• Journal of Microbiology and Biotechnology
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• v.3 no.4
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• pp.224-231
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• 1993

The nucleotide sequence of the xylanase gene (xynY) from alkalophilic Bacillus sp. YC-335 was determined and analyzed. An open reading frame of 1, 062 base pairs for xynY gene was observed and encoded for a protein of 354 amino acids with a molecular weight of 38, 915. S1 nuclease mapping showed that the transcription initiation sites of the xynY gene were different in Bacillus sp. YC-335 and Escherichia coli HB101 (pYS55). S1 mapping also showed that -10 region of the xynY gene recognized by RNA polymerases of E. coli and Bacillus sp. YC-335 were TACAGT and TATGAT , respectively. A ribosome binding site sequence with the free energy of -17.0 Kcal/mol was observed 9 base pairs upstream from the unusual initiation codon, TTG. The proposed signal sequence consisted of 27 amino acids, 2 of which were basic amino acid residues and 21 were hydrophobic amino acid residues. When the amino acid sequences of xylanases were compared, Bacillus sp. YC-335 xylanase showed more than 50% homology with xylanases from B. pumilus, B. subtilis, and B. circulans.

• Genomics & Informatics
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• v.15 no.4
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• pp.162-169
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• 2017

Metal binding proteins or metallo-proteins are important for the stability of the protein and also serve as co-factors in various functions like controlling metabolism, regulating signal transport, and metal homeostasis. In structural genomics, prediction of metal binding proteins help in the selection of suitable growth medium for overexpression's studies and also help in obtaining the functional protein. Computational prediction using machine learning approach has been widely used in various fields of bioinformatics based on the fact all the information contains in amino acid sequence. In this study, random forest machine learning prediction systems were deployed with simplified amino acid for prediction of individual major metal ion binding sites like copper, calcium, cobalt, iron, magnesium, manganese, nickel, and zinc.

• Journal of Microbiology
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• v.35 no.3
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• pp.159-164
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• 1997

The phylogenetic study of Penicilium chrysogenum was performed based on amino acid sequence comparison of chitin synthase. Phylogenetic trees were constructed with the deduced amino acid sequences of the highly conserved region of chitin synthease gene fragments amplified by PCR. The BlasP similarity searcch and the bootstrap analysis of the deduced amino acid sequences of chitin synthase from P. chrysogenum with those form other fungi showed a close evolutionary relationship of Penicillium to ascomycetous fungi, especially to genus Aspergilus. The result from bootstrap analysis of the deduced amino acid sequences of the Class II chitin synthase from ascomyceteous fungi supported the usefulness of the Class II chitin synthease for phylogenetic study of filamentous fungi.

• Proceedings of the Zoological Society Korea Conference
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• 1995.10b
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• pp.120-120
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• 1995

The total size of the pF AR1, a genomic clone of Frankia FaCI, was estimated to be about 44Kb by summation of the individual fragment length generated by single or double restriction enzymes. Southern hybridization analyses with Azotobacter vinelandii nif-genes as probes and partial sequencing analyses of the subclones revealed that organization of the nif-gene in the FaCI strain was nifV, H, D, K, E, N, X, W, B. The organization of the structural genes for nitrogenase is the same in this Frankia strain as it is in most other nitrogen-fixing prokaryotes but the positioning of the nifV-like gene relative to the nifHDK cluster differs. A consensus nif-promoter-like sequence, found at 5' of nifH, was not detected upstream of the niJV-like gene. nifV-like gene contained a ORF of 1206 NT encoding 401 amino acids. The nucleotide sequence and deduced amino acid sequence of the gene exhibit homology value of 65% and 41% with that from A vinelandii, respectively. The putative Shine-Dargamo sequences were present preceding nitK, nifH, D, K, and nifE, and in nitK gene putative start codon GTG was detected instead of A TG. The nucleotide and amino acid sequence of niIK of FaCI showed 82% and 76% homolgy with those of Frankia HFPCc 13, respectively. Amino acid sequence of niIK showed 69% and 61% homology with those of A vinelandii, Klebsiella pnewnoniae, respectively, while that of nifE 73% and 71%, respecti vely.i vely.

• The Plant Pathology Journal
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• v.16 no.4
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• pp.231-235
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• 2000

The 3,000 nucleotides of 3'-terminal region of the genomic RNA of a new isolate of carlavirus from a Korean native lily (Lilum lancitoium) was cloned and its nucleotide sequences were determined. The coat protein (CP) gene of the virus showed 72.0% to 72.8% nucleotide sequence identities and 86.9% to 88.0% amino acid sequence identities with those of the four strains (two Korean, one Dutch, and one Japanese isolates) of lily symptomless virus (LSV). Interestingly, different amino acid sequences between the new isolate and LSV strains were located at the N-terminal region of the CP. Pairwise amino acid sequence comparison of the CP gene revealed sequence identities of 22.0% to 71.1% between the virus and other 9 carlavirus species. The 25 kDa and 12 kDa proteins genes of the virus share 30.7% to 76.3% and 31.1% to 85.8% amino acid sequence identities, respectively, with those of 8 other carlaviruses. The 16 kDa protein gene of the virus shares 16.7% to 72.9% amino acid sequence identities with that of 9 other carlaviruses. These data indicate that the virus, designated as lily latent virus (LiLV), is a distinct of the Carlavirus genus and distinguished from the known strains of LSV.

