Bioinformatics Research on a New Protein Given the Sequence
نویسنده
چکیده
In this report, various bioinformatics tools were employed to find sequence and structure homologs of a protein given its sequence. These tools include BLAST, PSI-BLAST, PFAM, ClustalW, T-Coffee, SAM-T99, SAM-T02, SingalP, TMHMM, and RasMol. Further information about genetic and metabolic functions of this protein was gathered from multiple online databases, including Saccharomyces Genome Database (SGD), Yeast General Repository for Interaction Datasets(Yeast-GRID), Biomolecular Interaction Network Database (BIND), and Kyoto Encyclopedia of Genes and Genomes (KEGG). BLAST similarity search revealed the target is a known yeast protein named Dap1p (for DNA damage response protein related to membrane-associated progesterone receptors). The results from literature review and database searches indicate that Dap1p plays certain roles in DNA damage response, cell cycle arrest, and sterol metabolism. Based on the results obtained using aforementioned bioinformatics means, suggestions on how to further characterize the functions of Dap1p are provided at the end of this report.
منابع مشابه
Comparing the Bidirectional Baum-Welch Algorithm and the Baum-Welch Algorithm on Regular Lattice
A profile hidden Markov model (PHMM) is widely used in assigning protein sequences to protein families. In this model, the hidden states only depend on the previous hidden state and observations are independent given hidden states. In other words, in the PHMM, only the information of the left side of a hidden state is considered. However, it makes sense that considering the information of the b...
متن کاملComputational Identification of Micro RNAs and Their Transcript Target(s) in Field Mustard (Brassica rapa L.)
Background: Micro RNAs (miRNAs) are a pivotal part of non-protein-coding endogenous small RNA molecules that regulate the genes involved in plant growth and development, and respond to biotic and abiotic environmental stresses posttranscriptionally.Objective: In the present study, we report the results of a systemic search for identifi cation of new miRNAs in B. rapa using homology-based ...
متن کاملComparing various attributes of prolactin hormones in different species: application of bioinformatics tools
Prolactin is mainly secreted by the anterior pituitary and is able to stimulate mammary gland development and lactation in mammalians. Although prolactins share a common ancestral gene encoding, they show species specific characteristics and their efficiency may be different in various mammals. The importance of protein structures of all sequences of this hormone have been studied by various bi...
متن کاملIn Silico Analysis of Primary Sequence and Tertiary Structure of Lepidium Draba Peroxidase
Peroxidase enzymes are vastly applicable in industry and diagnosiss. Recently, we introduced a new kind of peroxidase gene from Lepidium draba (LDP). According to protein multiple sequence alignment results, LDP had 93% similarity and 88.96% identity with horseradish peroxidase C1A (HRP C1A). In the current study we employed in silico tools to determine, to which group of peroxidase enzymes LDP...
متن کاملCloning, molecular analysis and epitopics prediction of a new chaperone GroEL Brucella melitensis antigen
Objective(s):Brucellosis is a well-known domestic animal infectious disease, which is caused by Brucella bacterium. GroEL antigen increases Brucella survival and is one of the major antigens that stimulates the immune system. Hence, the objective of the present study was cloning and bioinformatics analysis of GroEL gene. Materials and Methods: The full-length open reading frame of this gene was...
متن کاملProtein Secondary Structure Prediction: a Literature Review with Focus on Machine Learning Approaches
DNA sequence, containing all genetic traits is not a functional entity. Instead, it transfers to protein sequences by transcription and translation processes. This protein sequence takes on a 3D structure later, which is a functional unit and can manage biological interactions using the information encoded in DNA. Every life process one can figure is undertaken by proteins with specific functio...
متن کامل