HAMAP database of microbial protein families
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More detailed information about this field from each metasource.
HAMAP database of microbial protein families
metasource: Fairsharing.org
version: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
HAMAP
metasource: Fairsharing.org
version: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
hamap
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
Names
More detailed information about this field from each metasource.
HAMAP database of microbial protein families
metasource: Fairsharing.orgversion: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
HAMAP
metasource: Fairsharing.orgversion: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
hamap
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
Names
More detailed information about this field from each metasource.
HAMAP database of microbial protein families
metasource: Fairsharing.orgversion: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
HAMAP
metasource: Fairsharing.orgversion: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
hamap
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.
Description
More detailed information about this field from each metasource.
HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.
metasource: Fairsharing.orgversion: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
High-quality Automated and Manual Annotation of microbial Proteomes
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
A system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. HAMAP is applied to bacterial, archaeal and eukaryotic proteins and used to annotate records in UniProtKB via UniProt's automatic annotation pipeline.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
Webpage:
https://hamap.expasy.org/Webpage
More detailed information about this field from each metasource.
https://hamap.expasy.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://www.expasy.org/sprot/hamap/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://hamap.expasy.org
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
Licence:
Name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by-nc/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
HAMAP in 2015: updates to the protein family classification and annotation system
PMID: 25348399
metasource: Fairsharing.org
version: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
HAMAP in 2013, new developments in the protein family classification and annotation system
PMID: 23193261
metasource: Fairsharing.org
version: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gku1002
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
HAMAP in 2015: updates to the protein family classification and annotation system
PMID: 25348399
metasource: Fairsharing.org
version: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
HAMAP in 2013, new developments in the protein family classification and annotation system
PMID: 23193261
metasource: Fairsharing.org
version: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gku1002
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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HAMAP in 2015: updates to the protein family classification and annotation system
PubMed citations: 64.
64 articles citing: HAMAP in 2015: updates to the protein family classification and annotation system
ContactPFP: Protein function prediction using predicted contact information. PMID:35875419
A de Novo ZMIZ1 Pathogenic Variant for Neurodevelopmental Disorder With Dysmorphic Facies and Distal Skeletal Anomalies. PMID:35432459
Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate. PMID:35418297
Prediction of Prophages and Their Host Ranges in Pathogenic and Commensal Neisseria Species. PMID:35418239
Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. PMID:34737728
Ambient Air Pollution Shapes Bacterial and Fungal Ivy Leaf Communities. PMID:34683409
Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class. PMID:34555022
Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. PMID:34475860
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. PMID:33963861
Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol. PMID:33902737
Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation. PMID:33763039
The InterPro protein families and domains database: 20 years on. PMID:33156333
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. PMID:32399560
Comparative genome sequence analysis of several species in the genus Tepidimonas and the description of a novel species Tepidimonas charontis sp. nov. PMID:32228748
An assessment of genome annotation coverage across the bacterial tree of life. PMID:32124724
A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. PMID:32103005
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat. PMID:31685928
Isolates from Colonic Spirochetosis in Humans Show High Genomic Divergence and Potential Pathogenic Features but Are Not Detected Using Standard Primers for the Human Microbiota. PMID:31405919
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
High-Quality Draft Genome Sequence of the Microcolonial Black Fungus Aeminium ludgeri DSM 106916. PMID:30948467
Anaerobic Degradation of Sulfated Polysaccharides by Two Novel Kiritimatiellales Strains Isolated From Black Sea Sediment. PMID:30833937
PIRSitePredict for protein functional site prediction using position-specific rules. PMID:30805646
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
Genome-Wide Identification and Transcriptional Regulation of Aquaporin Genes in Bread Wheat (Triticum aestivum L.) under Water Stress. PMID:30326657
Environmentally-driven gene content convergence and the Bacillus phylogeny. PMID:30285626
Updates in Rhea: SPARQLing biochemical reaction data. PMID:30272209
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. PMID:30165572
Functional Prediction of Hypothetical Transcription Factors of Escherichia coli K-12 Based on Expression Data. PMID:30050664
A Pathogen-Responsive Leucine Rich Receptor Like Kinase Contributes to Fusarium Resistance in Cereals. PMID:29997638
Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (Lolium perenne L.). PMID:29626084
Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger. PMID:29375499
Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria. PMID:29259581
Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism. PMID:29162929
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. PMID:29036270
MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data. PMID:28968784
The single cyclic nucleotide-specific phosphodiesterase of the intestinal parasite Giardia lamblia represents a potential drug target. PMID:28915270
BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation. PMID:28750104
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. PMID:28717205
Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. PMID:28581482
Bacterial Virus Ontology; Coordinating across Databases. PMID:28545254
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. PMID:28334975
Protein Bioinformatics Databases and Resources. PMID:28150231
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes. PMID:28025345
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. PMID:27899624
UniProt: the universal protein knowledgebase. PMID:27899622
Primer on the Gene Ontology. PMID:27812933
Computational prediction shines light on type III secretion origins. PMID:27713481
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. PMID:27382076
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. PMID:27363390
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. PMID:27153729
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. PMID:26994912
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
SugarBindDB, a resource of glycan-mediated host-pathogen interactions. PMID:26578555
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. PMID:26527724
A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes. PMID:26042526
UniProt: a hub for protein information. PMID:25348405 -
HAMAP in 2013, new developments in the protein family classification and annotation system
PubMed citations: 37.
37 articles citing: HAMAP in 2013, new developments in the protein family classification and annotation system
Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. PMID:35484634
An improved high-quality genome assembly and annotation of Tibetan hulless barley. PMID:32385314
Isolates from Colonic Spirochetosis in Humans Show High Genomic Divergence and Potential Pathogenic Features but Are Not Detected Using Standard Primers for the Human Microbiota. PMID:31405919
Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential. PMID:30410642
Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis. PMID:30381904
A Primer on Infectious Disease Bacterial Genomics. PMID:28590251
Noumeavirus replication relies on a transient remote control of the host nucleus. PMID:28429720
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. PMID:28193156
Decay of Sexual Trait Genes in an Asexual Parasitoid Wasp. PMID:28172869
Aberrant coordination geometries discovered in the most abundant metalloproteins. PMID:28142195
Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining. PMID:27390860
Misannotation Awareness: A Tale of Two Gene-Groups. PMID:27379147
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. PMID:26740739
Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity--a large-scale system analysis of decoded bacterial genomes. PMID:26459834
Diversity in protein domain superfamilies. PMID:26451979
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PMID:26366735
The history of the CATH structural classification of protein domains. PMID:26253692
Interaction networks for identifying coupled molecular processes in microbial communities. PMID:26180552
Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica. PMID:25956885
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. PMID:25888481
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes. PMID:25378302
HAMAP in 2015: updates to the protein family classification and annotation system. PMID:25348399
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. PMID:25271953
Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway. PMID:25210598
Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. PMID:25197483
Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). PMID:25007843
From sequence to enzyme mechanism using multi-label machine learning. PMID:24885296
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. PMID:24792157
Analysis of expressed genes of the bacterium 'Candidatus phytoplasma Mali' highlights key features of virulence and metabolism. PMID:24728201
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. PMID:24622611
InterProScan 5: genome-scale protein function classification. PMID:24451626
antibacTR: dynamic antibacterial-drug-target ranking integrating comparative genomics, structural analysis and experimental annotation. PMID:24438389
NECTAR: a database of codon-centric missense variant annotations. PMID:24297257
Activities at the Universal Protein Resource (UniProt). PMID:24253303
Ensembl Genomes 2013: scaling up access to genome-wide data. PMID:24163254
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. PMID:23505298 - http://dx.doi.org/10.1093/nar/gku1002
Tags:
Tags
More detailed information about this field from each metasource.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
sequence annotation
metasource: Fairsharing.org
version: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
prokaryotic genome databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
microbiology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
sequence analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
Tags
More detailed information about this field from each metasource.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
sequence annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: June 22, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
prokaryotic genome databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
microbiology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
sequence analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
protein sequence annotation polypeptide region genomics prokaryotic genome microbiology gene and protein families sequence analysis
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