ArticleProceedings of the National Academy of Sciences of the United States of America1995
Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications.
Article in Proceedings of the National Academy of Sciences of the United States of America, 1995. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- The structure and function of small nucleolar ribonucleoproteins.Nucleic acids research · 2007Review
- Identification and comparative analysis of sixteen fungal peptidyl-prolyl cis/trans isomerase repertoires.BMC genomics · 2006Article
- Birth and death of protein domains: a simple model of evolution explains power law behavior.BMC evolutionary biology · 2002Article
- Purified box C/D snoRNPs are able to reproduce site-specific 2'-O-methylation of target RNA in vitro.Molecular and cellular biology · 2002Article
- In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex.Proceedings of the National Academy of Sciences of the United States of America · 2002Article
- Lineage-specific gene expansions in bacterial and archaeal genomes.Genome research · 2001Article
- Global perspectives on proteins: comparing genomes in terms of folds, pathways and beyond.The pharmacogenomics journal · 2001Review
- The human tRNA(m(2)(2)G(26))dimethyltransferase: functional expression and characterization of a cloned hTRM1 gene.Nucleic acids research · 2000Article
- Predicting protein function by genomic context: quantitative evaluation and qualitative inferences.Genome research · 2000Article
- Regulation of expression of the yiaKLMNOPQRS operon for carbohydrate utilization in Escherichia coli: involvement of the main transcriptional factors.Journal of bacteriology · 2000Article
- A common regulator for the operons encoding the enzymes involved in D-galactarate, D-glucarate, and D-glycerate utilization in Escherichia coli.Journal of bacteriology · 2000Article
- Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution.The EMBO journal · 2000Article
- Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme.RNA (New York, N.Y.) · 1999Article
- Evolution of the structure and chromosomal distribution of histidine biosynthetic genes.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 1998Article
- The role of gene duplication in the evolution of purine nucleotide salvage pathways.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 1998Article
- The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of psi55 in both mitochondrial and cytoplasmic tRNAs.Nucleic acids research · 1997Article
- A structural census of the current population of protein sequences.Proceedings of the National Academy of Sciences of the United States of America · 1997Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A computer analysis of 2328 protein sequences comprising about 60% of the Escherichia coli gene products was performed using methods for database screening with individual sequences and alignment blocks. A high fraction of E. coli proteins--86%--shows significant sequence similarity to other proteins in current databases; about 70% show conservation at least at the level of distantly related bacteria, and about 40% contain ancient conserved regions (ACRs) shared with eukaryotic or Archaeal proteins. For > 90% of the E. coli proteins, either functional information or sequence similarity, or both, are available. Forty-six percent of the E. coli proteins belong to 299 clusters of paralogs (intraspecies homologs) defined on the basis of pairwise similarity. Another 10% could be included in 70 superclusters using motif detection methods. The majority of the clusters contain only two to four members. In contrast, nearly 25% of all E. coli proteins belong to the four largest superclusters--namely, permeases, ATPases and GTPases with the conserved "Walker-type" motif, helix-turn-helix regulatory proteins, and NAD(FAD)-binding proteins. We conclude that bacterial protein sequences generally are highly conserved in evolution, with about 50% of all ACR-containing protein families represented among the E. coli gene products. With the current sequence databases and methods of their screening, computer analysis yields useful information on the functions and evolutionary relationships of the vast majority of genes in a bacterial genome. Sequence similarity with E. coli proteins allows the prediction of functions for a number of important eukaryotic genes, including several whose products are implicated in human diseases.
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