A Novel Tool for Peptide Pattern Recognition Identifies 13 Subgroups of the GH61 Family

Peter Kamp Busk, Mette Lange, Lene Lange

Research output: Contribution to conference without publisher/journalPosterResearch

Abstract

Proteins of the glycosyl hydrolase family 61 (gh61) are important proteins for fungal degradation of biomass. There are 132 entries for gh61 in the CAZY database, no subfamilies have been defined and each fungus may have several gh61s with very different sequences.
Alignment of highly divergent sequences such as the gh61s is difficult to perform correctly and to interpret. Therefore, we developed an alignment-independent method for sequence comparison and used it to analyze 467 gh61-like sequences found in NCBI. The method divided the gh61-family into 13 comprehensive subgroups and identified the conserved sequence motifs of each group, thus providing a framework for additional analysis of this large and interesting protein family.
PCR primers based on the conserved sequences in the largest subgroup amplified new gh61-encoding sequences from 14 out of 14 fungi demonstrating that the conserved motifs can be used to identify new proteins.
Original languageEnglish
Publication date16 Mar 2011
Number of pages1
Publication statusPublished - 16 Mar 2011

Cite this

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title = "A Novel Tool for Peptide Pattern Recognition Identifies 13 Subgroups of the GH61 Family",
abstract = "Proteins of the glycosyl hydrolase family 61 (gh61) are important proteins for fungal degradation of biomass. There are 132 entries for gh61 in the CAZY database, no subfamilies have been defined and each fungus may have several gh61s with very different sequences. Alignment of highly divergent sequences such as the gh61s is difficult to perform correctly and to interpret. Therefore, we developed an alignment-independent method for sequence comparison and used it to analyze 467 gh61-like sequences found in NCBI. The method divided the gh61-family into 13 comprehensive subgroups and identified the conserved sequence motifs of each group, thus providing a framework for additional analysis of this large and interesting protein family. PCR primers based on the conserved sequences in the largest subgroup amplified new gh61-encoding sequences from 14 out of 14 fungi demonstrating that the conserved motifs can be used to identify new proteins.",
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A Novel Tool for Peptide Pattern Recognition Identifies 13 Subgroups of the GH61 Family. / Busk, Peter Kamp; Lange, Mette; Lange, Lene.

2011.

Research output: Contribution to conference without publisher/journalPosterResearch

TY - CONF

T1 - A Novel Tool for Peptide Pattern Recognition Identifies 13 Subgroups of the GH61 Family

AU - Busk, Peter Kamp

AU - Lange, Mette

AU - Lange, Lene

PY - 2011/3/16

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N2 - Proteins of the glycosyl hydrolase family 61 (gh61) are important proteins for fungal degradation of biomass. There are 132 entries for gh61 in the CAZY database, no subfamilies have been defined and each fungus may have several gh61s with very different sequences. Alignment of highly divergent sequences such as the gh61s is difficult to perform correctly and to interpret. Therefore, we developed an alignment-independent method for sequence comparison and used it to analyze 467 gh61-like sequences found in NCBI. The method divided the gh61-family into 13 comprehensive subgroups and identified the conserved sequence motifs of each group, thus providing a framework for additional analysis of this large and interesting protein family. PCR primers based on the conserved sequences in the largest subgroup amplified new gh61-encoding sequences from 14 out of 14 fungi demonstrating that the conserved motifs can be used to identify new proteins.

AB - Proteins of the glycosyl hydrolase family 61 (gh61) are important proteins for fungal degradation of biomass. There are 132 entries for gh61 in the CAZY database, no subfamilies have been defined and each fungus may have several gh61s with very different sequences. Alignment of highly divergent sequences such as the gh61s is difficult to perform correctly and to interpret. Therefore, we developed an alignment-independent method for sequence comparison and used it to analyze 467 gh61-like sequences found in NCBI. The method divided the gh61-family into 13 comprehensive subgroups and identified the conserved sequence motifs of each group, thus providing a framework for additional analysis of this large and interesting protein family. PCR primers based on the conserved sequences in the largest subgroup amplified new gh61-encoding sequences from 14 out of 14 fungi demonstrating that the conserved motifs can be used to identify new proteins.

M3 - Poster

ER -