Tag: MetaCyc

The evolutionary origin of host association in the Rickettsiales

Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021). CAS  PubMed  Article  Google Scholar  Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021). CAS  PubMed  PubMed Central  Article  Google Scholar  Strassert, J. F. H.,…

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Escherichia coli K-12 substr. MG1655 EC 2.7.1.180

BioCyc ID: RXN-14461 EC Number: 2.7.1.180 Enzymes and Genes: FAD:protein FMN transferase: ftp Reaction Locations: periplasmic space The reaction direction shown is in accordance with the direction in which it was curated. Mass balance status: Balanced. Enzyme Commission Primary Name: FAD:protein FMN transferase Enzyme Commission Synonyms: flavin transferase, apbE (gene…

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Escherichia coli K-12 substr. MG1655 GO:0033468

Escherichia coli K-12 substr. MG1655 Gene-Ontology-Terms Class: GO:0033468 – CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process Synonyms: CMP-KDO biosynthesis, CMP-KDO biosynthetic process, CMP-keto-3-deoxy-D-manno-octulosonic acid anabolism, CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthesis, CMP-keto-3-deoxy-D-manno-octulosonic acid formation, CMP-keto-3-deoxy-D-manno-octulosonic acid synthesis Definition: The chemical reactions and pathways resulting in the formation of CMP-keto-3-deoxy-D-manno-octulosonic acid, a substance composed of the acidic…

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Summary of Fusobacterium nucleatum MJR7757B, version 26.0

Summary of Fusobacterium nucleatum, Strain MJR7757B, version 26.0 Tier 3 Uncurated Database Summary: This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Fusobacterium nucleatum MJR7757B, as obtained from RefSeq (annotation date: 04-APR-2017). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software…

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Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

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Escherichia coli K-12 substr. MG1655 EC 7.2.2.8

BioCyc ID: RXN-14455 EC Number: 7.2.2.8 Transporters and Genes: Cu+ exporting P-type ATPase: copA Supersedes EC number: 3.6.3.54 Reaction Locations: inner membrane The reaction direction shown is in accordance with the direction in which it was curated. Most BioCyc compounds have been protonated to a reference pH value of 7.3….

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Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS  PubMed  Google Scholar  2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS  PubMed  Google Scholar …

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Escherichia coli K-12 substr. MG1655 GO:0042781

Escherichia coli K-12 substr. MG1655 Gene-Ontology-Terms Class: GO:0042781 – 3′-tRNA processing endoribonuclease activity Synonyms: 3′ tRNA processing endoribonuclease activity, 3′ tRNase activity, tRNA 3′ endonuclease activity Definition: Catalysis of the endonucleolytic cleavage of RNA, removing extra 3′ nucleotides from tRNA precursor, generating 3′ termini of tRNAs. A 3′-hydroxy group is…

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Escherichia coli K-12 substr. MG1655 EC 1.1.1.282

BioCyc ID: RXN-11174 EC Number: 1.1.1.282 Enzymes and Genes: shikimate dehydrogenase: ydiB The reaction direction shown is in accordance with the direction in which it was curated. Most BioCyc compounds have been protonated to a reference pH value of 7.3. Please see the PGDB Concepts Guide for more information. Mass…

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How to map enriched pathways on whole metacyc pathway map?

How to map enriched pathways on whole metacyc pathway map? 0 Hi there!!! I have a list of control enriched and a list of case enriched microbiome pathways (metacyc). Now I want to map them on the whole MetaCyc map to get the the enriched pathways on the whole network….

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kegg pathway database

Pathways that include all genes in gene_ids. Here the KEGG API operations are explained in comparison to these web tools. MODULE — modules or functional units of genes, BRITE — hierarchical classifications of biological entities, This page was last edited on 22 October 2020, at 18:43. The list can be…

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How to retrieve KO IDs for a list of genes?

How to retrieve KO IDs for a list of genes? 2 Hi, community!!! I have downloaded a list of genes from the MetaCyc database for some bacterial species. I want to find out their respective KO IDs. Can anyone please tell me how can I do that? Thanks KEGG database…

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