CD-Search: protein domain annotations on the fly
Computational Biology Branch, NCBI, National Library of Medicine, NIH, Building 38A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
* To whom correspondence should be addressed. Tel: +1 301 435 4919; Fax: +1 301 480 9241; Email: bauer{at}ncbi.nlm.nih.gov
Received February 19, 2004; Revised and Accepted April 21, 2004
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONUSING CD-SearchINTERPRETING RESULTSALTERNATIVE ROUTES TO CD-Search...FUTURE DEVELOPMENTSREFERENCES |
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We describe the Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences. CD-Search uses BLAST® heuristics to provide a fast, interactive service, and searches a comprehensive collection of domain models. Search results are displayed as domain architecture cartoons and pairwise alignments between the query and domain-model consensus sequences. Search results may be visualized in further detail by embedding the query sequence into multiple alignment displays and by mapping onto three-dimensional molecular graphic displays of known structures within the domain family. CD-Search can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONUSING CD-SearchINTERPRETING RESULTSALTERNATIVE ROUTES TO CD-Search...FUTURE DEVELOPMENTSREFERENCES |
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The accelerating growth of the amount of protein sequence data is continuing to result in an urgent need for rapid computational annotation of protein sequences. A variety of useful resources have emerged, many at the level of protein domains and/or protein families. CD-Search combines the sensitivity of carefully constructed search models based on multiple sequence alignments with the speed and significance statistics of the BLAST® software suite. The sources of CD-Search's alignment model data are imported collections, such as Pfam (1) and SMART (2), and automated alignments supplied with the Clusters of Orthologous Groups (COGs) classifications (3). Curators at the NCBI are adding in an ongoing manner models for ancient, phylogenetically widespread domain families with structure-based alignments and explicitly recorded subfamily hierarchies (4). Domain-model alignments are converted into position-specific scoring matrices (PSSMs); protein query sequences can be scanned against these PSSMs with RPS-BLAST, a variant of the Psi-BLAST algorithm (5).
We have built a web service which runs live searches against large collections of PSSM search models for protein queries supplied by users. Execution times vary with query sequence length and search database size, and typically lie in the range of a few to about twenty seconds. CD-Search uses BLAST® statistics to evaluate the significance of query–subject alignments, and returns E-values (expectation values), which can be interpreted analogously to those obtained with Psi-BLAST.
CD-Search reports graphical summaries of the search results, a tabular list of hits and individual pairwise alignments between the user query and search model consensus sequences. Consensus sequences are not used in the calculation per se. They serve as placeholders for columns in the position-specific scoring matrix, their length chosen approximately as the median length of domain sequences in the multiple alignment. The balloons showing domain footprints on the query sequence are linked to more extensive visualization. Following these links, users can embed the query sequence into individual domain alignment displays and change parameters to emphasize patterns of sequence conservation. Domain models curated at the NCBI may carry annotation of functional features, in which case specific conserved columns are highlighted. This should make it easier to understand whether key functional residues are present in a query sequence and help to rule out chance similarities in query–database hits at the borderline of significance. Many domain families are linked to three-dimensional (3D) structure. In these cases we offer alignment visualization including embedded user query sequences with NCBI's 3D structure viewer Cn3D (6).
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USING CD-Search |
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TOPABSTRACTINTRODUCTIONUSING CD-SearchINTERPRETING RESULTSALTERNATIVE ROUTES TO CD-Search...FUTURE DEVELOPMENTSREFERENCES |
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Searches can be submitted at the following URL: http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. The search page allows the user to set a variety of parameters.
- Search database: currently we mirror some of the imported collections, as well as an all-inclusive set, the default. The default search set will be replaced with a less redundant collection in the near future.
- Query sequences can be supplied as raw sequences, FASTA-formatted sequences or sequence identifiers [‘GI’ (genInfo identifier) numbers or accessions] valid in the NCBI's Entrez protein database (7).
- An E-value threshold can be set to vary the search sensitivity and specificity. The default is 0.01.