• Korean Journal of Microbiology
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• v.41 no.1
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• pp.13-17
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• 2005

The aim of this work was to investigate the N-terminal amino acid sequence of catechol 2,3-dioxygenase isolated from Delftia sp. JK-2, which could utilize aniline as sole carbon, nitrogen and energy source. Molecular weight of the enzyme was determined to approximately 35 kDa by SDS-PAGE. N-terminal amino acid sequence of C2,3O from strain JK-2 was $^1MGVMRIGHASLKVMDMDAAVRHYENV^{26}$, and exhibited high sequence similarity with that of C2,3O from Pseudomonas sp., Comamonas sp. JS765, Comamonas test-osteroni, or Burkholderia sp. RP007. Approximately 950-bp C2,3O was obtained through PCR using the primers derived from N-terminal amino acid sequence. Analysis of the DNA sequence revealed that the deduced 296 amino acid sequences were determined, and it showed $100\%$ identity with C2,3O from Pseudomonas sp. AW-2 and $97\%$ similarity with Comamonas sp. JS765.

• BMB Reports
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• v.37 no.2
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• pp.144-147
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• 2004

Molecular amplification and sequencing of genomic DNA that encodes camel polyubiquitin (PUBC1) was performed by a polymerase chain reaction (PCR) using various sets of primers. The amplification generated a number of DNA fragments, which were sequenced and compared with the polyubiquitin coding sequences of various species. One DNA fragment that conformed to 325 bp was found to be 95 and 88% homologous to the sequences of human polyubiquitin B and C, respectively. The DNA translated into 108 amino acids that corresponded to two fused units of ubiquitin with no intervening sequence, which indicates that it is a polyubiquitin and contains at least two units of ubiquitin. Although, variations were found in the nucleotide sequence when compared to those of other species, the amino acid sequence was 100% homologous to the polyubiquitin sequences of humans, mice, and rats. This is the first report of the polyubiquitin DNA coding sequence and its corresponding amino acid sequence from camels, amplified using direct genomic DNA preparations.

• Plant Resources
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• v.8 no.2
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• pp.110-115
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• 2005

Ribosomal protein complex with ribosomal RNA to form the subunits of the ribosome serve essential functions in protein synthesis. A full-length cDNA (PRPS4) encoding ribosomal protein S4 has been isolated and its nucleotide sequence determined in ginseng plant (Panax ginseng). A PRPS4 cDNA is 1105 nucleotides long and has an open reading frame of 792 bp with a deduced amino acid sequence of 264 residues (pI 10.67). The deduced amino acid sequence of PRPS4 matched to the previously reported ribosomal protein S4 genes. Their degree of amino acid identity ranged from 68 to $92\%$. Phylogenetic analysis based on the amino acid residues showed that the PRPS4 grouped with ribosomal protein S4 of S. tuberosum (CAA54095).

• Korean Journal of Plant Tissue Culture
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• v.24 no.2
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• pp.93-97
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• 1997

For the molecular genetic study of cold tolerance mechanism in plants, a cDNA encoding fatty acid desaturase (fad3), converting linoleic acid (18:2, $\omega$-6) to linolenic acid (18:3, $\omega$-3), was isolated from $\lambda$ZAPII Arabidopsis thaliana cDNA expression library by plaque hybridization using fad3 cDNA probe derived from Brassica napus. A 1.8 kb-EcoRI fragment from a lambda clone showing a strong positive hybridization signal was subcloned into pGEM7 and analyzed for its nucleotide sequence. From deduced amino acid sequences, the fad3 gene was revealed to have an open reading frame(ORF) consisting of 386 amino acids with a molecular mass of 44,075 Da. The fad3 gene was compared to chloroplast $\omega$-3 fatty acid desaturase (fad7) and endoplasmic reticulum Δ12 fatty acid desaturase (fad2) to show 70% and 58% amino acid sequence homology, respectively, Especially, amino acids of internal (82 to 151) and carboxy terminal (276 to 333) regions were highly conserved, implying their requisite role for enzymatic functioning of fatty acid desaturases. IPTG-induced fad3 cDNA expression in E. coli cells was suggested to be toxic to bacterial growth.

• Fisheries and Aquatic Sciences
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• v.6 no.3
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• pp.116-124
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• 2003

Isolation and cloning of seven-band grouper (Epinephelus septemfasciatus) growth hormone cDNA from pituitary gland revealed an open reading frame of 612 bp coding for a pre-growth hormone of 204 amino acids with a 17 amino acid putative signal peptide. Deduced amino acid sequence showed that there was one possible N-glycosylation site at $Asn^{l84}$ and four cysteine residues $(Cys^{52},\;Cys^{160},\;Cys^{177},\;Cys^{185})$ on t e same positions as in some other species where they were involved in the stabilization of the tertiary structure. The seven-band grouper growth hormone (sbgGH) presented a $99.5\%$ amino acid sequence identity with the growth hormone of Epinephelus coioides and contained the conserved hormone domain region. Comparison of growth hormone sequences from evolutionarily diverse species revealed 25 amino acid residues conserved in jawless fishes to modern mammals. It also revealed an evolutionary trend to retain the same polypeptide sequence even in the distantly related animals while allowing alterations to occur in polypeptides of the closely related species. In order to create a recombinant system to produce high levels of the growth hormone, it was expressed in Escherichia coli (BL21) cells. The gel analysis revealed theoretically expected molecular weights for both mature and pre-sbgGHs.