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izvor podataka: crosbi

An effective approach for annotation of protein families with low sequence similarity and conserved motifs : identifying GDSL hydrolases across the plant kingdom (CROSBI ID 224350)

Prilog u časopisu | izvorni znanstveni rad | međunarodna recenzija

Vujaklija, Ivan ; Bielen, Ana ; Paradžik, Tina ; Biđin, Siniša ; Goldstein, Pavle ; Vujaklija, Dušica An effective approach for annotation of protein families with low sequence similarity and conserved motifs : identifying GDSL hydrolases across the plant kingdom // BMC bioinformatics, 17 (2016), 91-1-91-18. doi: 10.1186/s12859-016-0919-7

Podaci o odgovornosti

Vujaklija, Ivan ; Bielen, Ana ; Paradžik, Tina ; Biđin, Siniša ; Goldstein, Pavle ; Vujaklija, Dušica

engleski

An effective approach for annotation of protein families with low sequence similarity and conserved motifs : identifying GDSL hydrolases across the plant kingdom

The massive accumulation of protein sequences arising from the rapid development of high- throughput sequencing, coupled with automatic annotation, results in high levels of incorrect annotations. In this study, we describe an approach to decrease annotation errors of protein families characterized by low overall sequence similarity. The GDSL lipolytic family comprises proteins with multifunctional properties and high potential for pharmaceutical and industrial applications. The number of proteins assigned to this family has increased rapidly over the last few years. In particular, the natural abundance of GDSL enzymes reported recently in plants indicates that they could be a good source of novel GDSL enzymes. We noticed that a significant proportion of annotated sequences lack specific GDSL motif(s) or catalytic residue(s). Here, we applied motif- based sequence analyses to identify enzymes possessing conserved GDSL motifs in selected proteomes across the plant kingdom. Motif-based HMM scanning (Viterbi decoding-VD and posterior decoding-PD) and the here described PD/VD protocol were successfully applied on 12 selected plant proteomes to identify sequences with GDSL motifs. A significant number of identified GDSL sequences were novel. Moreover, our scanning approach successfully detected protein sequences lacking at least one of the essential motifs (171/820) annotated by Pfam profile search (PfamA) as GDSL. Based on these analyses we provide a curated list of GDSL enzymes from the selected plants. Clans clustering and phylogenetic analyses helped us to gain a better insight into the evolutionary relationship of all identified GDSL sequences. Three novel GDSL subfamilies as well as unreported variations in GDSL motifs were discovered in this study. In addition, analyses of selected proteomes showed a remarkable expansion of GDSL enzymes in the lycophyte, Selaginella moellendorffii. Finally, we provide a general motif- HMM scanner which is easily accessible through the graphical user interface (http://compbio.math.hr/). Conclusions Our results show that scanning with a carefully parameterized motif- HMM is an effective approach for annotation of protein families with low sequence similarity and conserved motifs. The results of this study expand current knowledge and provide new insights into the evolution of the large GDSL-lipase family in land plants.

motif-HMM ; annotation errors ; low sequence similarity ; GDSL family ; plant kingdom

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Podaci o izdanju

17

2016.

91-1-91-18

objavljeno

1471-2105

10.1186/s12859-016-0919-7

Povezanost rada

Biologija, Matematika

Poveznice
Indeksiranost