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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Sequence Alignment

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Disease relevance of Sequence Alignment

  • Based on sequence alignments with other histidine kinases, we dissected the Salmonella enterica Mg2+-sensor PhoQ in different subdomains and examined by in vivo and in vitro assays its interaction with the associated response regulator PhoP [1].
  • Via sequence alignments, based upon the crystal structure of the closely related Pseudomonas glumae lipase, a model has been made of the secondary-structure elements in AcLipA [2].
  • This multiple sequence alignment of paramyxovirus HN proteins was used as an intermediate to align the morbillivirus hemagglutinin (H) proteins with neuraminidase [3].
  • We also constructed SNV-based gag-pol chimeric variants by replacing the SNV integrase with the HIV-1 integrase, based on multiple sequence alignments and domain analyses [4].
  • Sequence alignments and secondary-structure prediction for HPV-16 E1 and other superfamily 3 (SF3) viral helicases closely parallel the mapping data in suggesting that aa 439 to 623 constitute a discrete helicase domain [5].

High impact information on Sequence Alignment


Chemical compound and disease context of Sequence Alignment


Biological context of Sequence Alignment


Anatomical context of Sequence Alignment

  • Finally, sequence alignments suggest that all three linker subdomains are highly conserved among the large subfamily of histidine kinase-coupled sensory receptors that possess methylation sites for use in covalent adaptation [21].
  • We have used polymerase chain reaction and highly degenerate, inosine containing oligonucleotides derived from sequence alignments of the transmembrane regions 2 and 7 of a number of G-binding protein receptors including the lutropin/choriogonadotropin (LH/CG) receptors to amplify various cDNAs from human thyroid cDNA [22].
  • Multiple DNA and protein sequence alignments have been constructed for the human T-cell receptor alpha/delta, beta, and gamma (TCRA/D, B, and G) variable (V) gene segments [23].

Associations of Sequence Alignment with chemical compounds

  • Sequence alignment and modeling of interleukin (IL)-3R and IL-5R identified an arginine residue at the tip of a beta turn in a highly divergent context at the F'-G' loop, close to a conserved structural element, the WSXWS motif, suggesting the possibility of a ligand association mechanism similar to the one described herein for GMR [24].
  • Multiple sequence alignments have been made based on structural information; they indicate that there will be only a limited number of canonical conformations for the first and second CDR loops [25].
  • Sequence alignment of known SNAPs revealed only leucine 294 to be conserved in the final 10 amino acids of alpha-SNAP [26].
  • Multiple sequence alignment of these MIF homologues reveals additional invariant residues that span the entire polypeptide but are in close proximity to the N-terminal proline in the folded protein [27].
  • Sequence alignment of P4.2 with these two transglutaminases, however, revealed that P4.2 lacks the critical cysteine residue required for the enzymatic crosslinking of substrates [28].

Gene context of Sequence Alignment

  • Sequence alignments and secondary structure predictions verified that mHip1R belongs to the Sla2 protein family [29].
  • Analysis of sequence alignments with IL-1 beta from other mammalian species shows the interior to be very well conserved with the exterior residues markedly less so [30].
  • Sequence alignments show that Hk, together with mammalian Kv beta, represents an additional branch of the aldo-keto reductase superfamily [31].
  • Moreover, based on these structures and sequence alignment of the FGF family, we propose that the Pro-253 --> Arg mutation will indiscriminately increase the affinity of FGFR2 toward any FGF [32].
  • Using multiple sequence alignment, we identified two vertebrate-conserved TERT N-terminal regions containing vertebrate-specific residues that were required for human telomerase activity [33].

