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In silico characterization of pectate lyase protein sequences from different source organisms.

Dubey AK, Yadav S, Kumar M, Singh VK, Sarangi BK, Yadav D - Enzyme Res (2010)

Bottom Line: The phylogenetic tree constructed revealed different clusters based on different source organisms representing bacterial, fungal, plant, and nematode pectate lyases.The multiple accessions of bacterial, fungal, nematode, and plant pectate lyase protein sequences were placed closely revealing a sequence level similarity.The motif analysis revealed a conserved Pec_Lyase_C domain uniformly observed in all pectate lyases irrespective of variable sources suggesting its possible role in structural and enzymatic functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur 273 009, India.

ABSTRACT
A total of 121 protein sequences of pectate lyases were subjected to homology search, multiple sequence alignment, phylogenetic tree construction, and motif analysis. The phylogenetic tree constructed revealed different clusters based on different source organisms representing bacterial, fungal, plant, and nematode pectate lyases. The multiple accessions of bacterial, fungal, nematode, and plant pectate lyase protein sequences were placed closely revealing a sequence level similarity. The multiple sequence alignment of these pectate lyase protein sequences from different source organisms showed conserved regions at different stretches with maximum homology from amino acid residues 439-467, 715-816, and 829-910 which could be used for designing degenerate primers or probes specific for pectate lyases. The motif analysis revealed a conserved Pec_Lyase_C domain uniformly observed in all pectate lyases irrespective of variable sources suggesting its possible role in structural and enzymatic functions.

No MeSH data available.


Related in: MedlinePlus

(a) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 439–467. (b) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 715–816. (c) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 829–910.
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Related In: Results  -  Collection


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fig2: (a) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 439–467. (b) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 715–816. (c) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 829–910.

Mentions: The multiple sequence alignment of these protein sequences revealed conserved regions at different stretches, namely, from 439–467, 715–816, and 829–918 amino acid residues (Figures 2(a), 2(b), and 2(c)). This region could be used for designing degenerate primers or probes for PCR-based amplification or hybridization-based detection of pectate lyase sequences from different source organisms.


In silico characterization of pectate lyase protein sequences from different source organisms.

Dubey AK, Yadav S, Kumar M, Singh VK, Sarangi BK, Yadav D - Enzyme Res (2010)

(a) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 439–467. (b) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 715–816. (c) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 829–910.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2962914&req=5

fig2: (a) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 439–467. (b) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 715–816. (c) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 829–910.
Mentions: The multiple sequence alignment of these protein sequences revealed conserved regions at different stretches, namely, from 439–467, 715–816, and 829–918 amino acid residues (Figures 2(a), 2(b), and 2(c)). This region could be used for designing degenerate primers or probes for PCR-based amplification or hybridization-based detection of pectate lyase sequences from different source organisms.

Bottom Line: The phylogenetic tree constructed revealed different clusters based on different source organisms representing bacterial, fungal, plant, and nematode pectate lyases.The multiple accessions of bacterial, fungal, nematode, and plant pectate lyase protein sequences were placed closely revealing a sequence level similarity.The motif analysis revealed a conserved Pec_Lyase_C domain uniformly observed in all pectate lyases irrespective of variable sources suggesting its possible role in structural and enzymatic functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur 273 009, India.

ABSTRACT
A total of 121 protein sequences of pectate lyases were subjected to homology search, multiple sequence alignment, phylogenetic tree construction, and motif analysis. The phylogenetic tree constructed revealed different clusters based on different source organisms representing bacterial, fungal, plant, and nematode pectate lyases. The multiple accessions of bacterial, fungal, nematode, and plant pectate lyase protein sequences were placed closely revealing a sequence level similarity. The multiple sequence alignment of these pectate lyase protein sequences from different source organisms showed conserved regions at different stretches with maximum homology from amino acid residues 439-467, 715-816, and 829-910 which could be used for designing degenerate primers or probes specific for pectate lyases. The motif analysis revealed a conserved Pec_Lyase_C domain uniformly observed in all pectate lyases irrespective of variable sources suggesting its possible role in structural and enzymatic functions.

No MeSH data available.


Related in: MedlinePlus