Home LiteratureArticle Details
PMID: 8871566 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Searching databases of conserved sequence regions by aligning protein multiple-alignments.

Nucleic acids research ·Vol. 24 ·No. 19 ·1996-10-01 ·Pages 3836-45

Pietrokovski S

Abstract

A general searching method for comparing multiple sequence alignments was developed to detect sequence relationships between conserved protein regions. Multiple alignments are treated as sequences of amino acid distributions and aligned by comparing pairs of such distributions. Four different comparison measures were tested and the Pearson correlation coefficient chosen. The method is sensitive, detecting weak sequence relationships between protein families. Relationships are detected beyond the range of conventional sequence database searches, illustrating the potential usefulness of the method. The previously undetected relation between flavoprotein subunits of two oxidoreductase families points to the potential active site in one of the families. The similarity between the bacterial RecA, DnaA and Rad51 protein families reveals a region in DnaA and Rad51 proteins likely to bind and unstack single-stranded DNA. Helix--turn--helix DNA binding domains from diverse proteins are readily detected and shown to be similar to each other. Glycosylasparaginase and gamma-glutamyltransferase enzymes are found to be similar in their proteolytic cleavage sites. The method has been fully implemented on the World Wide Web at URL: http://blocks.fhcrc.org/blocks-bin/LAMAvsearch.

