title: An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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 analysis 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.
authors.affiliation: Faculty of Electrical Engineering and Computing, Unska 3, Zagreb, 10000, Croatia. ivan.vujaklija@gmail.com.
authors.forename: Ivan
authors.initials: I
authors.lastname: Vujaklija
authors.affiliation: Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, Zagreb, 10000, Croatia. abielen@pbf.hr.|Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, 10000, Croatia. abielen@pbf.hr.
authors.forename: Ana
authors.initials: A
authors.lastname: Bielen
authors.affiliation: Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, 10000, Croatia. Tina.Simunov@irb.hr.
authors.forename: Tina
authors.initials: T
authors.lastname: Paradžik
authors.affiliation: Faculty of Electrical Engineering and Computing, Unska 3, Zagreb, 10000, Croatia. sinisa@bidin.eu.
authors.forename: Siniša
authors.initials: S
authors.lastname: Biđin
authors.affiliation: Department of Mathematics, Faculty of Science, University of Zagreb, Bijenička 30, Zagreb, 10000, Croatia. payo@math.hr.
authors.forename: Pavle
authors.initials: P
authors.lastname: Goldstein
authors.affiliation: Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, 10000, Croatia. vujaklij@irb.hr.
authors.forename: Dušica
authors.initials: D
authors.lastname: Vujaklija
mesh_terms: D006867:Hydrolases; D010802:Phylogeny; D010944:Plants; D017434:Protein Structure, Tertiary; D011506:Proteins
chemical_list: D011506:Proteins; D006867:Hydrolases