ISfinder Mirror Site

ISCph1

Family IS630
Group

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

Accession number	Transposition	Origin	Host
NC_010831	ND	Chlorobium phaeobacteroides	Chlorobium phaeobacteroides BS1

DNA section

IS Length : 1216 bp

Ends

IR Length : 14/16

IRL : GTGTCACGTCACGCATGTAAAGTCGCATAAATAGCCATATATTGTTCTTC
IRR : CTGTCATGTCACGCATCAACTGACGGATAAAGGTGTTTGAGCTTGATTCG

Insertion site

Left flank	Direct repeat	Right flank	DR Length
CATATCACAG	TA	GTTTATTTTA	2

DNA sequence

GTGTCACGTCACGCATGTAAAGTCGCATAAATAGCCATATATTGTTCTTCATAATCAACCATAGGAGGATTGAATATGAAGAAGTACAAAGTCACCCTGA
CCGAGGAAGAACGACAAGAGCTTGATGCTCTGAGCAGTAAAGGAAAACACGCAGCACAAACTGTTTTGAATGCATTGATCCTGCTGGCCTGTGATGAGGG
CAAATTCCAGAAAGAGCGGTCAATCAATGAAGACATTGCACGGGTGCTGAACATCAGCATGAAGACGATTGACCGGGTAAAAAAGCGATTCGTGGAAGAA
GGCCTCAGCATGGCCCTTACCGGTAAGCCGTCCACACGGGTGTATAGTCGAAAAGCCGATGGAGATCTGGAAGCACACCTGGTAGCCTTGAGTTGCTCGG
AACCACCGGAAGGGCATCTGCGCTGGACCTTGAGGTTGCTTGCCGATAAGGCGGTAGAACTAAACTATGTCGAGAATATCTCTTACGAAACCGTACGCAG
GACTTTAAAAAAAACGTCCTTAAGCCATGGAAGCAAGTCGGCTGGGTGATTCCACCACTGCATGATGGCAATTTCGTGGCTCATATGGAGATGGTGCTGG
ATACCTATAAGCAGCCCTATGATCCTCTGTATCCCGTGGTCTGTATGGATGAATCGCCCAAGCAGTTGATAGCCGAAACGAGAATGCCGGTACCGGCACG
ACCCGGCCAGCTGGCCCGATATGATTATGAATACAGCCGGAAAGGCACGTGTAATATTTTTATCGCCAATGAACCGTTAGTCGGAAAACGAATGGTCAAG
GTGACCTCCAGCAGGAAAAAGGATGACTGGGCCCGGTTCCTTGCAGAGATTGCCAGTAAGTATAAGCATGCGGAACGGATCACGCTGGTGATGGACAACC
TCAATACGCATCAGCCCGGCTCATTATATCAGGCCTTTAAGCCGCAGGAAGCAAAGGCGTTACTTGACCGGTTCGAATTTGTCTACACCCCGAAACACGG
AAGTTGGCTCAATATGGCAGAGATCGAGCTGCGAGTTCTTTCAGGCCAGTGCCTGAACCGGCGCATTGACACAATCACAGAAGTTCGCTCAGAAGTCATG
GCCTGGGAGAAAGAACGGAACAACCTGAACGCAATAATCAACTGGCGCTTCACCACGGATAAGGCCCGAATCAAGCTCAAACACCTTTATCCGTCAGTTG
ATGCGTGACATGACAG

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
474 bp	157 aa	76	549	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MKKYKVTLTEEERQELDALSSKGKHAAQTVLNALILLACDEGKFQKERSINEDIARVLNISMKTIDRVKKRFVEEGLSMALTGKPSTRVYSRKADGDLEA
HLVALSCSEPPEGHLRWTLRLLADKAVELNYVENISYETVRRTLKKTSLSHGSKSAG

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
759 bp	252 aa	450	1208	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

GGRTKLCREYLLRNRTQDFKKNVLKPWKQVGWVIPPLHDGNFVAHMEMVLDTYKQPYDPLYPVVCMDESPKQLIAETRMPVPARPGQLARYDYEYSRKGT
CNIFIANEPLVGKRMVKVTSSRKKDDWARFLAEIASKYKHAERITLVMDNLNTHQPGSLYQAFKPQEAKALLDRFEFVYTPKHGSWLNMAEIELRVLSGQ
CLNRRIDTITEVRSEVMAWEKERNNLNAIINWRFTTDKARIKLKHLYPSVDA

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
1133 bp	377 aa	76	1208	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MKKYKVTLTEEERQELDALSSKGKHAAQTVLNALILLACDEGKFQKERSINEDIARVLNISMKTIDRVKKRFVEEGLSMALTGKPSTRVYSRKADGDLEA
HLVALSCSEPPEGHLRWTLRLLADKAVELNYVENISYETVRRTLKKNVLKPWKQVGWVIPPLHDGNFVAHMEMVLDTYKQPYDPLYPVVCMDESPKQLIA
ETRMPVPARPGQLARYDYEYSRKGTCNIFIANEPLVGKRMVKVTSSRKKDDWARFLAEIASKYKHAERITLVMDNLNTHQPGSLYQAFKPQEAKALLDRF
EFVYTPKHGSWLNMAEIELRVLSGQCLNRRIDTITEVRSEVMAWEKERNNLNAIINWRFTTDKARIKLKHLYPSVDA

Blast result :

Comments

ISCph1 is 84% aa similar to ISArch4. The third ORF is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.

References

1] ISfinder annotation (2010)
2] Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Ovchinnikova,G., Li,T., Liu,Z., Zhao,F., Overmann,J., Bryant,D.A. and Richardson,P. (2008) Direct submission GenBank.