Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
AAAS Promotion

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 24 October 1997:
Vol. 278. no. 5338, pp. 631 - 637
DOI: 10.1126/science.278.5338.631
Prev | Table of Contents | Next

Articles

A Genomic Perspective on Protein Families

Roman L. Tatusov, Eugene V. Koonin, * David J. Lipman

In order to extract the maximum amount of information from the rapidly accumulating genome sequences, all conserved genes need to be classified according to their homologous relationships. Comparison of proteins encoded in seven complete genomes from five major phylogenetic lineages and elucidation of consistent patterns of sequence similarities allowed the delineation of 720 clusters of orthologous groups (COGs). Each COG consists of individual orthologous proteins or orthologous sets of paralogs from at least three lineages. Orthologs typically have the same function, allowing transfer of functional information from one member to an entire COG. This relation automatically yields a number of functional predictions for poorly characterized genomes. The COGs comprise a framework for functional and evolutionary genome analysis.

The authors are with the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
*   To whom requests for reprints should be addressed. E-mail: koonin{at}ncbi.nlm.nih.gov

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes.
O. Gonzalez and R. Zimmer (2008)
Bioinformatics 24, 1257-1263
   Abstract »    Full Text »    PDF »
OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes.
L.-W. Jiang, K.-L. Lin, and C. L. Lu (2008)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
Vertebrate Genomes Code Excess Proteins with Charge Periodicity of 28 Residues.
R. Ke, N. Sakiyama, R. Sawada, M. Sonoyama, and S. Mitaku (2008)
J. Biochem. 143, 661-665
   Abstract »    Full Text »    PDF »
Near Intron Positions Are Reliable Phylogenetic Markers: An Application to Holometabolous Insects.
V. Krauss, C. Thummler, F. Georgi, J. Lehmann, P. F. Stadler, and C. Eisenhardt (2008)
Mol. Biol. Evol. 25, 821-830
   Abstract »    Full Text »    PDF »
The relative value of operon predictions.
R. W. W. Brouwer, O. P. Kuipers, and S. A. F. T. v. Hijum (2008)
Brief Bioinform
   Abstract »    Full Text »    PDF »
Gene Expression by the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough Grown on an Iron Electrode under Cathodic Protection Conditions.
S. M. Caffrey, H. S. Park, J. Been, P. Gordon, C. W. Sensen, and G. Voordouw (2008)
Appl. Envir. Microbiol. 74, 2404-2413
   Abstract »    Full Text »    PDF »
Proteogenomics: needs and roles to be filled by proteomics in genome annotation.
C. Ansong, S. O. Purvine, J. N. Adkins, M. S. Lipton, and R. D. Smith (2008)
Brief Funct Genomic Proteomic
   Abstract »    Full Text »    PDF »
The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota.
T. Kosaka, S. Kato, T. Shimoyama, S. Ishii, T. Abe, and K. Watanabe (2008)
Genome Res. 18, 442-448
   Abstract »    Full Text »    PDF »
Coevolution of gene families in prokaryotes.
O. X. Cordero, B. Snel, and P. Hogeweg (2008)
Genome Res. 18, 462-468
   Abstract »    Full Text »    PDF »
Genome evolution in cyanobacteria: The stable core and the variable shell.
T. Shi and P. G. Falkowski (2008)
PNAS 105, 2510-2515
   Abstract »    Full Text »    PDF »
A Botrytis cinerea Emopamil Binding Domain Protein, Required for Full Virulence, Belongs to a Eukaryotic Superfamily Which Has Expanded in Euascomycetes.
A. Gioti, J. M. Pradier, E. Fournier, P. Le Pecheur, C. Giraud, D. Debieu, J. Bach, P. Leroux, and C. Levis (2008)
Eukaryot. Cell 7, 368-378
   Abstract »    Full Text »    PDF »
