Protein database searches for multiple alignments.

Abstract:

:Protein database searches frequently can reveal biologically significant sequence relationships useful in understanding structure and function. Weak but meaningful sequence patterns can be obscured, however, by other similarities due only to chance. By searching a database for multiple as opposed to pairwise alignments, distant relationships are much more easily distinguished from background noise. Recent statistical results permit the power of this approach to be analyzed. Given a typical query sequence, an algorithm described here permits the current protein database to be searched for three-sequence alignments in less than 4 min. Such searches have revealed a variety of subtle relationships that pairwise search methods would be unable to detect.

authors

Altschul SF,Lipman DJ

doi

10.1073/pnas.87.14.5509

subject

Has Abstract

pub_date

1990-07-01 00:00:00

pages

5509-13

issue

14

eissn

0027-8424

issn

1091-6490

journal_volume

87

pub_type

杂志文章
  • Kinetic isotope effects in Ras-catalyzed GTP hydrolysis: evidence for a loose transition state.

    abstract::A remote labeling method has been developed to determine (18)O kinetic isotope effects (KIEs) in Ras-catalyzed GTP hydrolysis. Substrate mixtures consist of (13)C-depleted GTP and [(18)O,(13)C]GTP that contains (18)O at phosphoryl positions of mechanistic interest and (13)C at all carbon positions of the guanosine moi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0401675101

    authors: Du X,Black GE,Lecchi P,Abramson FP,Sprang SR

    更新日期:2004-06-15 00:00:00

  • Role of the F-box protein Skp2 in lymphomagenesis.

    abstract::The F-box protein Skp2 (S-phase kinase-associated protein 2) positively regulates the G(1)-S transition by controlling the stability of several G(1) regulators, such as the cell cycle inhibitor p27. We show here that Skp2 expression correlates directly with grade of malignancy and inversely with p27 levels in human ly...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.041475098

    authors: Latres E,Chiarle R,Schulman BA,Pavletich NP,Pellicer A,Inghirami G,Pagano M

    更新日期:2001-02-27 00:00:00

  • Crystal structure of the bacteriophage T4 late-transcription coactivator gp33 with the β-subunit flap domain of Escherichia coli RNA polymerase.

    abstract::Activated transcription of the bacteriophage T4 late genes, which is coupled to concurrent DNA replication, is accomplished by an initiation complex containing the host RNA polymerase associated with two phage-encoded proteins, gp55 (the basal promoter specificity factor) and gp33 (the coactivator), as well as the DNA...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1113328108

    authors: Twist KA,Campbell EA,Deighan P,Nechaev S,Jain V,Geiduschek EP,Hochschild A,Darst SA

    更新日期:2011-12-13 00:00:00

  • Microbial tryptophan metabolites regulate gut barrier function via the aryl hydrocarbon receptor.

    abstract::Inflammatory bowel diseases (IBDs), including Crohn's disease and ulcerative colitis, are associated with dysbiosis of the gut microbiome. Emerging evidence suggests that small-molecule metabolites derived from bacterial breakdown of a variety of dietary nutrients confer a wide array of host benefits, including amelio...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2000047117

    authors: Scott SA,Fu J,Chang PV

    更新日期:2020-08-11 00:00:00

  • NETSeq reveals heterogeneous nucleotide incorporation by RNA polymerase I.

    abstract::DNA sequence motifs that affect RNA polymerase transcription elongation are well studied in prokaryotic organisms and contribute directly to regulation of gene expression. Despite significant work on the regulation of eukaryotic transcription, the effect of DNA template sequence on RNA polymerase I (Pol I) transcripti...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1809421115

    authors: Clarke AM,Engel KL,Giles KE,Petit CM,Schneider DA

    更新日期:2018-12-11 00:00:00

  • Circadian clock protein Rev-erbα regulates neuroinflammation.

    abstract::Circadian dysfunction is a common attribute of many neurodegenerative diseases, most of which are associated with neuroinflammation. Circadian rhythm dysfunction has been associated with inflammation in the periphery, but the role of the core clock in neuroinflammation remains poorly understood. Here we demonstrate th...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1812405116

    authors: Griffin P,Dimitry JM,Sheehan PW,Lananna BV,Guo C,Robinette ML,Hayes ME,Cedeño MR,Nadarajah CJ,Ezerskiy LA,Colonna M,Zhang J,Bauer AQ,Burris TP,Musiek ES

