Microbial & comparative genomics最新文献_第7页

Theoretical indicators of enzyme reaction specificity from conserved information in amino acid sidechains. 从氨基酸侧链的保守信息判断酶反应特异性的理论指标。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/10906590050179765

P A Herring, J H Jackson

{"title":"Theoretical indicators of enzyme reaction specificity from conserved information in amino acid sidechains.","authors":"P A Herring, J H Jackson","doi":"10.1089/10906590050179765","DOIUrl":"https://doi.org/10.1089/10906590050179765","url":null,"abstract":"Amino acid sequences for 11 acetohydroxy acid synthase (EC 4.1.3.18; AHS) polypeptides with experimentally established activity were chosen for computational comparisons to detect conserved local information associated with reaction specificity for each sequence. Windowed analysis by Pearson product moment cross-correlation of six amino acid sidechain properties revealed locally conserved segments common to all proteins with AHS activity. Seven information segments were detected in the same arrangement in sequences for the large subunit polypeptides of prokaryotes, and in the sequences for single polypeptides of eukaryotic AHS. The information segments were numbered 1-7 according to sequential position, and sequence features such as cofactor binding sites were defined for specific segments. Extension of the information segment analysis to seven other proteins of the pyruvate decarboxylase superfamily permitted use of the content and organization of information segments to recognize four classes of enzyme reaction specificity. Estimates of information entropy, based upon a state space defined by reaction specificity, directly reflected the known reaction complexity for all but one enzyme examined. Our data suggest that development of information-segment models for enzyme superfamilies may improve the accuracy of inferring protein activity from sequence.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/10906590050179765","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21913737","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

A novel microarray strategy for detecting genes and pathways in microbes with unsequenced genomes. 一种新的微阵列策略用于检测基因组未测序的微生物中的基因和途径。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/OMI.1.2000.5.153

R. Ramarathnam, S. Subramaniam

引用次数: 3

Improving quality of expressed sequence tag (EST) databases: recovery of reversed, antisense cDNA sequences. 提高表达序列标签(EST)数据库的质量:恢复反向、反义cDNA序列。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/10906590050145230

E Navarro, L Espinosa

{"title":"Improving quality of expressed sequence tag (EST) databases: recovery of reversed, antisense cDNA sequences.","authors":"E Navarro, L Espinosa","doi":"10.1089/10906590050145230","DOIUrl":"https://doi.org/10.1089/10906590050145230","url":null,"abstract":"Expressed sequence tag (EST) databases contain a significant number (5-20%) of reversed, antisense, cDNA sequences that can be recognized by the label \"reversed clone: similarity on wrong strand\" in the annotations to the sequence. Despite this high number of altered sequences, no attempt has been made to explain the alteration in molecular terms, or to evaluate their effect on the quality of the information curated in EST databases. In this paper we try to explain the way these altered sequences are originated, and propose a plausible mechanism: a \"double priming\" of the first strand oligo-dT primer at both ends of nascent cDNAs. In this way, a symmetrical cDNA intermediate is generated, an intermediate that can be cloned after partial digestion with the restriction enzyme used for the directional cloning. Furthermore, when \"secondary\" priming takes place inside the cDNA, the chain synthesized is prone to be truncated prematurely, with the subsequent loss of upstream information. One of the most subtle effects of this cloning alteration is the generation of virtual open reading frames (ORFs) in sequences with no homologues available for comparison. Nevertheless, and according to our model and our data, the \"double priming mechanism\" does not shift the ORF effected, so antisense sequences should be considered as normal ones after a simple transformation in their inverse-complementary forms.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/10906590050145230","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21844606","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: 3

The periodic table of biology. 生物学的元素周期表。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/OMI.1.2000.5.179

G. Evans

引用次数: 9

A minimal tiling path cosmid library for functional analysis of the Pseudomonas aeruginosa PAO1 genome. 铜绿假单胞菌PAO1基因组功能分析的最小平铺路径cosmid文库。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/OMI.1.2000.5.189