Choosing BLAST options for better detection of orthologs as reciprocal best hits.
G. Moreno-Hagelsieb and K. Latimer (2008)
Bioinformatics 24, 319-324
   Abstract »    Full Text »    PDF »
AffyTrees: Facilitating Comparative Analysis of Affymetrix Plant Microarray Chips.
T. Frickey, V. A. Benedito, M. Udvardi, and G. Weiller (2008)
Plant Physiology 146, 377-386
   Abstract »    Full Text »    PDF »
Role of Hypermutability in the Evolution of the Genus Oenococcus.
A. M. Marcobal, D. A. Sela, Y. I. Wolf, K. S. Makarova, and D. A. Mills (2008)
J. Bacteriol. 190, 564-570
   Abstract »    Full Text »    PDF »
IMG/M: a data management and analysis system for metagenomes.
V. M. Markowitz, N. N. Ivanova, E. Szeto, K. Palaniappan, K. Chu, D. Dalevi, I-M. A. Chen, Y. Grechkin, I. Dubchak, I. Anderson, et al. (2008)
Nucleic Acids Res. 36, D534-D538
   Abstract »    Full Text »    PDF »
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.
V. M. Markowitz, E. Szeto, K. Palaniappan, Y. Grechkin, K. Chu, I-M. A. Chen, I. Dubchak, I. Anderson, A. Lykidis, K. Mavromatis, et al. (2008)
Nucleic Acids Res. 36, D528-D533
   Abstract »    Full Text »    PDF »
eggNOG: automated construction and annotation of orthologous groups of genes.
L. J. Jensen, P. Julien, M. Kuhn, C. von Mering, J. Muller, T. Doerks, and P. Bork (2008)
Nucleic Acids Res. 36, D250-D254
   Abstract »    Full Text »    PDF »
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.
A. Matsuya, R. Sakate, Y. Kawahara, K. O. Koyanagi, Y. Sato, Y. Fujii, C. Yamasaki, T. Habara, H. Nakaoka, F. Todokoro, et al. (2008)
Nucleic Acids Res. 36, D787-D792
   Abstract »    Full Text »    PDF »
AlterORF: a database of alternate open reading frames.
I. Pedroso, G. Rivera, F. Lazo, M. Chacon, F. Ossandon, F. A. Veloso, and D. S. Holmes (2008)
Nucleic Acids Res. 36, D517-D518
   Abstract »    Full Text »    PDF »
Low temperature (23 {degrees}C) increases expression of biofilm-, cold-shock- and RpoS-dependent genes in Escherichia coli K-12.
C. A. White-Ziegler, S. Um, N. M. Perez, A. L. Berns, A. J. Malhowski, and S. Young (2008)
Microbiology 154, 148-166
   Abstract »    Full Text »    PDF »
Evolution of the Chaperone/Usher Assembly Pathway: Fimbrial Classification Goes Greek.
S.-P. Nuccio and A. J. Baumler (2007)
Microbiol. Mol. Biol. Rev. 71, 551-575
   Abstract »    Full Text »    PDF »
Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi.
M. J. Cornell, I. Alam, D. M. Soanes, H. M. Wong, C. Hedeler, N. W. Paton, M. Rattray, S. J. Hubbard, N. J. Talbot, and S. G. Oliver (2007)
Genome Res. 17, 1809-1822
   Abstract »    Full Text »    PDF »
Genome-scale analysis of positionally relocated genes.
A. Bhutkar, S. M. Russo, T. F. Smith, and W. M. Gelbart (2007)
Genome Res. 17, 1880-1887
   Abstract »    Full Text »    PDF »
Host pathogen protein interactions predicted by comparative modeling.
F. P. Davis, D. T. Barkan, N. Eswar, J. H. McKerrow, and A. Sali (2007)
Protein Sci. 16, 2585-2596
   Abstract »    Full Text »    PDF »
Insights from Modeling Protein Evolution with Context-Dependent Mutation and Asymmetric Amino Acid Selection.
C. T. Saunders and P. Green (2007)
Mol. Biol. Evol. 24, 2632-2647
   Abstract »    Full Text »    PDF »
Analysis of Rare Amino Acid Replacements Supports the Coelomata Clade.
I. B. Rogozin, Y. I. Wolf, L. Carmel, and E. V. Koonin (2007)
Mol. Biol. Evol. 24, 2594-2597
   Abstract »    Full Text »    PDF »
Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in Escherichia coli.
S. Zuber, C. Ngom-Bru, C. Barretto, A. Bruttin, H. Brussow, and E. Denou (2007)
J. Bacteriol. 189, 8206-8214
   Abstract »    Full Text »    PDF »
Evolutionary analysis of enzymes using Chisel.
A. A. Rodriguez, T. Bompada, M. Syed, P. K. Shah, and N. Maltsev (2007)
