Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors

Journal of Molecular Biology

Volumn 321, Issue 1, 2002, Pages 7-20

  Mirny, Leonid A ^a   Gelfand, Mikhail S ^b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b Integrated Genomics   (Russian Federation)

Author keywords

Covariation; Mutual information; Orthologs; Paralogs; Transcription

Indexed keywords

PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; BACTERIAL MUTATION; CONTROLLED STUDY; CORRELATION ANALYSIS; DRUG DESIGN; GENOME; MOLECULAR RECOGNITION; NONHUMAN; ORTHOLOGY; PARALOGY; PREDICTION; PRIORITY JOURNAL; STATISTICAL MODEL; STATISTICAL SIGNIFICANCE;

BACTERIA (MICROORGANISMS);

EID: 0036352010     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00587-9     Document Type: Article

References (51)

1. Distinguishing homologous from analogous proteins
2. Homology a personal view on some of the problems
3. An apology for orthologs - Or brave new memes
4. Homologuephobia
5. Orthologs and paralogs - We need to get it right
6. Can sequence determine function?
7. Comparative genomics of the archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell
8. The cog database: A tool for genome-scale analysis of protein functions and evolution
9. Prediction of transcription regulatory sites in archaea by a comparative genomic approach
10. Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies
11. The use of gene clusters to infer functional coupling
12. Regulondb (version 3.2): Transcriptional regulation and operon organization in Escherichia coli k-12
13. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
14. Identifying DNA and protein patterns with statistically significant a ligments of multiple sequences
15. A comparative genomics approach to prediction of new members of regulons
16. Furilisin: A variant of subtilisin bpn' engineered for cleaving tribasic substrates
17. Secret life of genes
18. Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation
19. A method to predict functional residues in proteins
20. An evolutionary trace method defines binding surfaces common to protein families
21. Identification of functional surfaces of the zinc binding domains of intracellular receptors
22. Analysis and prediction of functional sub-types from protein sequence alignments
23. Mouse-human orthology relationships in an olfactory receptor gene cluster
24. Predicting ligand-binding function in families of bacterial receptors
25. The roles of residues 5 and 9 of the recognition helix of lac repressor in lac operator binding
26. Mutant lac repressors with new specificities hint at rules for protein-DNA recognition
27. The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions
28. The X-ray structure of the purr-guanine-purf operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated
29. Crystallographic analysis of lac repressor bound to natural operator o1
30. Evolutionarily conserved pathways of energetic connectivity in protein families
31. Al2co: Calculation of positional conservation in a protein sequence alignment
32. Lac repressor mutants with double or triple exchanges in the recognition helix bind specifically to lac operator variants with multiple exchanges
33. Evolution of an enzyme active site: The structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase
34. Super-sites within superfolds. Binding site similarity in the absence of homology
35. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
36. Software for analysis of bacterial genomes
37. The swiss-prot protein sequence database and its supplement trembl in 2000
38. Covariation of residues in the homeodomain sequence family
39. Matrixplot: Visualizing sequence constraints
40. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis
41. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum
42. Complete genome sequence of an m1 strain of Streptococcus pyogenes
43. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae
44. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae
45. The complete genome sequence of Escherichia coli k-12
46. Genome sequence of Yersinia pestis, the causative agent of plague
47. Whole-genome random sequencing and assembly of Haemophilus influenzae rd
48. Complete genome sequence of Pseudomonas aeruginosa pa01, an opportunistic pathogen