B. Huang, C. Whitchurch, L. Croft, S. Beatson, J. Mattick

{"title":"A minimal tiling path cosmid library for functional analysis of the Pseudomonas aeruginosa PAO1 genome.","authors":"B. Huang, C. Whitchurch, L. Croft, S. Beatson, J. Mattick","doi":"10.1089/OMI.1.2000.5.189","DOIUrl":"https://doi.org/10.1089/OMI.1.2000.5.189","url":null,"abstract":"Pseudomonas aeruginosa is an important pathogenic and environmental bacterium, with the most widely studied strain being PAO1. Using the PAO1 reference cosmid library and the recently completed PAO1 genome sequence, we have mapped a minimal tiling path across the genome using a two-step strategy. First, we sequenced both ends of a set of over 500 random and previously mapped clones to create a backbone. Second, we end-sequenced a second set of cosmid clones that were identified to lie within the larger gaps using hybridization of the reference library filters with probes designed against sequences at the center of each gap. The minimal tiling path was calculated using the program Domino (http://www.bit.uq.edu.au/download/), with the overlap between adjacent clones set to 5 kb (where possible) to minimize the chance of truncating genes. This yielded a minimal tiling cosmid library (334 clones) covering 93.7% of the genome in 57 contigs. This library has reduced to a workable set the number of clones required to represent the majority of the P. aeruginosa genome and gives the precise location of each cosmid, enabling most genes of interest to be located on clones without further screening. This library should prove a useful resource to accelerate functional analysis of the P. aeruginosa genome.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/OMI.1.2000.5.189","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60513999","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: 21

Chromosomal localization of single copy genes SRY and SOX3 by primed in situ labeling (PRINS). 引物原位标记(PRINS)对单拷贝基因SRY和SOX3的染色体定位。

Microbial & comparative genomics Pub Date : 2000-01-01 DOI: 10.1089/10906590050179756

J S Kadandale, Y Tunca, A T Tharapel

引用次数: 27

Computational analysis of the polymorphic membrane protein superfamily of Chlamydia trachomatis and Chlamydia pneumoniae. 沙眼衣原体和肺炎衣原体多态膜蛋白超家族的计算分析。

Microbial & comparative genomics Pub Date : 1999-01-01 DOI: 10.1089/omi.1.1999.4.187

J Grimwood, R S Stephens

{"title":"Computational analysis of the polymorphic membrane protein superfamily of Chlamydia trachomatis and Chlamydia pneumoniae.","authors":"J Grimwood, R S Stephens","doi":"10.1089/omi.1.1999.4.187","DOIUrl":"https://doi.org/10.1089/omi.1.1999.4.187","url":null,"abstract":"Whole sequence genome analysis is invaluable in providing complete profiles of related proteins and gene families. The genome sequences of the obligate intracellular bacteria Chlamydia trachomatis and Chlamydia pneumoniae both encode proteins with similarity to several 90-kDa Chlamydia psittaci proteins. These proteins are members of a large superfamily, C. trachomatis with 9 members and C. pneumoniae with 21 members. All polymorphic membrane protein (Pmp) are heterogeneous, both in amino acid sequence and in predicted size. Most proteins have apparent signal peptide leader sequences and hence are predicted to be localized to the outer membrane. The unifying features of all proteins are the conserved amino acid motifs GGAI and FXXN repeated in the N-terminal half of each protein. In both genomes, the pmp genes are clustered at various locations on the chromosome. Phylogenetic analysis suggests six related families, each with at least one C. trachomatis and one C. pneumoniae orthologue. One of these families has seen prolific expansion in C. pneumoniae, resulting in 13 protein paralogues. The maintenance of orthologues from each species suggests specific functions for the proteins in chlamydial biology.","PeriodicalId":79689,"journal":{"name":"Microbial & comparative genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1089/omi.1.1999.4.187","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21446716","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: 117

11th International Genome Sequencing and Analysis Conference. Miami Beach, Florida, USA. September 18-21, 1999. Abstracts. 第十一届国际基因组测序与分析会议。迈阿密海滩，美国佛罗里达州。1999年9月18-21日。摘要。

Microbial & comparative genomics Pub Date : 1999-01-01 DOI: 10.1089/omi.1.1999.4.75

引用次数: 0

Microbial genomes III: Sequencing, functional characterization, and comparative genomics. 微生物基因组III:测序、功能表征和比较基因组学。

Microbial & comparative genomics Pub Date : 1999-01-01 DOI: 10.1089/omi.1.1999.4.1

M Barnstead, D J Doyle

引用次数: 4

The Wolbachia Genome Consortium. 沃尔巴克氏体基因组联盟。

Microbial & comparative genomics Pub Date : 1999-01-01 DOI: 10.1089/omi.1.1999.4.161

B E Slatko, S L O'Neill, A L Scott, J L Werren, M L Blaxter

引用次数: 26