCCCGAAGTGAACGCTCTCGACAGGCCCTGCTGAAAACTGCCG
CGCTGCCCGCTGTGAAAACGCTGGAGCAATACGACTTCGCGTTTGCCACCGGCGTCCCCCGGGCACAGCTCCAGGAGCTGGCAGCACTGAGTTTTGTTGG
ACGTGCCGAGAACATCGTGTTCCTGGGGCCTAGTGGTGTAGGCAAGAGCCACCTGGCTATCGCCCTGGCCTACCGGGCAGTGATGGCCGGTATCAAAACC
CGCTTCGTCACGGCGGCTGACTTGATGCTGCAACTGACCGCTGCGCACCGCCAGGAACGGCTCAAGGAATACTTCAGTCGTGTGGTGATGGCCCCTGGGT
TGTTGGTCATCGATGAAATCGGCTACCTGCCGTTTGGTCGTGATGAAGCCAACCTGTTCTTCAATGTTGTCGCCAAGCGCTACGAGCAAGGCAGCCTGAT
CCTCACGAGTAACTTGCCGTTTACCCAGTGGGCCGGAACCTTTGCGGATGATCAAACACTGACAGCGGCCATGCTGGACAGGCTGTTACATCATGCCCAT
ATCGTGCAGATGACAGGTGAAAGCTATCGACTCAAGGACAAGCGCAAAGCAGGAACCAAATCTTCTCGGGCCGAACCGGCTCGAAAATATGAACCCGAGG
GGGGTCAAAACTAAGTTGGCGATTTAGCACGGAAGGGGGTCACTTTTTAGTTGGCGTTGACA

Protein section

ORF number : 2

ORF 1

Length		Begin	End	Strand	Fusion ORF
1023 bp	340 aa	86	1108	+	No

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MLTQEQSVEIKVLARQGHGIKFIARELGISRNTVRKYLRKARSLPSDKVRPARPCKIDPFKDYLHERIEAARPHWIPATVLLREITALGYSGGVSRLKAY
IRPFKRKAEEPVVRFETLPGKQIQVDFTTIRRGRQPLKAFVATLGFSRASFVRFSEREDSEAWLTGLREAFAYFGGVPEQALFDNAGTIITERDAFGEGQ
HRWHPRLAALADEFGFIPKVCRPYRAQTKGKVERFNGYLKGSFITPLAATLKSAGLTLDVVTANAHIGQWLDEVAHQRIHGTTGVQPAVRLAQEQQVLLP
LPTQSLRPQPAQGLRLGRVLPYESLQHPLSVYEQLLEVRA

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
658 bp	218 aa	1105	1762	+	No

ORF function : Accessory Gene
AG : IS21 helper

ORF sequence :

MNLQHARLTELCKGLKLERVGVDWPHLAQQAASGEDSFADFLEKLLAAETDARSERSRQALLKTAALPAVKTLEQYDFAFATGVPRAQLQELAALSFVGR
AENIVFLGPSGVGKSHLAIALAYRAVMAGIKTRFVTAADLMLQLTAAHRQERLKEYFSRVVMAPGLLVIDEIGYLPFGRDEANLFFNVVAKRYEQGSLIL
TSNLPFTQWAGTFADDQT

Blast result :

Comments

There are 22 copies of ISPsy4 in the chromosome of this strain, one of which is disrupted by an insertion sequence. There is one truncated copy in plasmid 1 and one intact copy in plasmid 2. Only one of the intact copies, which is located in the chromosome, lacks a target site duplication.
ISPsy23 name is also used to define partial ISPsy4 in the genome (only istB).

References

1] Buell,C.R., Joardar,V., Lindeberg,M., Selengut,J., Paulsen,I.T.,Gwinn,M.L., Dodson,R.J., Deboy,R.T., Durkin,A.S., Kolonay,J.F., Madupu,R., Daugherty,S., Brinkac,L., Beanan,M.J., Haft,D.H., Nelson,W.C., Davidsen,T., Zafar,N., Zhou,L., Liu,J., Yuan,Q., Khouri,H., Fedorova,N., Tran,B., Russell,D., Berry,K.,Utterback,T., Van Aken,S.E., Feldblyum,T.V., D'Ascenzo,M., Deng,W.L., Ramos,A.R., Alfano,J.R., Cartinhour,S., Chatterjee,A.K., Delaney,T.P., Lazarowitz,S.G., Martin,G.B., Schneider,D.J., Tang,X., Bender,C.L., White,O., Fraser,C.M. and Collmer,A. (2003) PNAS, 100 (18), 10181-10186 .