Protein sequences & data analysis最新文献

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Calculating percent identity between protein or DNA sequences with a word processor. 用文字处理器计算蛋白质或DNA序列之间的相同百分比。
Protein sequences & data analysis Pub Date : 1990-07-01
U S Ladror
{"title":"Calculating percent identity between protein or DNA sequences with a word processor.","authors":"U S Ladror","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Two macros, to calculate percentage identity between protein or DNA sequences using the Microsoft Word word processor, are described. The user prepares an alignment file of multiple sequences which is used by the macros to calculate number of matches, number of mismatches, total number of compared positions, and the percent identity. The macros are especially useful when alignment of multiple sequences is possible only by eye.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"3 3","pages":"267-71"},"PeriodicalIF":0.0,"publicationDate":"1990-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13551774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
N-terminal amino acid sequence analysis of small subunits of photosystem I reaction center complex from a thermophilic cyanobacterium, Synechococcus elongatus Nägeli. 嗜热蓝藻长聚球菌(Synechococcus elongatus)光系统I反应中心配合物的n端氨基酸序列分析Nägeli
Protein sequences & data analysis Pub Date : 1990-07-01
I Enami, H Kaiho, H Izumi, S Katoh, N Kotani, C S Jone, M Kamo, A Tsugita
{"title":"N-terminal amino acid sequence analysis of small subunits of photosystem I reaction center complex from a thermophilic cyanobacterium, Synechococcus elongatus Nägeli.","authors":"I Enami,&nbsp;H Kaiho,&nbsp;H Izumi,&nbsp;S Katoh,&nbsp;N Kotani,&nbsp;C S Jone,&nbsp;M Kamo,&nbsp;A Tsugita","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Four small subunits (14, 13, 10, and 8 kDa) of the photosystem I reaction center complex were isolated from a thermophilic cyanobacterium Synechococcus elongatus and their N-terminal amino acid sequences determined. Sequence analysis of the 10-kDa subunit revealed that the distribution of cysteine residues, Cys-X-X-Cys-X-X-Cys-X-X-X-Cys-Pro, is characteristic of bacterial-type ferredoxins, and that its partial sequence is highly homologous to that deduced from the chloroplast gene frx A of liverwort. This indicates that the 10-kDa polypeptide is an apoprotein carrying two iron-sulfur centers, FA and FB, assigned as [4Fe-4S] clusters, which mediated the light-activated transfer of electrons from P700 in photosystem I reaction center complex to soluble ferredoxin. The amino acid sequence of the 14-kDa polypeptide also showed similarity to that of the 20-kDa polypeptide from spinach chloroplast that can be chemically crosslinked with soluble ferredoxin. Thus, the 14-kDa polypeptide appears to be the ferredoxin 'docking' protein.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"3 3","pages":"257-62"},"PeriodicalIF":0.0,"publicationDate":"1990-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13274852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The following protein sequences were reprinted from the: protein sequence database of the Protein Identification Resource (PIR). 以下蛋白质序列转载自protein Identification Resource (PIR)的蛋白质序列数据库。
Protein sequences & data analysis Pub Date : 1990-07-01
W C Barker, L T Hunt, D G George, L S Yeh, H R Chen, M C Blomquist, E I Seibel-Ross, A Elzanowski, J K Bair, D A Ferrick
{"title":"The following protein sequences were reprinted from the: protein sequence database of the Protein Identification Resource (PIR).","authors":"W C Barker,&nbsp;L T Hunt,&nbsp;D G George,&nbsp;L S Yeh,&nbsp;H R Chen,&nbsp;M C Blomquist,&nbsp;E I Seibel-Ross,&nbsp;A Elzanowski,&nbsp;J K Bair,&nbsp;D A Ferrick","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"3 3","pages":"273-322"},"PeriodicalIF":0.0,"publicationDate":"1990-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13551775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The amino acid sequence of hemerythrin from Siphonosoma cumanense. 人类虹膜虫氯氰菊酯的氨基酸序列。
Protein sequences & data analysis Pub Date : 1990-06-01
T Uchida, H Yano, K Satake, I Kubota, A Tsugita