Analytical, diagnostic and therapeutic context of Sequence Alignment


  1. The H box-harboring domain is key to the function of the Salmonella enterica PhoQ Mg2+-sensor in the recognition of its partner PhoP. Castelli, M.E., Cauerhff, A., Amongero, M., Soncini, F.C., Vescovi, E.G. J. Biol. Chem. (2003) [Pubmed]
  2. Characterization of the extracellular lipase, LipA, of Acinetobacter calcoaceticus BD413 and sequence analysis of the cloned structural gene. Kok, R.G., van Thor, J.J., Nugteren-Roodzant, I.M., Brouwer, M.B., Egmond, M.R., Nudel, C.B., Vosman, B., Hellingwerf, K.J. Mol. Microbiol. (1995) [Pubmed]
  3. Sequence and structure alignment of Paramyxoviridae attachment proteins and discovery of enzymatic activity for a morbillivirus hemagglutinin. Langedijk, J.P., Daus, F.J., van Oirschot, J.T. J. Virol. (1997) [Pubmed]
  4. Cross-packaging of human immunodeficiency virus type 1 vector RNA by spleen necrosis virus proteins: construction of a new generation of spleen necrosis virus-derived retroviral vectors. Parveen, Z., Mukhtar, M., Goodrich, A., Acheampong, E., Dornburg, R., Pomerantz, R.J. J. Virol. (2004) [Pubmed]
  5. A C-terminal helicase domain of the human papillomavirus E1 protein binds E2 and the DNA polymerase alpha-primase p68 subunit. Masterson, P.J., Stanley, M.A., Lewis, A.P., Romanos, M.A. J. Virol. (1998) [Pubmed]
  6. Molybdenum-cofactor-containing enzymes: structure and mechanism. Kisker, C., Schindelin, H., Rees, D.C. Annu. Rev. Biochem. (1997) [Pubmed]
  7. The crystal structure and biological function of leukemia inhibitory factor: implications for receptor binding. Robinson, R.C., Grey, L.M., Staunton, D., Vankelecom, H., Vernallis, A.B., Moreau, J.F., Stuart, D.I., Heath, J.K., Jones, E.Y. Cell (1994) [Pubmed]
  8. AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Falnes, P.Ø., Johansen, R.F., Seeberg, E. Nature (2002) [Pubmed]
  9. Positional recognition of a tRNA determinant dependent on a peptide insertion. Lovato, M.A., Swairjo, M.A., Schimmel, P. Mol. Cell (2004) [Pubmed]
  10. Mediator-nucleosome interaction. Lorch, Y., Beve, J., Gustafsson, C.M., Myers, L.C., Kornberg, R.D. Mol. Cell (2000) [Pubmed]
  11. Complete amino acid sequence of streptokinase and its homology with serine proteases. Jackson, K.W., Tang, J. Biochemistry (1982) [Pubmed]
  12. Photoaffinity labeling with UMP of lysine 992 of carbamyl phosphate synthetase from Escherichia coli allows identification of the binding site for the pyrimidine inhibitor. Cervera, J., Bendala, E., Britton, H.G., Bueso, J., Nassif, Z., Lusty, C.J., Rubio, V. Biochemistry (1996) [Pubmed]
  13. Identification of the RNA-binding sites of the triple gene block protein 1 of bamboo mosaic potexvirus. Wung, C.H., Hsu, Y.H., Liou, D.Y., Huang, W.C., Lin, N.S., Chang, B.Y. J. Gen. Virol. (1999) [Pubmed]
  14. Ferric enterochelin transport in Yersinia enterocolitica: molecular and evolutionary aspects. Schubert, S., Fischer, D., Heesemann, J. J. Bacteriol. (1999) [Pubmed]
  15. Crystal structure of the Escherichia coli peptide methionine sulphoxide reductase at 1.9 A resolution. Tête-Favier, F., Cobessi, D., Boschi-Muller, S., Azza, S., Branlant, G., Aubry, A. Structure (2000) [Pubmed]
  16. XRCC2 and XRCC3, new human Rad51-family members, promote chromosome stability and protect against DNA cross-links and other damages. Liu, N., Lamerdin, J.E., Tebbs, R.S., Schild, D., Tucker, J.D., Shen, M.R., Brookman, K.W., Siciliano, M.J., Walter, C.A., Fan, W., Narayana, L.S., Zhou, Z.Q., Adamson, A.W., Sorensen, K.J., Chen, D.J., Jones, N.J., Thompson, L.H. Mol. Cell (1998) [Pubmed]
  17. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Saxonov, S., Berg, P., Brutlag, D.L. Proc. Natl. Acad. Sci. U.S.A. (2006) [Pubmed]
  18. ECgene: genome-based EST clustering and gene modeling for alternative splicing. Kim, N., Shin, S., Lee, S. Genome Res. (2005) [Pubmed]
  19. Essential histidine at the active site of sorghum leaf NADP-dependent malate dehydrogenase. Lemaire, M., Schmitter, J.M., Issakidis, E., Miginiac-Maslow, M., Gadal, P., Decottignies, P. J. Biol. Chem. (1994) [Pubmed]