    更新日期:2019-03-12 00:00:00

  • Pronounced climatic variations in Alaska during the last two millennia.

    abstract::Paired oxygen-isotopic analyses of abiotic carbonate and benthic-ostracode shells from lake sediments provide a continuous quantitative record of growing-season temperature for the past 2000 years in the northwestern foothills of the Alaska Range. This record reveals three time intervals of comparable warmth: anno Dom...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.181333798

    authors: Hu FS,Ito E,Brown TA,Curry BB,Engstrom DR

    更新日期:2001-09-11 00:00:00

  • Shifting transition states in the unfolding of a large ankyrin repeat protein.

    abstract::The 33-amino-acid ankyrin motif comprises a beta-turn followed by two anti-parallel alpha-helices and a loop and tandem arrays of the motif pack in a linear fashion to produce elongated structures characterized by short-range interactions. In this article we use site-directed mutagenesis to investigate the kinetic unf...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0705300105

    authors: Werbeck ND,Rowling PJ,Chellamuthu VR,Itzhaki LS

    更新日期:2008-07-22 00:00:00

  • Measuring the forces involved in polyvalent adhesion of uropathogenic Escherichia coli to mannose-presenting surfaces.

    abstract::Mechanisms of bacterial pathogenesis have become an increasingly important subject as pathogens have become increasingly resistant to current antibiotics. The adhesion of microorganisms to the surface of host tissue is often a first step in pathogenesis and is a plausible target for new antiinfective agents. Examinati...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.230451697

    authors: Liang MN,Smith SP,Metallo SJ,Choi IS,Prentiss M,Whitesides GM

    更新日期:2000-11-21 00:00:00

  • Multivariate proteomic analysis of murine embryonic stem cell self-renewal versus differentiation signaling.

    abstract::A number of extracellular stimuli, including soluble cytokines and insoluble matrix factors, are known to influence murine embryonic stem cell self-renewal and differentiation behavioral responses via intracellular signaling pathways, but their net effects in combination are difficult to understand. To gain insight co...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0308768101

    authors: Prudhomme W,Daley GQ,Zandstra P,Lauffenburger DA

    更新日期:2004-03-02 00:00:00

  • Aberrant calcium signaling by transglutaminase-mediated posttranslational modification of inositol 1,4,5-trisphosphate receptors.

    abstract::The inositol 1,4,5-trisphosphate receptor (IP3R) in the endoplasmic reticulum mediates calcium signaling that impinges on intracellular processes. IP3Rs are allosteric proteins comprising four subunits that form an ion channel activated by binding of IP3 at a distance. Defective allostery in IP3R is considered crucial...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1409730111

    authors: Hamada K,Terauchi A,Nakamura K,Higo T,Nukina N,Matsumoto N,Hisatsune C,Nakamura T,Mikoshiba K

    更新日期:2014-09-23 00:00:00

  • A rate threshold mechanism regulates MAPK stress signaling and survival.

    abstract::Cells are exposed to changes in extracellular stimulus concentration that vary as a function of rate. However, how cells integrate information conveyed from stimulation rate along with concentration remains poorly understood. Here, we examined how varying the rate of stress application alters budding yeast mitogen-act...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2004998118

    authors: Johnson AN,Li G,Jashnsaz H,Thiemicke A,Kesler BK,Rogers DC,Neuert G

    更新日期:2021-01-12 00:00:00

  • Placental overgrowth in mice lacking the imprinted gene Ipl.

    abstract::The Ipl (Tssc3) gene lies in an extended imprinted region of distal mouse chromosome 7, which also contains the Igf2 gene. Expression of Ipl is highest in placenta and yolk sac, where its mRNA is derived almost entirely from the maternal allele. Ipl encodes a small cytoplasmic protein with a pleckstrin-homology (PH) d...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.122039999

    authors: Frank D,Fortino W,Clark L,Musalo R,Wang W,Saxena A,Li CM,Reik W,Ludwig T,Tycko B

    更新日期:2002-05-28 00:00:00

  • Changes in cyclic nucleotide metabolism in aorta and heart of neurogenically hypertensive rats: possible trigger mechanism of hypertension.

    abstract::Changes in cyclic nucleotide metabolism similar to those characteristic of the chronic forms of hypertension were observed in an acute neurogenic form of hypertension in rats produced by electrolytic lesions of the nucleus tractus solitarii. These changes that were evident 2 hr after the lesions were made included dec...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.72.6.2135

    authors: Amer MS,Doba N,Reis DJ

    更新日期:1975-06-01 00:00:00

  • Benzo[a]pyrene diol epoxide-DNA cis adduct formation through a trans chlorohydrin intermediate.