{"title":"The amino acid sequence of hemerythrin from Siphonosoma cumanense.","authors":"T Uchida,&nbsp;H Yano,&nbsp;K Satake,&nbsp;I Kubota,&nbsp;A Tsugita","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The amino acid sequence of hemerythrin from Siphonosoma cumanense was determined. The sequence consists of 113 amino acid residues. High homology is conserved in the regions of amino acid residues coordinating two iron atoms as its active site. The invariant sequences observed from the proteins in the same family were considerably altered except for the residues in the active site.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"3 2","pages":"141-7"},"PeriodicalIF":0.0,"publicationDate":"1990-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13511293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computer-assisted analysis of chromosomal locations and transcriptional directions of Escherichia coli genes. 大肠杆菌基因染色体位置和转录方向的计算机辅助分析。
Protein sequences & data analysis Pub Date : 1990-06-01
H Watanabe, T Kunisawa
{"title":"Computer-assisted analysis of chromosomal locations and transcriptional directions of Escherichia coli genes.","authors":"H Watanabe,&nbsp;T Kunisawa","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We present a computer-assisted method for locating and orienting nucleotide sequence segments on a large restriction map by comparing restriction fragment lengths. This method is based on the observation that long restriction fragments are rare and, therefore, the longest restriction fragments serve as effective discriminators. The method was applied to Escherichia coli genes, and chromosomal locations and transcriptional directions for more than 500 genes were determined.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"3 2","pages":"149-56"},"PeriodicalIF":0.0,"publicationDate":"1990-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13346951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The following protein sequences were reprinted from the protein sequence database of the Protein Identification Resource (PIR). 以下蛋白质序列转载自蛋白质鉴定资源(protein Identification Resource, PIR)的蛋白质序列数据库。
Protein sequences & data analysis Pub Date : 1990-06-01
W C Barker, L T Hunt, D G George, L S Yeh, H R Chen, M C Blomquist, E I Seibel-Ross, A Elzanowski, J K Bair, D A Ferrick
{"title":"The following protein sequences were reprinted from the protein sequence database of the Protein Identification Resource (PIR).","authors":"W C Barker,&nbsp;L T Hunt,&nbsp;D G George,&nbsp;L S Yeh,&nbsp;H R Chen,&nbsp;M C Blomquist,&nbsp;E I Seibel-Ross,&nbsp;A Elzanowski,&nbsp;J K Bair,&nbsp;D A Ferrick","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"3 2","pages":"163-256"},"PeriodicalIF":0.0,"publicationDate":"1990-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13511296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Escherichia coli K12 genomic database. 大肠杆菌K12基因组数据库。
Protein sequences & data analysis Pub Date : 1990-06-01
T Kunisawa, M Nakamura, H Watanabe, J Otsuka, A Tsugita, L S Yeh, D G George, W C Barker
{"title":"Escherichia coli K12 genomic database.","authors":"T Kunisawa,&nbsp;M Nakamura,&nbsp;H Watanabe,&nbsp;J Otsuka,&nbsp;A Tsugita,&nbsp;L S Yeh,&nbsp;D G George,&nbsp;W C Barker","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We have compiled the genomic nucleic acid sequence data of Escherichia coli K12 available from the existing major data collections and from the literature. The collected data are structured as a database for easy access and analysis. The sequence segments in the database are ordered by genetic map position. Sequence redundancy has been completely removed by combining overlapping sequences; therefore, our sequence data are amenable to statistical analysis. We have specified with a plus or minus (+ or -) on which of the two DNA strands the segment exists. The database currently contains a total of 954,392 bp, which corresponds to about 20% of the entire genome size. The sequence data are available on request.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"3 2","pages":"157-62"},"PeriodicalIF":0.0,"publicationDate":"1990-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13346825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Estimation of protein secondary structure from circular dichroism spectra: a critical examination of the CONTIN program. 从圆二色光谱估计蛋白质二级结构:对CONTIN程序的关键检查。
Protein sequences & data analysis Pub Date : 1990-03-01
A Bobba, P Cavatorta, M Attimonelli, P Riccio, L Masotti, E Quagliariello