Bioinformatics 23, 2961-2968
   Abstract »    Full Text »    PDF »
The Essential tacF Gene Is Responsible for the Choline-Dependent Growth Phenotype of Streptococcus pneumoniae.
M. Damjanovic, A. S. Kharat, A. Eberhardt, A. Tomasz, and W. Vollmer (2007)
J. Bacteriol. 189, 7105-7111
   Abstract »    Full Text »    PDF »
Functional Genomics of the Chicken A Model Organism.
L. A. Cogburn, T. E. Porter, M. J. Duclos, J. Simon, S. C. Burgess, J. J. Zhu, H. H. Cheng, J. B. Dodgson, and J. Burnside (2007)
Poult. Sci. 86, 2059-2094
   Abstract »    Full Text »    PDF »
The anatomy of microbial cell state transitions in response to oxygen.
A. K. Schmid, D. J. Reiss, A. Kaur, M. Pan, N. King, P. T. Van, L. Hohmann, D. B. Martin, and N. S. Baliga (2007)
Genome Res. 17, 1399-1413
   Abstract »    Full Text »    PDF »
Solution structure of the hypothetical protein TA0095 from Thermoplasma acidophilum: A novel superfamily with a two-layer sandwich architecture.
E. Leon, A. Yee, A. R. Ortiz, J. Santoro, M. Rico, and M. A. Jimenez (2007)
Protein Sci. 16, 2278-2286
   Abstract »    Full Text »    PDF »
Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough.
S. M. Caffrey, H.-S. Park, J. K. Voordouw, Z. He, J. Zhou, and G. Voordouw (2007)
J. Bacteriol. 189, 6159-6167
   Abstract »    Full Text »    PDF »
Cell-Wide Responses to Low-Oxygen Exposure in Desulfovibrio vulgaris Hildenborough.
A. Mukhopadhyay, A. M. Redding, M. P. Joachimiak, A. P. Arkin, S. E. Borglin, P. S. Dehal, R. Chakraborty, J. T. Geller, T. C. Hazen, Q. He, et al. (2007)
J. Bacteriol. 189, 5996-6010
   Abstract »    Full Text »    PDF »
OMA Browser Exploring orthologous relations across 352 complete genomes.
A. Schneider, C. Dessimoz, and G. H. Gonnet (2007)
Bioinformatics 23, 2180-2182
   Abstract »    Full Text »    PDF »
Human Body Temperature (37{degrees}C) Increases the Expression of Iron, Carbohydrate, and Amino Acid Utilization Genes in Escherichia coli K-12.
C. A. White-Ziegler, A. J. Malhowski, and S. Young (2007)
J. Bacteriol. 189, 5429-5440
   Abstract »    Full Text »    PDF »
YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity.
U. Mechold, G. Fang, S. Ngo, V. Ogryzko, and A. Danchin (2007)
Nucleic Acids Res. 35, 4552-4561
   Abstract »    Full Text »    PDF »
Low Concentrations of Bile Salts Induce Stress Responses and Reduce Motility in Bacillus cereus ATCC 14570.
S. M. Kristoffersen, S. Ravnum, N. J. Tourasse, O. A. Okstad, A.-B. Kolsto, and W. Davies (2007)
J. Bacteriol. 189, 5302-5313
   Abstract »    Full Text »    PDF »
BLASTO: a tool for searching orthologous groups.
Y. Zhou and L. F. Landweber (2007)
Nucleic Acids Res. 35, W678-W682
   Abstract »    Full Text »    PDF »
COMPASS server for remote homology inference.
R. I. Sadreyev, M. Tang, B.-H. Kim, and N. V. Grishin (2007)
Nucleic Acids Res. 35, W653-W658
   Abstract »    Full Text »    PDF »
KAAS: an automatic genome annotation and pathway reconstruction server.
Y. Moriya, M. Itoh, S. Okuda, A. C. Yoshizawa, and M. Kanehisa (2007)
Nucleic Acids Res. 35, W182-W185
   Abstract »    Full Text »    PDF »
Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization.
N. H. Putnam, M. Srivastava, U. Hellsten, B. Dirks, J. Chapman, A. Salamov, A. Terry, H. Shapiro, E. Lindquist, V. V. Kapitonov, et al. (2007)
Science 317, 86-94
   Abstract »    Full Text »    PDF »
SpxB Regulates O-Acetylation-dependent Resistance of Lactococcus lactis Peptidoglycan to Hydrolysis.
P. Veiga, C. Bulbarela-Sampieri, S. Furlan, A. Maisons, M.-P. Chapot-Chartier, M. Erkelenz, P. Mervelet, P. Noirot, D. Frees, O. P. Kuipers, et al. (2007)
J. Biol. Chem. 282, 19342-19354
   Abstract »    Full Text »    PDF »
