• Microbiology and Biotechnology Letters
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• v.18 no.3
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• pp.309-316
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• 1990

The sequence of a 1795 bp restriction fragment containing the B. circulans F-2 gene for NaC1- dependent $\alpha$-amylase (CI-amylase) is reported. The probable coding region of the gene is 1005 base pairs (335 amino acida) long. The NaC1-dependent $\alpha$-amylase (el-amy) sequence shows an open reading frame (ORF) with the translated molecular weight of about 38, 006, which correspond to a molecular weight of about 35, 000 (Mi). The gene is preceded by the sequence resembling promoter for the vegetative B, subtitis RNA polymerases. These are followed by the sequences resembling a B. subtilis ribosome binding site 5 nucleotides before the first codon of the gene. Homologous regions with other amylases were found. The N-terminal sequences of the mature proteins expressed in E. eoli were identical to the N-terminal sequences which are anaIysed.

• BMB Reports
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• v.32 no.4
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• pp.409-413
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• 1999

The cDNA encoding CMP-NeuAc:lactosylceramide ${\alpha}2$,3-sialyltransferase (GM3 synthase) was isolated from a human fetal brain cDNA library using sequence information obtained from amino acid sequences found in the conserved regions of the previously-cloned mouse GM3 synthase (mST3Gal V) and human sialyltransferases. The cDNA sequence included an open reading frame coding for 362 amino acids, and the primary structure of this enzyme predicted all the structural features characteristic of other sialyltransferases, including a type II membrane protein topology and both sialylmotifs. Comparative analysis of this cDNA with mST3Gal V showed 85% and 86% identity of the nucleotide and amino acid residues, respectively. The expression of this gene is highly restricted in both human fetal and adult tissues.

• Journal of Microbiology and Biotechnology
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• v.11 no.4
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• pp.668-676
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• 2001

Pseudomonas sp. strain SY5 is a PCB-degrading bacterium [24] that includes two different enzymes (BphC1 and BphC2) encoding 2,3-dihdroxybiphenyl 1,2-dioxygenase and BphD encoding 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase. The bphC1 and bphC2 genes were found to consist of 897 based encoding 299 amino acids and 882 bases encoding 294 amino acids, respectively, whereas the bphD gene consisted of 861 bases encoding 287 amino acids. According to a homology search, a 50% and 39% similarity between the bphC1 and bphC2 genes at the nucleotide and amino acid level was shown, respectively. The bphC1 gene showed a 38% and 45% similarity at the amino acid level to Alcaligenes eutrophus A5 and Rhodococcus rhodochrous, respectively, whereas, bphC2 showed a 95% and 43% similarity, respectively. A comparison of the deduced amino acid sequence of the bphD product of Pseudomonas sp. SY5 with that of A. eutrophus A5, Pseudomons sp. KKS102, and LB400 showed a sequence identity of 92, 92, and 79%, respectively. Strain SY5 was originally isolated from municipal sewage containing recalcitrant organic compounds an found to have a high degradability of various aromatic compounds [23]. The current study found that strain SY5 had two extradiol-type dioxygenases, which did not hybridize with each other as they had a low similarity, yet a similar structure of evolutionarily conserved amino acids residues for catalytic activity between BphC1 and BphC2 was observed.

• BMB Reports
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• v.37 no.5
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• pp.574-581
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• 2004

The full-length cDNA of the lumbrokinase fraction 6 (F6) protease gene of Lumbricus rubellus was amplified using an mRNA template, sequenced and expressed in E. coli cells. The F6 protease gene consisted of pro- and mature sequences by gene sequence analysis, and the protease was translated and modified into active mature polypeptide by N-terminal amino acid sequence analysis of the F6 protease. The pro-region of F6 protease consisted of the 44 residues from methionine-1 to lysine-44, and the mature polypeptide sequence (239 amino acid residues and one stop codon; 720 bp) started from isoleucine-45 and continued to the terminal residue. F6 protease gene clones having pro-mature sequence and mature sequence produced inclusion bodies in E. coli cells. When inclusion bodies were orally administrated rats, generated thrombus weight in the rat' venous was reduced by approximately 60% versus controls. When the inclusion bodies were solubilized in pepsin and/or trypsin solutions, the solubilized enzymes showed hemolytic activity in vitro. It was concluded the F6 protease has hemolytic activity, and that it is composed of pro- and mature regions.

• Korean Journal of Microbiology
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• v.30 no.5
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• pp.397-402
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• 1992

The cDNA of RNA segment coding for VP7 of human rotavirus isolated from patient's stool at Seoul area was synthesized, amplified by polymerase chain reaction, field in with Klenow fragment of DNA polymerase I and cloned into pUC19. The cDNA sequence was determined and compared with that of VP7 coding RNA segments of group A rotaviruses isolates in foreign country. Over 90% sequence homology was found with serotyppe I sepcific WA1 and RE9 strains. Comparative analysis of the deduced amino acid sequences within the two variable regions (amino acid residue 87 through 101 and 208 through 221) with WA1 and RE9 strains also showed high degree of sequence similarity with each other.

