<i>In Silico</i>Characterization of Histidine Acid Phytase Sequences

Kumar, Vinod; Singh, Gopal; Verma, Amit; Agrawal, Sanjeev

doi:10.1155/2012/845465

Cited by 21 publications

(13 citation statements)

References 38 publications

(38 reference statements)

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“…The protein sequences, which were shown to exhibit phytase activities, were selected for in silico study. Their characterization for homology, phylogenetic relationship, functional domain and other biochemical properties was carried out using freely available bioinformatic tools following the methodology of Kumar et al (2012). For domain search, the Pfam site (http: //www.sanger.ac.uk/software/pfam/search.html) was used.…”

Section: Methodsmentioning

confidence: 99%

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An insight into protein sequences of PTP-like cysteine phytases

2014

Nus Biosci

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Abstract. Kumar V, Agrawal S. 2014. An insight into protein sequences of PTP-like cysteine phytases. Nusantara Bioscience 6: 102-106. Protein tyrosine phosphatase like cysteine phytases (CPhy) are novel phytases reported in the ruminant microbial community and suggested to play major role in phytate-phosphorus hydrolysis in animal feed. These phytases are very promising to be used in animal feed applications for monogastric animals. Present study deals with utilization of sequence information of 40 CPhy reference protein sequences for their sequential characterization for conserved regions, phylogenetic relationship, biochemical features, superfamily and functional motifs therein. The study reveals that CPhy, not well characterized class of phytases, contains conserved sequence feature which may be important catalytic residues. Five major clusters observed in phylogenetic tree with Clostridium sp. as largest cluster. Reported motifs might be used for diversity and expression analysis of CPhy enzymes.

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Section: Methodsmentioning

confidence: 99%

“…In addition to this, in silico characterization of protein sequences of HAPhy and BPPhy class of phytases has been reported recently (Kumar et al 2012;Kumar et al 2014a). These studies have been suggested to be useful in further genetic engineering and classification in important groups of phytases.…”

Section: Introductionmentioning

confidence: 99%

An insight into protein sequences of PTP-like cysteine phytases

2014

Nus Biosci

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“…This is produced by bacteria [95], fungi [96], and plants [97] with tremendous diversity in various agro-climatic and environmental conditions. Four classes of phytases, namely, (HAPhy), (BPPhy), (PAPhy), and (CPhy), have been reported in the literature based on catalytic and sequence features [98]. These have also been categorized as 3-phytase and 4/6-phytase based on initial site of action and liberation of inorganic phosphate from phytate structure [99].…”

Section: Beneficial Microbes For Sustainable Agriculturementioning

confidence: 99%

Beneficial microbiomes: Biodiversity and potential biotechnological applications for sustainable agriculture and human health

Yadav¹,

Kumar²,

Kumar³

et al. 2017

J App Biol Biotech

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The beneficial microbes plays an important role in medical, industrial, and agricultural processes. The precious microbes belong to different groups including archaea, bacteria, and fungi which can be sort out from different habitat such as extreme environments (acidic, alkaline, drought, pressure, salinity, and temperatures) and associated with plants (epiphytic, endophytic, and rhizospheric) and human. The beneficial microbes exhibited multifunctional plant growth promoting (PGP) attributes such as N 2 -fixation, solubilization of micronutrients (phosphorus, potassium and zinc), and production of siderophores, antagonistic substances, antibiotic, auxin, and gibberellins. These microbes could be applied as biofertilizers for native as well as crops growing at diverse extreme habitat. Microbes with PGP attributes of N 2 -fixation, P-, and K-solubilization could be used at a place of NPK chemical fertilizers. Agriculturally, important microbes with Fe-and Zn-solubilizing attributes can be used for biofortification of micronutrients in different cereal crops. The biofertilizers are an eco-friendly technology and bioresources for sustainable agriculture and human health. In general, the concentrations of micronutrient in different crops are not adequate for human nutrition in diets. Hence, consumption of such cereal-based diet may result in micronutrient malnutrition and related severe health complications. The biofortification approach is getting much attention to increase the availability of micronutrients, especially Fe and Zn in the major food crops. The beneficial microbes can be used as probiotic as functional foods for human health. Probiotics microbes such as Bifidobacterium, Lactobacillus, Methanobrevibacter, Methanosphaera, and Saccharomyces are increasingly being used as dietary supplements in functional food products. The microbes with beneficial properties could be utilized for sustainable agriculture and human health.

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“…The sequence data about 50 sequences were found to be reliable for phylogenetic analysis as well as for data mining approach [23][24][25]. After complete alignment of the sequences by Clustal-W tool integrated with MEGA 4 software, boot-strapping was performed for 1000 times.…”

Section: Analysis Of Phylogenetic Consequencesmentioning

confidence: 99%

Computational Phylogenetic Study and Data Mining Approach to Laccase Enzyme Sequences

Satpathy¹,

Behera²,

Padhi³

et al. 2013

J Phylogen Evolution Biol

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Currently data mining is an essential tool to discover the hidden data and important patterns from a large data set. The present work is a pilot study that compares the result of sequence based phylogenetic study and some of the physicochemical and structural feature based clustering of Laccase enzyme sequences. Total of 50 homologous sequences were obtained specific to each of the organism like plant, fungi and bacteria. Multiple sequences alignment of sequences was performed followed by phylogenetic tree construction and consistency study also to observe the major clusters. Again the major domain and motif analysis was done to support the study in the divergence pattern of Laccase enzyme sequences. There after 13 numbers of physicochemical and structural features were computed for each enzyme sequences. Then data normalisation and k-means clustering technique revealed that the fungi, bacteria and plant were obtained in three distinct clusters. The analysis indicates that the result of sequence based classification is in a good agreement with physicochemical basis of classification of proteins. The methods can be further optimised for different clustering algorithm to obtain specific physicochemical features that would help to classification of proteins.

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In SilicoCharacterization of Histidine Acid Phytase Sequences

Cited by 21 publications

References 38 publications

An insight into protein sequences of PTP-like cysteine phytases

An insight into protein sequences of PTP-like cysteine phytases

Beneficial microbiomes: Biodiversity and potential biotechnological applications for sustainable agriculture and human health

Computational Phylogenetic Study and Data Mining Approach to Laccase Enzyme Sequences

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