    abstract::Alkylation of DNA by 7r,8t-dihydroxy,9t,10t-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (anti-BPDE) forms mainly trans adducts (with respect to the C-9/10 positions). We recently described a halide-catalyzed pathway that preferentially generates cis adducts and now report that the trans chlorohydrin of anti-BPDE (trans-BP...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.5.1749

    authors: Meehan T,Wolfe AR,Negrete GR,Song Q

    更新日期:1997-03-04 00:00:00

  • Bone patterning is altered in the regenerating zebrafish caudal fin after ectopic expression of sonic hedgehog and bmp2b or exposure to cyclopamine.

    abstract::Amputation of the zebrafish caudal fin stimulates regeneration of the dermal skeleton and reexpression of sonic hedgehog (shh)-signaling pathway genes. Expression patterns suggest a role for shh signaling in the secretion and patterning of the regenerating dermal bone, but a direct role has not been demonstrated. We e...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.122571799

    authors: Quint E,Smith A,Avaron F,Laforest L,Miles J,Gaffield W,Akimenko MA

    更新日期:2002-06-25 00:00:00

  • Tetrodotoxin-sensitive sodium channels in normal human fibroblasts and normal human glia-like cells.

    abstract::Tetrodotoxin-sensitive sodium channels are detectable in normal human fibroblasts and in "glia-like" cells at appreciable levels when compared to what is observed in established neuronal cell lines in culture. Two- to 3-fold stimulations of sodium influx are observed in the presence of 0.2 mM veratridine and scorpion ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.76.12.6425

    authors: Munson R Jr,Westermark B,Glaser L

    更新日期:1979-12-01 00:00:00

  • Identification of an adhesion factor for chondrocytes.

    abstract::The attachment of chondrocytes to collagen substrates is stimulated by serum but not by fibronectin. The active material in serum was partially purified and was shown to be a protein by its sensitivity to trypsin and heat and its chromatographic properties. This factor, which we have named chondronectin, is distinct f...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.1.385

    authors: Hewitt AT,Kleinman HK,Pennypacker JP,Martin GR

    更新日期:1980-01-01 00:00:00

  • Development of CD4+ T cells expressing a nominally MHC class I-restricted T cell receptor by two different mechanisms.

    abstract::Differences in T cell receptor (TCR) signaling initiated by interactions among TCRs, coreceptors, and self-peptide-MHC complexes determine the outcome of CD4 versus CD8 lineage of T cell differentiation. The H-2Ld and Kbm3 alloreactive 2C TCR is positively selected by MHC class I Kb and a yet-to-be identified nonclass...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0510561103

    authors: Ge Q,Holler PD,Mahajan VS,Nuygen T,Eisen HN,Chen J

    更新日期:2006-02-07 00:00:00

  • Control of the initiation of DNA synthesis in 3T3 cells: low-molecular weight nutrients.

    abstract::Sparse 3T3 cells, in excess serum, become quiescent in the early G(1) (or G(0)) phase of the cell cycle if the cells are cultured in low concentrations of amino acids, glucose, or phosphate ion. These quiescent cells then initiate DNA synthesis if the concentration of the limiting nutrient is increased. In normal medi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.71.8.2942

    authors: Holley RW,Kiernan JA

    更新日期:1974-08-01 00:00:00

  • Modified recombination and transmission of mitochondrial genetic markers in rho minus mutants of Saccharomyces cerevisiae.

    abstract::A large number of primary petite (rho-) clones were isolated after ethidium bromide mutagenesis of various grande (rho+) strains of S. cerevisiae that contained the mitochondrial genetic markers, CR, ER, OIR (or OIIR), and PR. From the frequency of coretention of markers in the petites, we have deduced a probable circ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.73.12.4608

    authors: Boltin-Fukuhara M,Fukuhara H

    更新日期:1976-12-01 00:00:00

  • A localized differentiation-inducing-factor sink in the front of the Dictyostelium slug.