MeSH Terms
Amino Acid Sequence Aspartylglucosylaminase/chemistry,metabolism Catalysis Conserved Sequence DNA Nucleotidyltransferases/chemistry,metabolism DNA, Single-Stranded/metabolism DNA-Binding Proteins/chemistry,metabolism Databases, Factual Flavin-Adenine Dinucleotide/metabolism Helix-Turn-Helix Motifs Hydrolysis Proteins/chemistry,metabolism Sequence Homology, Amino Acid Transposases gamma-Glutamyltransferase/chemistry,metabolism
Chemicals
DNA, Single-Stranded DNA-Binding Proteins Proteins Flavin-Adenine Dinucleotide gamma-Glutamyltransferase DNA Nucleotidyltransferases Transposases Aspartylglucosylaminase
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Pietrokovski S
Fred Hutchinson Cancer Research Center, Seattle, WA 98104, USA.
References (70)
70 references, click to expand
  1. Molecular cloning and sequence analysis of Flavobacterium meningosepticum glycosylasparaginase: a single gene encodes the alpha and beta subunits.
    Arch Biochem Biophys. 1995 Jan 10;316(1):399-406 PMID: 7840643
  2. Effect of site-directed mutations on processing and activity of gamma-glutamyltranspeptidase of Escherichia coli K-12.
    J Biochem. 1995 Jul;118(1):75-80 PMID: 8537328
  3. Comparison of methods for searching protein sequence databases.
    Protein Sci. 1995 Jun;4(6):1145-60 PMID: 7549879
  4. Gibbs motif sampling: detection of bacterial outer membrane protein repeats.
    Protein Sci. 1995 Aug;4(8):1618-32 PMID: 8520488
  5. gamma-Glutamyl transpeptidase. What does the organization and expression of a multipromoter gene tell us about its functions?
    Am J Pathol. 1995 Nov;147(5):1175-85 PMID: 7485380
  6. Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications.
    Proc Natl Acad Sci U S A. 1995 Dec 5;92(25):11921-5 PMID: 8524875
  7. Activation of glycosylasparaginase. Formation of active N-terminal threonine by intramolecular autoproteolysis.
    J Biol Chem. 1996 Jan 19;271(3):1732-7 PMID: 8576176
  8. Structure of the active ternary complex of pig heart lactate dehydrogenase with S-lac-NAD at 2.7 A resolution.
    J Mol Biol. 1981 Sep 15;151(2):289-307 PMID: 7338899
  9. FAD-binding site of glutathione reductase.
    J Mol Biol. 1982 Sep 15;160(2):287-308 PMID: 7175934
  10. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold.
    EMBO J. 1982;1(8):945-51 PMID: 6329717
  11. Protein-DNA recognition.
    Annu Rev Biochem. 1984;53:293-321 PMID: 6236744
  12. Characterization of a processing protease that converts the precursor form of gamma-glutamyltranspeptidase to its subunits.
    Biochem Int. 1984 Apr;8(4):581-8 PMID: 6148085
  13. Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint.
    J Mol Biol. 1986 Jan 5;187(1):101-7 PMID: 3959077
  14. Profile analysis: detection of distantly related proteins.
    Proc Natl Acad Sci U S A. 1987 Jul;84(13):4355-8 PMID: 3474607
  15. Systematic method for the detection of potential lambda Cro-like DNA-binding regions in proteins.
    J Mol Biol. 1987 Apr 5;194(3):557-64 PMID: 3625774
  16. Refined crystal structure of dogfish M4 apo-lactate dehydrogenase.
    J Mol Biol. 1987 Dec 5;198(3):445-67 PMID: 3430615
  17. Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome.
    Cell. 1988 Mar 11;52(5):743-55 PMID: 2830993
  18. A flexible method to align large numbers of biological sequences.
    J Mol Evol. 1988 Dec-1989 Feb;28(1-2):161-9 PMID: 3148736
  19. RNA recognition and translational regulation by a homeodomain protein.
    Nature. 1996 Feb 22;379(6567):694-9 PMID: 8602214
  20. Evolutionary conservation of RecA genes in relation to protein structure and function.
    J Bacteriol. 1996 Apr;178(7):1881-94 PMID: 8606161
  21. Homologous DNA pairing promoted by a 20-amino acid peptide derived from RecA.
    Science. 1996 May 10;272(5263):868-72 PMID: 8629021
  22. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer.
    Science. 1996 Mar 1;271(5253):1247-54 PMID: 8638105
  23. recA-like genes from three archaean species with putative protein products similar to Rad51 and Dmc1 proteins of the yeast Saccharomyces cerevisiae.
    Nucleic Acids Res. 1996 Jun 1;24(11):2125-32 PMID: 8668545
  24. Blocks database and its applications.
    Methods Enzymol. 1996;266:88-105 PMID: 8743679
  25. Using substitution probabilities to improve position-specific scoring matrices.
    Comput Appl Biosci. 1996 Apr;12(2):135-43 PMID: 8744776
  26. Determining residue-base interactions between AraC protein and araI DNA.
    J Mol Biol. 1989 Oct 20;209(4):607-22 PMID: 2531226
  27. Automatic generation of primary sequence patterns from sets of related protein sequences.
    Proc Natl Acad Sci U S A. 1990 Jan;87(1):118-22 PMID: 2296575
  28. The N-terminal domain of the insertion sequence 30 transposase interacts specifically with the terminal inverted repeats of the element.
    J Biol Chem. 1990 Mar 5;265(7):3757-62 PMID: 2154486
  29. Protein database searches for multiple alignments.
    Proc Natl Acad Sci U S A. 1990 Jul;87(14):5509-13 PMID: 2196570
  30. Improved detection of helix-turn-helix DNA-binding motifs in protein sequences.
    Nucleic Acids Res. 1990 Sep 11;18(17):5019-26 PMID: 2402433
  31. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  32. Sequence logos: a new way to display consensus sequences.
    Nucleic Acids Res. 1990 Oct 25;18(20):6097-100 PMID: 2172928
  33. Cloning and sequence analysis of a cDNA for human glycosylasparaginase. A single gene encodes the subunits of this lysosomal amidase.