Characterization of a Novel Bile-Inducible Operon Encoding a Two-Component Regulatory System in Lactobacillus acidophilus.
E. A. Pfeiler, M. A. Azcarate-Peril, and T. R. Klaenhammer (2007)
J. Bacteriol. 189, 4624-4634
   Abstract »    Full Text »    PDF »
Reconstruction of highly heterogeneous gene-content evolution across the three domains of life.
W. Iwasaki and T. Takagi (2007)
Bioinformatics 23, i230-i239
   Abstract »    Full Text »    PDF »
Automatic genome-wide reconstruction of phylogenetic gene trees.
I. Wapinski, A. Pfeffer, N. Friedman, and A. Regev (2007)
Bioinformatics 23, i549-i558
   Abstract »    Full Text »    PDF »
A sub-proteome of Arabidopsis thaliana mature stems trapped on Concanavalin A is enriched in cell wall glycoside hydrolases.
Z. Minic, E. Jamet, L. Negroni, P Arsene der Garabedian, M. Zivy, and L. Jouanin (2007)
J. Exp. Bot. 58, 2503-2512
   Abstract »    Full Text »    PDF »
CTX-BLAST: context sensitive version of protein BLAST.
A. Gambin and P. Wojtalewicz (2007)
Bioinformatics 23, 1686-1688
   Abstract »    Full Text »    PDF »
The Early Response to Acid Shock in Lactobacillus reuteri Involves the ClpL Chaperone and a Putative Cell Wall-Altering Esterase.
T. Wall, K. Bath, R. A. Britton, H. Jonsson, J. Versalovic, and S. Roos (2007)
Appl. Envir. Microbiol. 73, 3924-3935
   Abstract »    Full Text »    PDF »
The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host cell interaction genes.
N.-H. Cho, H.-R. Kim, J.-H. Lee, S.-Y. Kim, J. Kim, S. Cha, S.-Y. Kim, A. C. Darby, H.-H. Fuxelius, J. Yin, et al. (2007)
PNAS 104, 7981-7986
   Abstract »    Full Text »    PDF »
Identification of Lactobacillus sakei Genes Induced during Meat Fermentation and Their Role in Survival and Growth.
E. Hufner, T. Markieton, S. Chaillou, A.-M. Crutz-Le Coq, M. Zagorec, and C. Hertel (2007)
Appl. Envir. Microbiol. 73, 2522-2531
   Abstract »    Full Text »    PDF »
Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R.
H. Yukawa, C. A. Omumasaba, H. Nonaka, P. Kos, N. Okai, N. Suzuki, M. Suda, Y. Tsuge, J. Watanabe, Y. Ikeda, et al. (2007)
Microbiology 153, 1042-1058
   Abstract »    Full Text »    PDF »
Essentiality of Ribosomal and Transcription Antitermination Proteins Analyzed by Systematic Gene Replacement in Escherichia coli.
M. Bubunenko, T. Baker, and D. L. Court (2007)
J. Bacteriol. 189, 2844-2853
   Abstract »    Full Text »    PDF »
Hierarchical classification of functionally equivalent genes in prokaryotes.
H. Wu, F. Mao, V. Olman, and Y. Xu (2007)
Nucleic Acids Res. 35, 2125-2140
   Abstract »    Full Text »    PDF »
Assessment of phylogenomic and orthology approaches for phylogenetic inference.
B. E. Dutilh, V. van Noort, R. T. J. M. van der Heijden, T. Boekhout, B. Snel, and M. A. Huynen (2007)
Bioinformatics 23, 815-824
   Abstract »    Full Text »    PDF »
Ecdysozoan Clade Rejected by Genome-Wide Analysis of Rare Amino Acid Replacements.
I. B. Rogozin, Y. I. Wolf, L. Carmel, and E. V. Koonin (2007)
Mol. Biol. Evol. 24, 1080-1090
   Abstract »    Full Text »    PDF »
The c-Myc Target Gene Rcl (C6orf108) Encodes a Novel Enzyme, Deoxynucleoside 5'-monophosphate N-Glycosidase.
Y. K. Ghiorghi, K. I. Zeller, C. V. Dang, and P. A. Kaminski (2007)
J. Biol. Chem. 282, 8150-8156
   Abstract »    Full Text »    PDF »
FNR Is a Global Regulator of Virulence and Anaerobic Metabolism in Salmonella enterica Serovar Typhimurium (ATCC 14028s).
R. C. Fink, M. R. Evans, S. Porwollik, A. Vazquez-Torres, J. Jones-Carson, B. Troxell, S. J. Libby, M. McClelland, and H. M. Hassan (2007)
J. Bacteriol. 189, 2262-2273
   Abstract »    Full Text »    PDF »
TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities.
