Tag: MetaCyc
Improved species level bacterial characterization from rhizosphere soil of wilt infected Punica granatum
The soil samples were collected from an orchard situated in Karnataka, India, which were categorized based on their stage of infection (ISI, ASI) and compared with a healthy sample (HSC). Physical examination of the plants, with respect to their roots, leaves, stem and fruits, revealed the presence of root knots…
A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters
Revsbech, N. P. et al. Determination of ultra-low oxygen concentrations in oxygen minimum zones by the STOX sensor. Limnol. Oceanogr.: Methods. 7, 371-381. (2009). Wright, J. J., Konwar, K. M. & Hallam, S. J. Microbial ecology of expanding oxygen minimum zones. Nat. Rev. Microbiol. 10, 381–394 (2012). Article CAS PubMed …
ANCOM-BC OF THE METABOLIC PATHWAYS DIFFERENTIALLY ABUNDANT BETWEEN TREATMENTS: SUPPLEMENTARY RESULTS TABLE 2.5.2
Table S2.5.2: ANCOM-BC analysis showing the differentially abundant predicted metabolic pathways (MetaCyc) in the subsoil layer (3-4 cm beside the amendment). S2.5.2A: Planted soils with deep-banded amendment (DBA) compared to unplanted soils with DBA. S2.5.2B: Planted soils with DBA compared to planted soils without DBA. School School of Agriculture, Biomedicine…
Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota
Detailed reconstruction of the infant gut bacterial composition A total of 10,935 publicly available datasets, retrieved from 40 cohorts from various geographical origins, were subjected to microbial profiling based on short-read taxonomic classification down to the species level (Supplementary Table 1). Collected data were filtered based on a number of…
Long-Read Metagenomics and CAZyme Discovery
La Rosa SL, Ostrowski MP, Vera-Ponce de León A, McKee LS, Larsbrink J, Eijsink VG, Lowe EC, Martens EC, Pope PB (2022) Glycan processing in gut microbiomes. Curr Opin Microbiol 67:102143. doi.org/10.1016/j.mib.2022.102143 CrossRef CAS PubMed Google Scholar Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette…
Comparison of fecal and blood metabolome reveals inconsistent associations of the gut microbiota with cardiometabolic diseases
Study cohorts This study was based on the Guangzhou Nutrition and Health Study (GNHS). The detailed description of GNHS cohort could be found in previous studies22,23. Briefly, a total of 4048 Chinese participants aged 40–75 years living in the urban area of Guangzhou, China, for at least 5 years were…
Leveraging 16S rRNA data to uncover vaginal microbial signatures in women with cervical cancer
1 Introduction Cervical cancer (CC) remains the fourth most common cancer in women worldwide, with 604,127 new cases in 2020 and more than 341,831 deaths, accounting for nearly 8% of all female cancer-related deaths annually (Sung et al., 2021). This common infection-related neoplasm and its premalignant precursor are caused by high-risk…
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.,…
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…
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…
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…
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…
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….
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 …
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…
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…
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….
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…
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…