    FEBS Lett. 1990 Dec 10;276(1-2):232 PMID: 2265705
  34. The RecA protein: structure and function.
    Crit Rev Biochem Mol Biol. 1990;25(6):415-56 PMID: 2292186
  35. Glycosaparaginase from human leukocytes. Inactivation and covalent modification with diazo-oxonorvaline.
    J Biol Chem. 1991 Mar 25;266(9):5860-9 PMID: 2005122
  36. Studies on Phe-228 and Leu-307 recombinant mutants of porcine kidney D-amino acid oxidase: expression, purification, and characterization.
    J Biochem. 1991 Jan;109(1):171-7 PMID: 1673125
  37. Database of homology-derived protein structures and the structural meaning of sequence alignment.
    Proteins. 1991;9(1):56-68 PMID: 2017436
  38. PROSITE: a dictionary of sites and patterns in proteins.
    Nucleic Acids Res. 1991 Apr 25;19 Suppl:2241-5 PMID: 2041810
  39. The SWISS-PROT protein sequence data bank.
    Nucleic Acids Res. 1991 Apr 25;19 Suppl:2247-9 PMID: 2041811
  40. Amino acid substitution matrices from an information theoretic perspective.
    J Mol Biol. 1991 Jun 5;219(3):555-65 PMID: 2051488
  41. Identification of active site residues of Escherichia coli fumarate reductase by site-directed mutagenesis.
    J Biol Chem. 1991 Jul 25;266(21):13572-9 PMID: 1856194
  42. Automated assembly of protein blocks for database searching.
    Nucleic Acids Res. 1991 Dec 11;19(23):6565-72 PMID: 1754394
  43. Structure of the recA protein-ADP complex.
    Nature. 1992 Jan 23;355(6358):374-6 PMID: 1731253
  44. Latent proteinase activity of gamma-glutamyl transpeptidase light subunit.
    J Biol Chem. 1979 Jun 25;254(12):4942-5 PMID: 36377
  45. Identification of common molecular subsequences.
    J Mol Biol. 1981 Mar 25;147(1):195-7 PMID: 7265238
  46. DMC1: a meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression.
    Cell. 1992 May 1;69(3):439-56 PMID: 1581960
  47. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein.
    Cell. 1992 May 1;69(3):457-70 PMID: 1581961
  48. Dynamic programming algorithms for biological sequence comparison.
    Methods Enzymol. 1992;210:575-601 PMID: 1584052
  49. The sequence of the flavoprotein subunit of bovine heart succinate dehydrogenase.
    J Biol Chem. 1992 Jun 5;267(16):11553-8 PMID: 1375942
  50. Detection of Caenorhabditis transposon homologs in diverse organisms.
    New Biol. 1992 Apr;4(4):382-8 PMID: 1320399
  51. Transcription factors: structural families and principles of DNA recognition.
    Annu Rev Biochem. 1992;61:1053-95 PMID: 1497306
  52. Cloning and sequencing of IS1086, an Alcaligenes eutrophus insertion element related to IS30 and IS4351.
    J Bacteriol. 1992 Dec;174(24):8133-8 PMID: 1334071
  53. Molecular basis of allosteric activation of bacterial L-lactate dehydrogenase.
    J Mol Biol. 1993 Mar 5;230(1):21-7 PMID: 8450537
  54. Ancient conserved regions in new gene sequences and the protein databases.
    Science. 1993 Mar 19;259(5102):1711-6 PMID: 8456298
  55. Structural relationship of bacterial RecA proteins to recombination proteins from bacteriophage T4 and yeast.
    Science. 1993 Mar 26;259(5103):1892-6 PMID: 8456313
  56. Similarity of the yeast RAD51 filament to the bacterial RecA filament.
    Science. 1993 Mar 26;259(5103):1896-9 PMID: 8456314
  57. A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication.
    Nucleic Acids Res. 1993 Jun 11;21(11):2541-7 PMID: 8332451
  58. Aspartylglycosaminuria: protein chemistry and molecular biology of the most common lysosomal storage disorder of glycoprotein degradation.
    FASEB J. 1993 Oct;7(13):1247-56 PMID: 8405810
  59. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
    Science. 1993 Oct 8;262(5131):208-14 PMID: 8211139
  60. Yeast chromosome III: new gene functions.
    EMBO J. 1994 Feb 1;13(3):493-503 PMID: 8313894
  61. The initiator protein DnaA: evolution, properties and function.
    Biochim Biophys Acta. 1994 Mar 1;1217(2):111-30 PMID: 8110826
  62. Protein family classification based on searching a database of blocks.
    Genomics. 1994 Jan 1;19(1):97-107 PMID: 8188249
  63. Improved sensitivity of profile searches through the use of sequence weights and gap excision.
    Comput Appl Biosci. 1994 Feb;10(1):19-29 PMID: 8193951
  64. Detecting patterns in protein sequences.
    J Mol Biol. 1994 Jun 24;239(5):698-712 PMID: 8014990
  65. Modular arrangement of proteins as inferred from analysis of homology.
    Protein Sci. 1994 Mar;3(3):482-92 PMID: 8019419
  66. Homologous genetic recombination: the pieces begin to fall into place.
    Crit Rev Microbiol. 1994;20(2):125-42 PMID: 8080625
  67. PRINTS--a database of protein motif fingerprints.
    Nucleic Acids Res. 1994 Sep;22(17):3590-6 PMID: 7937065
  68. Position-based sequence weights.
    J Mol Biol. 1994 Nov 4;243(4):574-8 PMID: 7966282
  69. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
    Nucleic Acids Res. 1994 Nov 11;22(22):4673-80 PMID: 7984417
  70. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks.
    Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):12091-5 PMID: 7991589
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/24.19.3836
Published
1996-10-01
Pages
3836-45
Language
English
Region
England
NLM ID
0411011
PMCID
PMC146152
Subset
IM
Grants
NIGMS NIH HHS · GM29009 · United States
Corrections
ErratumIn
-
External Links
PubMed source DOI: 10.1093/nar/24.19.3836 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2