- A filter for low-complexity regions in the query sequence is turned on by default. This reduces the likelihood of false-positive hits.
- The search heuristic can be switched from the default mode (multiple hits, one pass) to slightly more sensitive and more time-consuming options (single hit, one pass or two passes).
- Output formatting options allow the user to limit the number of hits returned, reduce redundancy in the graphical results summary, modify its size and change the style of the pairwise alignments.
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INTERPRETING RESULTS |
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TOPABSTRACTINTRODUCTIONUSING CD-SearchINTERPRETING RESULTSALTERNATIVE ROUTES TO CD-Search...FUTURE DEVELOPMENTSREFERENCES |
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Figure 1 shows the top of a CD-Search results page. The page lists the version of RPS-BLAST used in the process, repeats information about the query sequence and displays statistics on the search database used.
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The graphical results summary comes with a text box which reports such details as accessions, short names and E-values as the mouse pointer is placed over one of the balloons representing an individual hit. The query sequence is drawn as a black bar on the top of the image, with a ruler indicating its length. Sections colored in cyan have been filtered out as low-complexity regions in the database search. RPS-BLAST, the search engine behind CD-Search, typically does not extend alignments into these regions. Alignment details are shown in individual pairwise alignment displays in the bottom part of the page, where low-complexity regions are again explicitly indicated.
The individual balloons are assigned colors according to a fixed schema. The best scoring hit is colored red; the second-best scoring hit is colored blue; for example see the online help document for details. Hits to conserved domain models that are identified as related by the CDART resource (8) are given the same color. The redundancy present in the all-inclusive search set of the CDD (Conserved Domain Database) is readily visible in this example. Balloons are drawn so that they extend from the first to the last residue of the alignment footprints on the query sequence. These alignments may contain gapped-out regions, which are visible in the pairwise alignment displays at the bottom of the page but are not indicated in the graphical summary.
Balloons may have jagged edges. A jagged edge at the N- or C-terminus of a domain footprint indicates that >20% of the domain model's extent is missing from the RPS-BLAST pairwise alignment. Pairwise alignment displays at the bottom of the page list exact percentages of the domain models that were used in the alignment. In the example shown in Figure 1, the jagged edges indicate partial hits to N- and C-terminal parts of zinc-dependent metalloprotase domains (the partial hits are caused by the insertion of additional domains).
Balloons may also have indentations, such as the best scoring hit in the example shown in Figure 1. Indentations indicate that a repeat structure has been detected algorithmically in the search model; in Figure 1, the alignment model labeled ‘HX’ spans four copies of hemopexin-repeats.
Clicking on a balloon invokes a multiple alignment view which adds the matching fragment of the query sequence, aligned according to the RPS-BLAST algorithm. An example is shown in Figure 2. The user can modify conservation thresholds used for coloring columns in the alignment to better identify conserved sites, and can select subsets of family-member sequences to be included in the display. By default, alignment rows most similar to the query sequence are chosen. In many conserved domain models curated at the NCBI, conserved functional motifs have been recorded as features of that model. A feature's address is a set of columns in the multiple alignment. Features are highlighted with hash marks printed on top of the alignment blocks. Features are recorded together with evidence, which may consist of citations or specialized 3D displays. The evidence viewer is found at the bottom of the multiple alignment display (not shown in Figure 2). These alignment display options are intended to assist the user in predicting whether a query sequence is a true and/or functional member of the domain family (and in particular to allow users to better discriminate between chance similarities and actual homology when the statistical significance places a similarity in a ‘twilight zone’).
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A powerful aid in studying query–subject relationships is the availability of 3D information. A large proportion of domain models can be linked to one or several 3D structures, and the NCBI's 3D structure viewer, Cn3D, can be used to interactively visualize the structure together with the multiple alignment of a domain family. Information about annotated features can be accessed from within Cn3D, and this combination provides a unique set of tools to hypothesize about the effects of sequence variation on otherwise conserved sites, such as catalytic sets of residues or binding interfaces.