{"title":"Estimation of protein secondary structure from circular dichroism spectra: a critical examination of the CONTIN program.","authors":"A Bobba,&nbsp;P Cavatorta,&nbsp;M Attimonelli,&nbsp;P Riccio,&nbsp;L Masotti,&nbsp;E Quagliariello","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The computer program CONTIN uses the Provencher and Glöckner procedure to calculate protein secondary structure from circular dichroism spectra. We have tested this program with peptides and proteins in which unfolding was either induced by denaturing treatment or was already present. Results indicate that the program does not clearly discriminate between the ordered and the unordered states of a protein.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"3 1","pages":"7-10"},"PeriodicalIF":0.0,"publicationDate":"1990-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13464487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Examination of protein sequence homologies. VII. The complementary molecular coevolution of ribosomal proteins equivalent to Escherichia coli L7/L12 and L10. 蛋白质序列同源性检查。7相当于大肠杆菌L7/L12和L10的核糖体蛋白的互补分子协同进化。
Protein sequences & data analysis Pub Date : 1990-03-01
E Otaka, K Suzuki, T Hashimoto
{"title":"Examination of protein sequence homologies. VII. The complementary molecular coevolution of ribosomal proteins equivalent to Escherichia coli L7/L12 and L10.","authors":"E Otaka,&nbsp;K Suzuki,&nbsp;T Hashimoto","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Recently reported P1, P2 and metabacteria line sequences of transposition-type 'A' proteins, equivalent to Escherichia coli ribosomal protein L7/L12, were examined using a correlation method which evaluates the sequence similarity quantitatively. As the sequences could be aligned along the alignment previously constructed for 25 various 'A' proteins, the inclusive alignment further supports the previous claims concerning the rule of \"preservation units\" and the transpositional regeneration for metabacterial and eukaryotic 'A' proteins. Yeasts contain multispecies of P1 and P2 line genes and their P1 line sequences show low correlation coefficient values compared to other P1 line sequences, indicating a great evolutionary distance between lower and higher eukaryotes. Five sequences of protein P0 from metabacteria, yeast, and human, of which about 20 residues at the C termini are homologous with those of their own transposition-type 'A' proteins, were similarly examined. The N-terminal three-quarters of the sequences align naturally and the first two-thirds of the alignment could involve the E. coli L10 (EL10) sequence. An alignment of the remaining sequences at the C termini was established, relying on the well-matching sequence similarities between the metabacteria 'A' protein and their P0 protein sequences. Finally, the C-terminal halves of P0 protein sequences corresponded with almost overall sequences of the transposition-type 'A' proteins. The gene fusion of a protein might have resulted in the formation of the P0 proteins. A coupling of this gene fusion and the transposition of prototype 'A' proteins may have given rise to the complementary molecular transformations required for the development toward higher organism cells.(ABSTRACT TRUNCATED AT 250 WORDS)</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"3 1","pages":"11-9"},"PeriodicalIF":0.0,"publicationDate":"1990-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13332677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Hemerythrin from Lingula unguis consists of two different subunits, alpha and beta. 菊酰氰菊酯由α和β两个不同的亚基组成。
Protein sequences & data analysis Pub Date : 1990-03-01
K Satake, M Yugi, M Kamo, H Kihara, A Tsugita
{"title":"Hemerythrin from Lingula unguis consists of two different subunits, alpha and beta.","authors":"K Satake,&nbsp;M Yugi,&nbsp;M Kamo,&nbsp;H Kihara,&nbsp;A Tsugita","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Hemerythrin, a non-heme Fe-protein, of Lingula unguis has an octamer structure. We demonstrated that the protein is composed of two distinct subunits (alpha and beta), in equal amounts by investigation of their composition and partial terminal sequence. The cross-linking reaction of the native protein with dithiobis-(succinimidyl propionate) provided evidence for the presence of a dimer composed of alpha and beta subunits.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"3 1","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"1990-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13464485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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