    abstract::Differentiation-inducing factor 1 [DIF-1; 1-(3,5-dichloro-2,6-dihydroxy-4-methoxyphenyl)-hexan-1-one] induces stalk cell differentiation during Dictyostelium development. It is present as a gradient in the multicellular slug, its lowest concentration being in the anterior. Here we demonstrate the existence of a locali...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.90.2.487

    authors: Kay RR,Large S,Traynor D,Nayler O

    更新日期:1993-01-15 00:00:00

  • Formation of hybrid complexes between Ca and the ionophores bromolasalocid (Br-X537A) and A23187.

    abstract::The ionophores A23187 and bromolasalocid (Br-X537A) acted synergistically in translocating Ca(2+) from an aqueous into an organic immiscible phase or in mediating Ca(2+) transport across the organic phase, the effects obtained in the simultaneous presence of both ionophores being greater than those expected from a sum...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.78.1.279

    authors: Deleers M,Gelbcke M,Malaisse WJ

    更新日期:1981-01-01 00:00:00

  • Top-down versus bottom-up and the Ruritanian bean bug.

    abstract::In a recent article, Hunter uses the late George Varley and George Gradwell's long-term data on the winter moth (Operophtera brumata) and green tortrix (Tortrix viridana) populations to propose a method of quantifying the relative importance of top-down effects (because of natural enemies) and bottom-up effects (becau...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.18.10661

    authors: Hassell MP,Crawley MJ,Godfray HC,Lawton JH

    更新日期:1998-09-01 00:00:00

  • Electrochemical and homogeneous electron transfers to the Alzheimer amyloid-beta copper complex follow a preorganization mechanism.

    abstract::Deciphering the electron transfer reactivity characteristics of amyloid β-peptide copper complexes is an important task in connection with the role they are assumed to play in Alzheimer's disease. A systematic analysis of this question with the example of the amyloid β-peptide copper complex by means of its electroche...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1011315107

    authors: Balland V,Hureau C,Savéant JM

    更新日期:2010-10-05 00:00:00

  • Brain-derived neurotrophic factor: subcellular compartmentalization and interneuronal transfer as visualized with anti-peptide antibodies.

    abstract::The recent cloning of a second member of the nerve growth factor family, brain-derived neurotrophic factor (BDNF), has prompted investigation into the cells that express this factor's mRNA and protein. In the present study, antibodies raised against unique peptide sequences within the porcine BDNF protein detect BDNF-...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.21.9843

    authors: Wetmore C,Cao YH,Pettersson RF,Olson L

    更新日期:1991-11-01 00:00:00

  • Solubilization and purification of the alpha 1-adrenergic receptor using a novel affinity resin.

    abstract::The highly selective alpha 1-adrenergic receptor antagonist prazosin was used to identify binding sites having alpha-adrenergic specificity in rat hepatic plasma membranes. Solubilization of the membrane-bound receptors was achieved by incubation with the nonionic detergent digitonin, and binding activity was assayed ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.79.7.2186

    authors: Graham RM,Hess HJ,Homcy CJ

    更新日期:1982-04-01 00:00:00

  • Dynorphin A and cAMP-dependent protein kinase independently regulate neuronal calcium currents.

    abstract::The kappa-selective opioid peptide dynorphin A (DYN) inhibits neuronal adenylate cyclase activity and reduces neuronal voltage-dependent calcium currents. It is not yet known, however, whether the regulation of calcium channel activity is dependent on or independent of the adenylate cyclase/cAMP system. We used the wh...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.18.7025

    authors: Gross RA,Moises HC,Uhler MD,Macdonald RL

    更新日期:1990-09-01 00:00:00

  • Native topology determines force-induced unfolding pathways in globular proteins.

    abstract::Single-molecule manipulation techniques reveal that stretching unravels individually folded domains in the muscle protein titin and the extracellular matrix protein tenascin. These elastic proteins contain tandem repeats of folded domains with beta-sandwich architecture. Herein, we propose by stretching two model sequ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.97.13.7254

    authors: Klimov DK,Thirumalai D

    更新日期:2000-06-20 00:00:00

  • Differential brain activity states during the perception and nonperception of illusory motion as revealed by magnetoencephalography.

    abstract::We studied visual perception using an annular random-dot motion stimulus called the racetrack. We recorded neural activity using magnetoencephalography while subjects viewed variants of this stimulus that contained no inherent motion or various degrees of embedded motion. Subjects reported seeing rotary motion during ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章,随机对照试验

    doi:10.1073/pnas.1009857108

    authors: Crowe DA,Leuthold AC,Georgopoulos AP

    更新日期:2010-12-28 00:00:00