An example is shown in Figure 3. The Cn3D viewer is launched by clicking the button labeled ‘View 3D Structure’ on alignment display pages (Figure 2). Cn3D needs to be installed locally as a helper application; for details follow the link labeled ‘download Cn3D’ on the alignment display pages (Figure 2). The set of sequences displayed, together with the embedded query, the consensus and a representative 3D structure, can be controlled using the options next to the ‘Subset Rows’ button. By default, Cn3D will be launched with 10 aligned rows; sequences from the alignment model are picked as the ones most similar to the query (judged by the number of identical residues, according to the aligned footprint). For domain-alignment models curated at NCBI, several 3D structures may be shown at once, with structure super-positions precalculated in the curation process. Cn3D allows the user to interactively highlight residues in either the 3D or alignment view; highlights will immediately transfer to the other view. Cn3D also allows the user to explore prerecorded annotation of conserved features, feature evidence and prerecorded links to literature.
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ALTERNATIVE ROUTES TO CD-Search RESULTS |
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TOPABSTRACTINTRODUCTIONUSING CD-SearchINTERPRETING RESULTSALTERNATIVE ROUTES TO CD-Search...FUTURE DEVELOPMENTSREFERENCES |
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Conserved domain Searches have been precalculated for all but the newest proteins in the Entrez database. If a protein has been found to contain conserved domains, a link labeled ‘Domains’ is available on Entrez document summaries. Following this link, users are shown a simplified CD-Search results page which contains the graphical results summary only. From this point, the view can be expanded to give detailed search results.
By default, protein query sequences are sent to CD-Search when regular protein-BLAST searches are submitted at http://www.ncbi.nlm.nih.gov/BLAST/. While users wait for the protein-BLAST search to complete, results from the domain analysis may already be visible. BLAST's intermediate search page will show a graphical summary of the CD-Search outcome, which again can be expanded into a full view.
Users can download CD-Search databases and run RPS-BLAST locally, provided they download and install the NCBI toolkit to build local versions of the BLAST programs. Detailed instructions for downloading and configuring a set of several search databases can be found at ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/README.
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FUTURE DEVELOPMENTS |
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TOPABSTRACTINTRODUCTIONUSING CD-SearchINTERPRETING RESULTSALTERNATIVE ROUTES TO CD-Search...FUTURE DEVELOPMENTSREFERENCES |
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Over time we plan to replace non-curated domain families with hierarchies of extensively curated models. The default display styles for CD-Search hits will become less redundant and more informative, since organizing related families in hierarchies will allow us to better understand the meaning of overlapping domain footprints. Consequently we shall be able to implement changes in display styles which may improve the resource's user-friendliness.
We will also be able to provide better support for local RPS-BLAST search database construction. Those who wish to will be able to customize specialized search sets.
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Notes |
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The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.
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REFERENCES |
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TOPABSTRACTINTRODUCTIONUSING CD-SearchINTERPRETING RESULTSALTERNATIVE ROUTES TO CD-Search...FUTURE DEVELOPMENTSREFERENCES |
|---|
- Bateman,A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths-Jones,S., Khanna,A., Marshall,M., Moxon,S., Sonnhammer,E.L., Studholme,D.J., Yates,C. and Eddy,S.R. ( (2004) ) The Pfam protein families database. Nucleic Acids Res., , 32, , 138–141.
- Letunic,I., Copley,R.R., Schmidt,S., Ciccarelli,F.D., Doerks,T., Shultz,J., Ponting,C.P. and Bork,P. ( (2004) ) SMART 4.0: towards genomic data integration. Nucleic Acids Res., , 32, , 142–144.