  20. Direct binding of p130(Cas) to the guanine nucleotide exchange factor C3G. Kirsch, K.H., Georgescu, M.M., Hanafusa, H. J. Biol. Chem. (1998) [Pubmed]
  21. Cysteine and disulfide scanning reveals two amphiphilic helices in the linker region of the aspartate chemoreceptor. Butler, S.L., Falke, J.J. Biochemistry (1998) [Pubmed]
  22. Molecular cloning of a human thyrotropin receptor cDNA fragment. Use of highly degenerate, inosine containing primers derived from aligned amino acid sequences of a homologous family of glycoprotein hormone receptors. Huang, G.C., Page, M.J., Roberts, A.J., Malik, A.N., Spence, H., McGregor, A.M., Banga, J.P. FEBS Lett. (1990) [Pubmed]
  23. Human T-cell receptor variable gene segment families. Arden, B., Clark, S.P., Kabelitz, D., Mak, T.W. Immunogenetics (1995) [Pubmed]
  24. Crucial role of the residue R280 at the F'-G' loop of the human granulocyte/macrophage colony-stimulating factor receptor alpha chain for ligand recognition. Rajotte, D., Cadieux, C., Haman, A., Wilkes, B.C., Clark, S.C., Hercus, T., Woodcock, J.A., Lopez, A., Hoang, T. J. Exp. Med. (1997) [Pubmed]
  25. Conserved motifs in T-cell receptor CDR1 and CDR2: implications for ligand and CD8 co-receptor binding. Arden, B. Curr. Opin. Immunol. (1998) [Pubmed]
  26. Stimulation of NSF ATPase activity by alpha-SNAP is required for SNARE complex disassembly and exocytosis. Barnard, R.J., Morgan, A., Burgoyne, R.D. J. Cell Biol. (1997) [Pubmed]
  27. Direct link between cytokine activity and a catalytic site for macrophage migration inhibitory factor. Swope, M., Sun, H.W., Blake, P.R., Lolis, E. EMBO J. (1998) [Pubmed]
  28. Molecular cloning of human protein 4.2: a major component of the erythrocyte membrane. Sung, L.A., Chien, S., Chang, L.S., Lambert, K., Bliss, S.A., Bouhassira, E.E., Nagel, R.L., Schwartz, R.S., Rybicki, A.C. Proc. Natl. Acad. Sci. U.S.A. (1990) [Pubmed]
  29. An actin-binding protein of the Sla2/Huntingtin interacting protein 1 family is a novel component of clathrin-coated pits and vesicles. Engqvist-Goldstein, A.E., Kessels, M.M., Chopra, V.S., Hayden, M.R., Drubin, D.G. J. Cell Biol. (1999) [Pubmed]
  30. Crystallographic refinement of interleukin 1 beta at 2.0 A resolution. Priestle, J.P., Schär, H.P., Grütter, M.G. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  31. A potassium channel beta subunit related to the aldo-keto reductase superfamily is encoded by the Drosophila hyperkinetic locus. Chouinard, S.W., Wilson, G.F., Schlimgen, A.K., Ganetzky, B. Proc. Natl. Acad. Sci. U.S.A. (1995) [Pubmed]
  32. Structural basis for fibroblast growth factor receptor 2 activation in Apert syndrome. Ibrahimi, O.A., Eliseenkova, A.V., Plotnikov, A.N., Yu, K., Ornitz, D.M., Mohammadi, M. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  33. Functional multimerization of human telomerase requires an RNA interaction domain in the N terminus of the catalytic subunit. Moriarty, T.J., Huard, S., Dupuis, S., Autexier, C. Mol. Cell. Biol. (2002) [Pubmed]
  34. Arabidopsis VILLIN1 generates actin filament cables that are resistant to depolymerization. Huang, S., Robinson, R.C., Gao, L.Y., Matsumoto, T., Brunet, A., Blanchoin, L., Staiger, C.J. Plant Cell (2005) [Pubmed]
  35. PANTHER: a library of protein families and subfamilies indexed by function. Thomas, P.D., Campbell, M.J., Kejariwal, A., Mi, H., Karlak, B., Daverman, R., Diemer, K., Muruganujan, A., Narechania, A. Genome Res. (2003) [Pubmed]
  36. Selective loss of either the epimerase or kinase activity of UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase due to site-directed mutagenesis based on sequence alignments. Effertz, K., Hinderlich, S., Reutter, W. J. Biol. Chem. (1999) [Pubmed]
  37. Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction. Erb, R.W., Wagner-Döbler, I. Appl. Environ. Microbiol. (1993) [Pubmed]
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