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Links tagged with 'archaeal proteins'

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COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/

Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

CytoscapeTool Content

http://www.cytoscape.org/

Protein > Interactions, Pathways, Enzymes

Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimited files containing mRNA expression profiles. The nodes of the interaction networks can be filtered by such variables as GO annotations and number of interactions.

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tagsalgorithms archaeal proteins bacteriophage lambda biological models computational biology data mining gene expression profiling gene regulatory networks genomics halobacterium messenger rna neural networks (computer) phenotype protein interaction mapping proteins proteomics software design stochastic processes

GDAPTool Content

http://www.doe-mbi.ucla.edu/Services/GDAP

Protein > Biochemical Features
Protein > Sequence Features

The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.

NAR Web Server Issue 2004
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tagsarchaeal genome archaeal proteins bacterial genome bacterial proteins cysteine disulfides protein sequence analysis statistical data interpretation

MEROPSDatabase Content

http://merops.sanger.ac.uk/

Protein > Databases

The MEROPS database is a collection of peptidases. The database has a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. The database can distinguish one peptidase from another through identifying the specificity of the peptidase in terms of where it will cleave substrates and with which inhibitors it will interact.

NAR Database Issue 2010
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tagsamino acid sequence amino acid sequence homology animals archaeal proteins computational biology genetic databases genomics humans molecular sequence data peptide hydrolases protein databases tertiary protein structure viral genome

MiSTDatabase Content

http://genomics.ornl.gov/mist/

Model Organisms > Databases
Protein > Databases

The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; novel, high-quality domain models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern, biologist-friendly web interface.

NAR Database Issue 2010
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tagsarchaea archaeal genome archaeal proteins bacteria bacterial genome bacterial proteins computational biology genetic databases protein databases signal transduction tertiary protein structure

P2CSDatabase Content

http://www.p2cs.org

Protein > Databases

P2CS is a database for prokaryotic two-component systems (TCSs). The database annotates and classifies TCS proteins from completely sequenced prokaryotic genomes and metagenomes. TCS complements can be browsed by metagenome, replicon or sequence cluster (and these genesets are available for download by users). A variety of database-wide or taxon-specific searches are also supported. Each TCS protein is fully annotated with sequence-feature information including replicon context, while properties of the predicted proteins can be queried against several external prediction servers to suggest homologues, interaction networks, sub-cellular localization and domain complements. There is also a CGView representation of the distribution of TCS genes around a replicon, categorization of TCS genes based on gene organization, an expanded domain-based classification scheme, a P2CS 'gene cart' and categorization on the basis of sequence clusters.

NAR Database Issue 2011
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tagsarchaeal genome archaeal proteins bacterial genome bacterial proteins intercellular signaling peptides and proteins molecular sequence annotation protein databases protein kinases

PSORTdbDatabase Content

http://db.psort.org

Protein > Databases

PSORTdb (part of the PSORT family) is a database of protein subcellular localizations for bacteria and archaea that contains both information determined through laboratory experimentation (ePSORTdb dataset) and computational predictions (cPSORTdb dataset).

This content is being maintained by fionabrinkman.

NAR Database Issue 2011
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tagsarchaeal proteins bacterial proteins computational biology intracellular space membrane proteins molecular sequence data protein databases protein sequence analysis proteome

Swiss-Prot and TrEMBLDatabase Content

http://us.expasy.org/sprot/

Protein > Sequence Data

Swiss-Prot is a curated database of protein sequences that are highly annotated and have a minimal level of redundancy. TrEMBL is a supplement to Swiss-Prot, containing computer-annotated translations of EMBL sequences.

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tagsanimal models animals archaeal proteins bacterial proteins humans plant proteins protein databases proteins proteome proteomics systems integration terminology as topic

TADBDatabase Content

http://bioinfo-mml.sjtu.edu.cn/TADB/

Other Molecules > Databases

TADB is an integrated database that provides comprehensive information about Type 2 toxin-antitoxin (TA) loci. TADB offers both predicted and experimentally supported Type 2 TA loci-relevant data. A broad range of similarity search, sequence alignment, genome context browser and phylogenetic tools are readily accessible via TADB.

NAR Database Issue 2011
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tagsarchaea archaeal genome archaeal proteins bacteria bacterial genome bacterial proteins bacterial toxins biological toxins genetic databases genetic loci

VKCDBDatabase Content

http://vkcdb.biology.ualberta.ca

DNA > Databases
Protein > Databases

The Voltage-gated K(+) Channel DataBase (VKCDB) contains full-length or nearly full-length unique channel sequences from Bacteria, Archaea and Eukaryotes. Corresponding nucleotide sequences of the open reading frames corresponding to the amino acid sequences are now available and can be extracted in parallel with sets of protein sequences. Channels are categorized into subfamilies by phylogenetic analysis and by using hidden Markov model analyses. The retrieval function of the web interface allows retrieval of entries that contain a substantial fraction of the core structural elements of VKCs, fragmentary entries, or both. The full database can be downloaded as either a MySQL dump or as an XML dump from the web site.

NAR Database Issue 2011
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tagsarchaeal proteins bacterial proteins open reading frames phylogeny protein databases protein sequence analysis voltage-gated potassium channels