- Tatusov,R.L, Fedorova,N.D., Jackson,J.D., Jacobs,A.R., Kiryutin,B., Koonin,E.V, Krylov,D.M., Mazumder,R., Mekhedov,S.L., Nikolskaya,A.N., Rao,B.S., Smirnov,S., Sverdlov,A.V., Vasudevan,S., Wolf,Y.I., Yin,J.J. and Natale,D.A. ( (2003) ) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, , 4, , 41.[CrossRef][Medline]
- Marchler-Bauer,A., Anderson,J.B., DeWeese-Scott,C., Fedorova,N.D., Geer,L.Y., He,S., Hurwitz,D.I., Jackson,J.D., Jacobs,A.R., Lanczycki,C.J., Liebert,C.A., Liu,C., Madej,T., Marchler,G.H., Mazumder,R., Nikolskaya,A.N., Panchenko,A.R., Rao,B.S., Shoemaker,B.A., Simonyan,V., Song,J.S., Thiessen,P.A., Vasudevan,S., Wang,Y., Yamashita,R.A., Yin,J.J. and Bryant,S.H. ( (2003) ) CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res., , 31, , 383–387.
[Abstract/Free Full Text] - Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. ( (1997) ) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., , 25, , 3389–3402.
[Abstract/Free Full Text] - Wang,Y., Geer,L.Y., Chappey,C., Kans,J.A. and Bryant,S.H. ( (2000) ) Cn3D: sequence and structure views for Entrez. Trends Biochem. Sci., , 25, , 300–302.[CrossRef][Web of Science][Medline]
- Wheeler,D.L., Church,D.M., Edgar,R., Federhen,S., Helmberg,W., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Sequeira,E., Suzek,T.O., Tatusova,T.A. and Wagner,L. ( (2004) ) Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res., , 32, , 35–40.
[Abstract/Free Full Text] - Geer,L.Y., Domrachev,M., Lipman,D.J. and Bryant,S.H. ( (2002) ) CDART: protein domain homology by domain architecture. Genome Res., , 12, , 1619–1623.
[Abstract/Free Full Text] - Wilhelm,S.M., Collier,I.E., Marmer,B.L, Eisen,A.Z., Grant,G.A. and Goldberg,G.I. ( (1989) ) SV40-transformed human lung fibroblasts secrete a 92-kDa type IV collagenase which is identical to that secreted by normal human macrophages. J. Biol. Chem., , 264, , 17213–17221.
[Abstract/Free Full Text]
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|
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M. Harper, J. D. Boyce, A. D. Cox, F. St. Michael, I. W. Wilkie, P. J. Blackall, and B. Adler Pasteurella multocida Expresses Two Lipopolysaccharide Glycoforms Simultaneously, but Only a Single Form Is Required for Virulence: Identification of Two Acceptor-Specific Heptosyl I Transferases Infect. Immun., August 1, 2007; 75(8): 3885 - 3893. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. W. Brown, R. A. E. Butchko, M. Busman, and R. H. Proctor The Fusarium verticillioides FUM Gene Cluster Encodes a Zn(II)2Cys6 Protein That Affects FUM Gene Expression and Fumonisin Production Eukaryot. Cell, July 1, 2007; 6(7): 1210 - 1218. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-K. Kim and L. L. McCarter ScrG, a GGDEF-EAL Protein, Participates in Regulating Swarming and Sticking in Vibrio parahaemolyticus J. Bacteriol., June 1, 2007; 189(11): 4094 - 4107. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. Penas, A. Hervas-Aguilar, T. Munera-Huertas, E. Reoyo, M. A. Penalva, H. N. Arst Jr., and J. Tilburn Further Characterization of the Signaling Proteolysis Step in the Aspergillus nidulans pH Signal Transduction Pathway Eukaryot. Cell, June 1, 2007; 6(6): 960 - 970. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. S. Papadopoulos and R. Agarwala COBALT: constraint-based alignment tool for multiple protein sequences Bioinformatics, May 1, 2007; 23(9): 1073 - 1079. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Y. Niv, D. R. Ripoll, J. A. Vila, A. Liwo, E. S. Vanamee, A. K. Aggarwal, H. Weinstein, and H. A. Scheraga Topology of Type II REases revisited; structural classes and the common conserved core Nucleic Acids Res., April 1, 2007; 35(7): 2227 - 2237. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Zayni, K. Steiner, A. Pfostl, A. Hofinger, P. Kosma, C. Schaffer, and P. Messner The dTDP-4-dehydro-6-deoxyglucose reductase encoding fcd gene is part of the surface layer glycoprotein glycosylation gene cluster of Geobacillus tepidamans GS5-97T Glycobiology, April 1, 2007; 17(4): 433 - 443. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Freshour, R. Yokoyama, and D. R. Mitchell Chlamydomonas Flagellar Outer Row Dynein Assembly Protein Oda7 Interacts with Both Outer Row and I1 Inner Row Dyneins J. Biol. Chem., February 23, 2007; 282(8): 5404 - 5412. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. P. Samuel, C.-H. Song, J. Wei, E. A. Roberts, J. L. Dahl, C. E. Barry III, E.-K. Jo, and R. L. Friedman Expression, production and release of the Eis protein by Mycobacterium tuberculosis during infection of macrophages and its effect on cytokine secretion Microbiology, February 1, 2007; 153(2): 529 - 540. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Yook and J. Hodgkin Mos1 Mutagenesis Reveals a Diversity of Mechanisms Affecting Response of Caenorhabditis elegans to the Bacterial Pathogen Microbacterium nematophilum Genetics, February 1, 2007; 175(2): 681 - 697. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Bitto, C. A. Bingman, G. E. Wesenberg, J. G. McCoy, and G. N. Phillips Jr. From the Cover: Structure of aspartoacylase, the brain enzyme impaired in Canavan disease PNAS, January 9, 2007; 104(2): 456 - 461. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Steele, K. Ziebell, Y. Zhang, A. Benson, P. Konczy, R. Johnson, and V. Gannon Identification of Escherichia coli O157:H7 Genomic Regions Conserved in Strains with a Genotype Associated with Human Infection Appl. Envir. Microbiol., January 1, 2007; 73(1): 22 - 31. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. W. Rozsa, K. M. Scott, H. Pawar, J. R. Samples, M. K. Wirtz, and J. E. Richards Differential Expression Profile Prioritization of Positional Candidate Glaucoma Genes: The GLC1C Locus Arch Ophthalmol, January 1, 2007; 125(1): 117 - 127. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. D. Allaire, B. Ritter, S. Thomas, J. L. Burman, A. Yu. Denisov, V. Legendre-Guillemin, S. Q. Harper, B. L. Davidson, K. Gehring, and P. S. McPherson Connecdenn, A Novel DENN Domain-Containing Protein of Neuronal Clathrin-Coated Vesicles Functioning in Synaptic Vesicle Endocytosis J. Neurosci., December 20, 2006; 26(51): 13202 - 13212. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Kolkenbrock, K. Parschat, B. Beermann, H.-J. Hinz, and S. Fetzner N-Acetylanthranilate Amidase from Arthrobacter nitroguajacolicus Ru61a, an {alpha}/{beta}-Hydrolase-Fold Protein Active towards Aryl-Acylamides and -Esters, and Properties of Its Cysteine-Deficient Variant J. Bacteriol., December 15, 2006; 188(24): 8430 - 8440. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Shipkowski and J. E. Brenchley Bioinformatic, Genetic, and Biochemical Evidence that Some Glycoside Hydrolase Family 42 {beta}-Galactosidases Are Arabinogalactan Type I Oligomer Hydrolases Appl. Envir. Microbiol., December 1, 2006; 72(12): 7730 - 7738. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Birtle and C. P. Ponting Meisetz and the birth of the KRAB motif Bioinformatics, December 1, 2006; 22(23): 2841 - 2845. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. W. Overton, R. Whitehead, Y. Li, L. A. S. Snyder, N. J. Saunders, H. Smith, and J. A. Cole Coordinated Regulation of the Neisseria gonorrhoeae-truncated Denitrification Pathway by the Nitric Oxide-sensitive Repressor, NsrR, and Nitrite-insensitive NarQ-NarP J. Biol. Chem., November 3, 2006; 281(44): 33115 - 33126. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Ruiz, C. Lenox, M. Radermacher, and K. P. Mintz Novel Surface Structures Are Associated with the Adhesion of Actinobacillus actinomycetemcomitans to Collagen. Infect. Immun., November 1, 2006; 74(11): 6163 - 6170. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. L. Gibson, A. P. White, S. D. Snyder, S. Martin, C. Heiss, P. Azadi, M. Surette, and W. W. Kay Salmonella Produces an O-Antigen Capsule Regulated by AgfD and Important for Environmental Persistence. J. Bacteriol., November 1, 2006; 188(22): 7722 - 7730. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Lindroos, O. Vinnere, A. Mira, D. Repsilber, K. Naslund, and S. G. E. Andersson Genome Rearrangements, Deletions, and Amplifications in the Natural Population of Bartonella henselae J. Bacteriol., November 1, 2006; 188(21): 7426 - 7439. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. J. Billington and B. H. Jost Multiple Genetic Elements Carry the Tetracycline Resistance Gene tet(W) in the Animal Pathogen Arcanobacterium pyogenes Antimicrob. Agents Chemother., November 1, 2006; 50(11): 3580 - 3587. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Stapleton, J. W. Carlson, and S. E. Celniker RNA editing in Drosophila melanogaster: New targets and functional consequences RNA, November 1, 2006; 12(11): 1922 - 1932. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Yang, G. A. Tuskan, and Z.-M. Cheng Divergence of the Dof Gene Families in Poplar, Arabidopsis, and Rice Suggests Multiple Modes of Gene Evolution after Duplication Plant Physiology, November 1, 2006; 142(3): 820 - 830. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Kessler, G. Sezonov, J. I. Guijarro, N. Desnoues, T. Rose, M. Delepierre, S. D. Bell, and D. Prangishvili A novel archaeal regulatory protein, Sta1, activates transcription from viral promoters Nucleic Acids Res., October 18, 2006; 34(17): 4837 - 4845. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Caraveo, D. B. van Rossum, R. L. Patterson, S. H. Snyder, and S. Desiderio Action of TFII-I outside the nucleus as an inhibitor of agonist-induced calcium entry. Science, October 6, 2006; 314(5796): 122 - 125. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Naikare, K. Palyada, R. Panciera, D. Marlow, and A. Stintzi Major Role for FeoB in Campylobacter jejuni Ferrous Iron Acquisition, Gut Colonization, and Intracellular Survival. Infect. Immun., October 1, 2006; 74(10): 5433 - 5444. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Berarducci, M. Ikoma, S. Stamatis, M. Sommer, C. Grose, and A. M. Arvin Essential Functions of the Unique N-Terminal Region of the Varicella-Zoster Virus Glycoprotein E Ectodomain in Viral Replication and in the Pathogenesis of Skin Infection J. Virol., October 1, 2006; 80(19): 9481 - 9496. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Nielsen, D. Maric, P. Lau, J. L. Barker, and L. D. Hudson Identification of a Novel Oligodendrocyte Cell Adhesion Protein Using Gene Expression Profiling J. Neurosci., September 27, 2006; 26(39): 9881 - 9891. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Fan, S. Lechno-Yossef, S. Ehira, T. Kaneko, M. Ohmori, N. Sato, S. Tabata, and C. P. Wolk Signal Transduction Genes Required for Heterocyst Maturation in Anabaena sp. Strain PCC 7120. J. Bacteriol., September 1, 2006; 188(18): 6688 - 6693. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Sambanthamoorthy, M. S. Smeltzer, and M. O. Elasri Identification and characterization of msa (SA1233), a gene involved in expression of SarA and several virulence factors in Staphylococcus aureus. Microbiology, September 1, 2006; 152(Pt 9): 2559 - 2572. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Zhao, A. K. Charnley, Z. Wang, Y. Yin, Z. Li, Y. Li, Y. Cao, G. Peng, and Y. Xia Identification of an Extracellular Acid Trehalase and Its Gene Involved in Fungal Pathogenesis of Metarizium anisopliae. J. Biochem., September 1, 2006; 140(3): 319 - 327. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. T. Larson, D. Reiter, M. Young, and C. M. Lawrence Structure of A197 from Sulfolobus Turreted Icosahedral Virus: a Crenarchaeal Viral Glycosyltransferase Exhibiting the GT-A Fold. J. Virol., August 1, 2006; 80(15): 7636 - 7644. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. H. Thomas Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants Genome Res., August 1, 2006; 16(8): 1017 - 1030. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. M. Joshi, A. K. Pandey, N. Capite, S. M. Fortune, E. J. Rubin, and C. M. Sassetti Characterization of mycobacterial virulence genes through genetic interaction mapping PNAS, August 1, 2006; 103(31): 11760 - 11765. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Prosseda, M. C. Latella, M. Casalino, M. Nicoletti, S. Michienzi, and B. Colonna Plasticity of the Pjunc Promoter of ISEc11, a New Insertion Sequence of the IS1111 Family J. Bacteriol., July 1, 2006; 188(13): 4681 - 4689. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Tangrot, L. Wang, B. Kagstrom, and U. H. Sauer FISH--family identification of sequence homologues using structure anchored hidden Markov models. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W10 - W14. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Novatchkova, G. Schneider, R. Fritz, F. Eisenhaber, and A. Schleiffer DOUTfinder--identification of distant domain outliers using subsignificant sequence similarity. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W214 - W218. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Ganesan, P. Dobrowolski, and B. C. Weimer Identification of the Leucine-to-2-Methylbutyric Acid Catabolic Pathway of Lactococcus lactis. Appl. Envir. Microbiol., June 1, 2006; 72(6): 4264 - 4273. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Y. Galperin Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J. Bacteriol., June 1, 2006; 188(12): 4169 - 4182. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Virag and S. D. Harris Functional Characterization of Aspergillus nidulans Homologues of Saccharomyces cerevisiae Spa2 and Bud6 Eukaryot. Cell, June 1, 2006; 5(6): 881 - 895. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Xiao, J. Hsieh, R. L. Nugent, D. J. Coughlin, C. A. Fierke, and D. R. Engelke Functional characterization of the conserved amino acids in Pop1p, the largest common protein subunit of yeast RNases P and MRP RNA, June 1, 2006; 12(6): 1023 - 1037. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Gibbs, V. V. Smeianov, J. L. Steele, P. Upcroft, and B. A. Efimov Two Families of Rep-Like Genes That Probably Originated by Interspecies Recombination Are Represented in Viral, Plasmid, Bacterial, and Parasitic Protozoan Genomes Mol. Biol. Evol., June 1, 2006; 23(6): 1097 - 1100. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. R. Hoen, K. C. Park, N. Elrouby, Z. Yu, N. Mohabir, R. K. Cowan, and T. E. Bureau Transposon-Mediated Expansion and Diversification of a Family of ULP-like Genes Mol. Biol. Evol., June 1, 2006; 23(6): 1254 - 1268. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. S. Barry and J. J. Giovannoni From The Cover: Ripening in the tomato Green-ripe mutant is inhibited by ectopic expression of a protein that disrupts ethylene signaling PNAS, May 16, 2006; 103(20): 7923 - 7928. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Nagasaki, M. Arita, T. Nishizawa, M. Suwa, and O. Gotoh Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns Bioinformatics, May 15, 2006; 22(10): 1211 - 1216. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. C. Gunesekere, C. M. Kahler, C. S. Ryan, L. A. S. Snyder, N. J. Saunders, J. I. Rood, and J. K. Davies Ecf, an Alternative Sigma Factor from Neisseria gonorrhoeae, Controls Expression of msrAB, Which Encodes Methionine Sulfoxide Reductase. J. Bacteriol., May 1, 2006; 188(10): 3463 - 3469. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. T. Poulos, K. F. J. Tang, C. R. Pantoja, J. R. Bonami, and D. V. Lightner Purification and characterization of infectious myonecrosis virus of penaeid shrimp. J. Gen. Virol., April 1, 2006; 87(Pt 4): 987 - 996. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Bulgheresi, I. Schabussova, T. Chen, N. P. Mullin, R. M. Maizels, and J. A. Ott A New C-Type Lectin Similar to the Human Immunoreceptor DC-SIGN Mediates Symbiont Acquisition by a Marine Nematode Appl. Envir. Microbiol., April 1, 2006; 72(4): 2950 - 2956. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. L. Grochowski, H. Xu, and R. H. White Identification of Lactaldehyde Dehydrogenase in Methanocaldococcus jannaschii and Its Involvement in Production of Lactate for F420 Biosynthesis. J. Bacteriol., April 1, 2006; 188(8): 2836 - 2844. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Eggenhofer, R. Rachel, M. Haslbeck, and B. Scharf MotD of Sinorhizobium meliloti and Related {alpha}-Proteobacteria Is the Flagellar-Hook-Length Regulator and Therefore Reassigned as FliK J. Bacteriol., March 15, 2006; 188(6): 2144 - 2153. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Y. James, P. Srivilai, U. Kues, and R. Vilgalys Evolution of the Bipolar Mating System of the Mushroom Coprinellus disseminatus From Its Tetrapolar Ancestors Involves Loss of Mating-Type-Specific Pheromone Receptor Function Genetics, March 1, 2006; 172(3): 1877 - 1891. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Chen and T. D. Schneider Comparative analysis of tandem T7-like promoter containing regions in enterobacterial genomes reveals a novel group of genetic islands Nucleic Acids Res., February 21, 2006; 34(4): 1133 - 1147. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. S. Bulmer and R. H. Crozier Variation in Positive Selection in Termite GNBPs and Relish Mol. Biol. Evol., February 1, 2006; 23(2): 317 - 326. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. F. Fricke, H. Seedorf, A. Henne, M. Kruer, H. Liesegang, R. Hedderich, G. Gottschalk, and R. K. Thauer The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis J. Bacteriol., January 15, 2006; 188(2): 642 - 658. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-Y. Zhang, J. Zou, Q. Bao, W.-L. Chen, L. Wang, H. Yang, and C.-C. Zhang A Lithium-Sensitive and Sodium-Tolerant 3'-Phosphoadenosine-5'-Phosphatase Encoded by halA from the Cyanobacterium Arthrospira platensis Is Closely Related to Its Counterparts from Yeasts and Plants Appl. Envir. Microbiol., January 1, 2006; 72(1): 245 - 251. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. E. Price, S. J. Reid, A. J. M. Driessen, and V. R. Abratt The Bifidobacterium longum NCIMB 702259T ctr Gene Codes for a Novel Cholate Transporter Appl. Envir. Microbiol., January 1, 2006; 72(1): 923 - 926. [Abstract] [Full Text] [PDF]
|
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|
|
|
|
D. Ware, Y. Jiang, W. Lin, and E. Swiatlo Involvement of potD in Streptococcus pneumoniae Polyamine Transport and Pathogenesis Infect. Immun., January 1, 2006; 74(1): 352 - 361. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Merighi, A. Carroll-Portillo, A. N. Septer, A. Bhatiya, and J. S. Gunn Role of Salmonella enterica Serovar Typhimurium Two-Component System PreA/PreB in Modulating PmrA-Regulated Gene Transcription J. Bacteriol., January 1, 2006; 188(1): 141 - 149. [Abstract] [Full Text] [PDF]
|
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|
 |
|
 N. Froese, M. Schwarzer, I. Niedick, U. Frischmann, M. Koster, A. Kroger, P. P. Mueller, M. Nourbakhsh, B. Pasche, J. Reimann, et al. Innate Immune Responses in NF-{kappa}B-Repressing Factor-Deficient Mice Mol. Cell. Biol., January 1, 2006; 26(1): 293 - 302. [Abstract] [Full Text] [PDF]
|
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|
 |
|
 L. G. Puente, D. J. Borris, J.-F. Carriere, J. F. Kelly, and L. A. Megeney Identification of Candidate Regulators of Embryonic Stem Cell Differentiation by Comparative Phosphoprotein Affinity Profiling Mol. Cell. Proteomics, January 1, 2006; 5(1): 57 - 67. [Abstract] [Full Text] [PDF]
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