• Journal of Life Science
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• v.9 no.4
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• pp.341-347
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• 1999

Insects use chitinolytic enzyme to digest chitin in the exoskelton during the molting process. We have isolated and sequenced a chitinase-encoding cDNA from the silkworm, Bombyx mandarina, compared its sequenced with genes encoding chitinolytic enzymes from other sources. The insert DNA in the clone is 2,675 nucleotides long with an open reading frame of 1,695 uncletides that encodes a protein of 565 amino acids with a molecuar weight of 63.4 kDa. The 3' -untranslated region of 889 nucleotides is AT-rich and contains two putative polyadenylation signals. The N-terminal sequence of the encoded protein contains numerous hydrophobic residues characteristic of a leader peptide. The amino acid alignment revealed that the endo-$\beta$-N-acetylglucosaminidase had 83% and 97% homology with M. sexta and B. mori, respectively. The deduced amino acid had two highly conserved region at the amino acid residues 97-111 and 139-148 that were related to the existing chitinase.

• Journal of Microbiology and Biotechnology
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• v.16 no.12
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• pp.1935-1939
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• 2006

The gene encoding the extracellular medium-chain-length poly(3-hydroxyalkanoate) (MCL-PHA) depolymerase of Pseudomonas luteola Ml3-4, $phaZ_{plu}$, was cloned and analyzed. It was found to be 849 bp, with a deduced protein of 282 amino acids, and was revealed to have a typical leader peptide at its N terminus. The amino acid sequence of $PhaZ_{plu}$ revealed relatively low identity (69 to 72%) with those of other Pseudomonas MCL-PHA depolymerases. In comparison with the amino acid sequences of all available MCL-PHA depolymerases, the depolymerase was found to consist of three domains in sequential order; signal peptide, an N-terminal substrate binding domain, and a catalytic domain, indicating that $PhaZ_{plu}$ belongs to the type IV depolymerases family. The enzyme also contained Asn as an oxyanion hole amino acid.

• Journal of the Korean Society of Food Science and Nutrition
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• v.3 no.1
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• pp.53-68
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• 1974

The thiohydantoin derivative derived from amino acid was used for the stepwise sequence analysis of peptide or protein from the carboxyl termini. Recently, SUZUKI reported the mass spectrometric identification about a part of these compounds. In this paper, was described the mass spectrometric identification of thiohydantoins derived from 20 amino acids. Mass spectra were obtained with a mass spectrometer, JEOL model JMS-06H and samples were introduced with a direct inlet probe. The molecular ion peaks and fragment ion peaks were identified easily, because these peaks appeared differently every amino acids and specially, it was easy discrimination between leucine and isoleucine. It is suggested that mass spectrometry was one of the useful methods to identify thiohydantoins derived from amino acids.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.244-249
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• 2004

There have been many attempts to predict the secondary structure content of a protein from its primary sequence, which serves as the first step in a series of bioinformatics processes to gain knowledge of the structure and function of a protein. Most of them assumed that prediction relying on the information of the amino acid composition of a protein can be successful. Several approaches expanded the amount of information by including the pair amino acid composition of two adjacent residues. Recent methods achieved a remarkable improvement in prediction accuracy by using this expanded composition information. The overall average errors of two successful methods were 6.1% and 3.4%. This work was motivated by the observation that evolutionarily related proteins share the similar structure. After manipulating the values of the frequency matrix obtained by running PSI-BLAST, inputs of an artificial neural network were constructed by taking the ratio of the amino acid composition of the evolutionarily related proteins with a query protein to the background probability. Although we did not utilize the expanded composition information of amino acid pairs, we obtained the comparable accuracy, with the overall average error being 3.6%.

• Journal of Sericultural and Entomological Science
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• v.41 no.3
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• pp.147-153
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• 1999

Chitinolytic enzymes such as ${\beta}$-N-acetylglucosaminidase are major hydrolases involved in insect molting. We have isolated, sequenced a CDNA encoding ${\beta}$-N-acetylglucosaminidase from the silkworm, Bombyx mandarina, and compared its sequence with genes encoding chitinolytic enyzmes from other sources. The insert DNA in the clone is 3,284 nucleotides long with an open reading frame of 1,788 nucleotides that encodes a protein of 596 amino acids with a molecular weight of 68.2 kDa. There is a 3’-untranslated region composed with 1.479 nucleotides and are several potential polyadenylation signals. The predicted amino acid sequence apparently contains a leader peptide of 23 amino acids. A search of the amino acids sequence databases for sequences similarities to other ${\beta}$-N-acetylglucosaminidases or ${\beta}$-N-acetylhexosaminidases. The highest similarity matched with the enzyme from B. mori, which has a sequence identity of 95%. On the other hand, the identity between the B. mandarina enzyme and those from M. sexta and human are 70% and 24%, respectively.