S. Gu, I. Anderson, V. Kunin, M. Cipriano, S. Minovitsky, G. Weber, N. Amenta, B. Hamann, and I. Dubchak (2007)
Bioinformatics 23, 764-766
   Abstract »    Full Text »    PDF »
The SXT Conjugative Element and Linear Prophage N15 Encode Toxin-Antitoxin-Stabilizing Systems Homologous to the tad-ata Module of the Paracoccus aminophilus Plasmid pAMI2.
L. Dziewit, M. Jazurek, L. Drewniak, J. Baj, and D. Bartosik (2007)
J. Bacteriol. 189, 1983-1997
   Abstract »    Full Text »    PDF »
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.
M. G. Smith, T. A. Gianoulis, S. Pukatzki, J. J. Mekalanos, L. N. Ornston, M. Gerstein, and M. Snyder (2007)
Genes & Dev. 21, 601-614
   Abstract »    Full Text »    PDF »
The Seventh International Conference on the Genetics of Streptococci, Lactococci, and Enterococci.
R. A. Burne, D. E. Bessen, J. R. Broadbent, and J.-P. Claverys (2007)
J. Bacteriol. 189, 1209-1218
   Full Text »    PDF »
Evolutionary Genomics of Lactic Acid Bacteria.
K. S. Makarova and E. V. Koonin (2007)
J. Bacteriol. 189, 1199-1208
   Full Text »    PDF »
Genome-Wide Screening of Genes Required for Swarming Motility in Escherichia coli K-12.
T. Inoue, R. Shingaki, S. Hirose, K. Waki, H. Mori, and K. Fukui (2007)
J. Bacteriol. 189, 950-957
   Abstract »    Full Text »    PDF »
Global Gene Expression Profiling of Asymptomatic Bacteriuria Escherichia coli during Biofilm Growth in Human Urine.
V. Hancock and P. Klemm (2007)
Infect. Immun. 75, 966-976
   Abstract »    Full Text »    PDF »
SAGA: a subgraph matching tool for biological graphs.
Y. Tian, R. C. McEachin, C. Santos, D. J. States, and J. M. Patel (2007)
Bioinformatics 23, 232-239
   Abstract »    Full Text »    PDF »
Operon prediction in Pyrococcus furiosus.
T. T. Tran, P. Dam, Z. Su, F. L. Poole II, M. W. W. Adams, G. T. Zhou, and Y. Xu (2007)
Nucleic Acids Res. 35, 11-20
   Abstract »    Full Text »    PDF »
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs).
E. A. O'Brien, L. B. Koski, Y. Zhang, L. Yang, E. Wang, M. W. Gray, G. Burger, and B. F. Lang (2007)
Nucleic Acids Res. 35, D445-D451
   Abstract »    Full Text »    PDF »
Xanthusbase: adapting wikipedia principles to a model organism database.
B. I. Arshinoff, G. Suen, E. M. Just, S. M. Merchant, W. A. Kibbe, R. L. Chisholm, and R. D. Welch (2007)
Nucleic Acids Res. 35, D422-D426
   Abstract »    Full Text »    PDF »
PATRIC: The VBI PathoSystems Resource Integration Center.
E. E. Snyder, N. Kampanya, J. Lu, E. K. Nordberg, H. R. Karur, M. Shukla, J. Soneja, Y. Tian, T. Xue, H. Yoo, et al. (2007)
Nucleic Acids Res. 35, D401-D406
   Abstract »    Full Text »    PDF »
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
L. H. Greene, T. E. Lewis, S. Addou, A. Cuff, T. Dallman, M. Dibley, O. Redfern, F. Pearl, R. Nambudiry, A. Reid, et al. (2007)
Nucleic Acids Res. 35, D291-D297
   Abstract »    Full Text »    PDF »
A Phytophthora infestans Cystatin-Like Protein Targets a Novel Tomato Papain-Like Apoplastic Protease.
M. Tian, J. Win, J. Song, R. van der Hoorn, E. van der Knaap, and S. Kamoun (2007)
Plant Physiology 143, 364-377
   Abstract »    Full Text »    PDF »
Bacterial Postgenomics: the Promise and Peril of Systems Biology{triangledown}.
G. Suen, J. S. Jakobsen, B. S. Goldman, M. Singer, A. G. Garza, and R. D. Welch (2006)
J. Bacteriol. 188, 7999-8004
   Full Text »    PDF »
Bioinformatic, Genetic, and Biochemical Evidence that Some Glycoside Hydrolase Family 42 {beta}-Galactosidases Are Arabinogalactan Type I Oligomer Hydrolases.
S. Shipkowski and J. E. Brenchley (2006)
Appl. Envir. Microbiol. 72, 7730-7738
   Abstract »    Full Text »    PDF »


ADVERTISEMENT
Click Me!

ADVERTISEMENT
Click Me!

To Advertise     Find Products