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Tag: Pfam
KEGG T01015: 4329963
Entry 4332822 CDS T01015 Name (RefSeq) LOW QUALITY PROTEIN: nuclear cap-binding protein subunit 1-like KO K12882 nuclear cap-binding protein subunit 1 Organism osa Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa03013 Nucleocytoplasmic transport osa03015 mRNA surveillance pathway osa03040 Spliceosome Brite KEGG Orthology (KO) [BR:osa00001] 09120 Genetic Information Processing 09121 Transcription 03040 Spliceosome 4332822 09122 Translation 03013 Nucleocytoplasmic transport 4332822 03015 mRNA…
KEGG T01710: 100306272
Entry 100782702 CDS T01710 Symbol COX2 Name (RefSeq) cytochrome c oxidase subunit 2, mitochondrial KO K02261 cytochrome c oxidase subunit 2 Organism gmx Glycine max (soybean) Pathway gmx00190 Oxidative phosphorylation gmx01100 Metabolic pathways Brite KEGG Orthology (KO) [BR:gmx00001] 09100 Metabolism 09102 Energy metabolism 00190 Oxidative phosphorylation 100782702 (COX2) 09180 Brite Hierarchies 09182 Protein families: genetic information processing 03029 Mitochondrial biogenesis…
KEGG T08053: IA203_01755
Entry IA203_01755 CDS T08053 Name (GenBank) UDP-N-acetylmuramate dehydrogenase KO K00075 UDP-N-acetylmuramate dehydrogenase [EC:1.3.1.98] Organism cwk Corynebacterium wankanglinii Pathway cwk00520 Amino sugar and nucleotide sugar metabolism cwk00550 Peptidoglycan biosynthesis cwk01100 Metabolic pathways cwk01250 Biosynthesis of nucleotide sugars Brite KEGG Orthology (KO) [BR:cwk00001] 09100 Metabolism 09101 Carbohydrate metabolism 00520 Amino sugar and nucleotide sugar metabolism IA203_01755 09107 Glycan biosynthesis and…
KEGG T09148: BWI76_09435
Entry BWI76_09435 CDS T09148 Name (GenBank) glutaredoxin, GrxA family KO K03674 glutaredoxin 1 Organism klm Klebsiella sp. M5al Brite KEGG Orthology (KO) [BR:klm00001] 09180 Brite Hierarchies 09182 Protein families: genetic information processing 03110 Chaperones and folding catalysts [BR:klm03110] BWI76_09435Chaperones and folding catalysts [BR:klm03110] Protein folding catalysts Protein disulfide isomerase BWI76_09435 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam: Glutaredoxin Glrx-like Thioredoxin_3…
A super-pangenome of the North American wild grape species | Genome Biology
Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…
How to filter hmmer output and get needed enzymes
How to filter hmmer output and get needed enzymes 0 This is a part of my file. You can see the output for KI0314_NODE_20043_length_7522_cov_1.691954_4. Glyco_hydro_43 PF04616.18 KI0314_NODE_20043_length_7522_cov_1.691954_4 – 2.3e-43 148.8 4.0 3.5e-43 148.2 4.0 1.3 1 0 0 1 1 1 1 Glycosyl hydrolases family 43 GH43_C2 PF17851.5 KI0314_NODE_20043_length_7522_cov_1.691954_4 –…
Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa)
Identification of the AP2/ERF transcription factors in lettuce genome To identify AP2/ERF family genes in lettuce, we queried the lettuce genomic protein database (version 8) using the Pfam model (PF00847) of the AP2 domain. This search led us to discover 223 genes that showed a significant match with the AP2…
Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome
Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article ADS CAS PubMed Google Scholar Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…
Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath
Bacterial strains We used P. putida strains S12, DOT-T1E, F1 (kindly gifted by Grant Rybnicky), ATCC 12633 (purchased from ATCC), JUb85 (kindly provided by Samuel Buck), EM383 (kindly gifted by Huseyin Tas), p106 (kindly provided by Carey-Ann Burnham), and KT2440 (obtained from lab stocks). An overnight culture of each P….
Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457
Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…
Curated model organism gene functional annotations
Curated model organism gene functional annotations 0 Hi, I’m working with a model organism for the first time – C. elegans nematodes – and have created a list of differential expressed genes from some RNAseq data the lab had. One of the things I like to do is look for…
Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces
Batinovic, S. et al. Bacteriophages in natural and artificial environments. Pathogens 8, 100. doi.org/10.3390/pathogens8030100 (2019). Article PubMed PubMed Central Google Scholar Mushegian, A. R. Are there 10^31 virus particles on earth, or more, or fewer?. J. Bacteriol. 202(9), 2020. doi.org/10.1128/JB.00052-20 (2020). Article Google Scholar Kutter, E. & Sulakvelidze, A. Bacteriophages:…
Page not found at /GeneAnnotation/?id=Ash020296&type=Apostasia
Page not found at /GeneAnnotation/?id=Ash020296&type=Apostasia Using the URLconf defined in orchidbase6.urls, Django tried these URL patterns, in this order: ^admin/ ^home/ ^ ^tools/ [name=”tools”] ^ ^help/ [name=”Help”] ^ ^download/ [name=”download”] ^ ^Phalaenopsis_home/ [name=”Phalaenopsis_2020″] ^ ^Dendrobium_home/ [name=”Dendrobium_2020″] ^ ^Apostasia_home/ [name=”Apostasia_2020″] ^ ^Vpompona_home/ [name=”Vpompona_2020″] ^ ^Vshenzhenica_home/ [name=”Vshenzhenica_2020″] ^ ^Pguangdongensis_home/ [name=”Pguangdongensis_2020″] ^ ^Pzijinensis_home/…
A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera
Jiao, Y. N. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011). Article PubMed Google Scholar Levin, D. A. Polyploidy and novelty in flowering plants. Am. Nat. 122, 1–25 (1983). Article Google Scholar Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of…
Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses
Honegger, R. The lichen symbiosis: What is so spectacular about it?. Lichenologist 30, 193–212 (1998). Article Google Scholar Grube, M. & Berg, G. Microbial consortia of bacteria and fungi with focus on the lichen symbiosis. Fung. Biol. Rev. 23, 72–85 (2009). Article Google Scholar Spribille, T. et al. Basidiomycete yeasts…
KEGG T01005: 473325
Entry 473325 CDS T01005 Symbol RNASE2 Name (RefSeq) non-secretory ribonuclease precursor KO K01168 pancreatic ribonuclease [EC:4.6.1.18] Organism ptr Pan troglodytes (chimpanzee) Brite KEGG Orthology (KO) [BR:ptr00001] 09180 Brite Hierarchies 09182 Protein families: genetic information processing 03019 Messenger RNA biogenesis [BR:ptr03019] 473325 (RNASE2) 04131 Membrane trafficking [BR:ptr04131] 473325 (RNASE2)Enzymes [BR:ptr01000] 4. Lyases 4.6 Phosphorus-oxygen lyases 4.6.1 Phosphorus-oxygen lyases (only sub-subclass identified to date) 4.6.1.18 pancreatic ribonuclease 473325 (RNASE2)Messenger…
How to get multiple protein domain database domain name from id’s
How to get multiple protein domain database domain name from id’s 0 Hello i got a blast2go output with a column with id’s from multiple databases suported by interpro but i need the domain names so i can filter the data someone know how can i do it? My data…
KEGG T01007: 415125
Entry 415125 CDS T01007 Symbol FGFR2 Name (RefSeq) fibroblast growth factor receptor 2 precursor KO K05093 fibroblast growth factor receptor 2 [EC:2.7.10.1] Organism cfa Canis lupus familiaris (dog) Pathway cfa01521 EGFR tyrosine kinase inhibitor resistance cfa04010 MAPK signaling pathway cfa04014 Ras signaling pathway cfa04015 Rap1 signaling pathway cfa04020 Calcium signaling pathway cfa04144 Endocytosis…
KEGG T02994: 18601618
Entry 18601618 CDS T02994 Name (RefSeq) alpha-glucan phosphorylase 1 KO K00688 glycogen phosphorylase [EC:2.4.1.1] Organism tcc Theobroma cacao (cacao) Pathway tcc00500 Starch and sucrose metabolism tcc01100 Metabolic pathways tcc01110 Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:tcc00001] 09100 Metabolism 09101 Carbohydrate metabolism 00500 Starch and sucrose metabolism 18601618Enzymes [BR:tcc01000] 2. Transferases 2.4 Glycosyltransferases 2.4.1 Hexosyltransferases 2.4.1.1 glycogen phosphorylase 18601618 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT…
KEGG T00196: STH138
Entry STH138 CDS T00196 Name (GenBank) putative N-acetyl-mannosamine transferase KO K05946 N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase [EC:2.4.1.187] Organism sth Symbiobacterium thermophilum Pathway sth00552 Teichoic acid biosynthesis Brite KEGG Orthology (KO) [BR:sth00001] 09100 Metabolism 09107 Glycan biosynthesis and metabolism 00552 Teichoic acid biosynthesis STH138 09180 Brite Hierarchies 09181 Protein families: metabolism 01003 Glycosyltransferases [BR:sth01003] STH138Enzymes [BR:sth01000] 2. Transferases 2.4 Glycosyltransferases 2.4.1 Hexosyltransferases 2.4.1.187 N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase STH138Glycosyltransferases [BR:sth01003] Polysaccharide Bacterial polysaccharide (excluding LPS) STH138 BRITE hierarchy SSDB…
Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants
Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…
KEGG T02920: 102247935
Entry 102247935 CDS T02920 Symbol TRMT44 Name (RefSeq) tRNA methyltransferase 44 homolog (S. cerevisiae) KO K15447 tRNASer (uridine44-2′-O)-methyltransferase [EC:2.1.1.211] Organism myb Myotis brandtii (Brandt’s bat) Brite KEGG Orthology (KO) [BR:myb00001] 09180 Brite Hierarchies 09182 Protein families: genetic information processing 03016 Transfer RNA biogenesis [BR:myb03016] 102247935 (TRMT44)Enzymes [BR:myb01000] 2. Transferases 2.1 Transferring one-carbon groups 2.1.1 Methyltransferases 2.1.1.211 tRNASer (uridine44-2′-O)-methyltransferase 102247935 (TRMT44)Transfer RNA biogenesis [BR:myb03016] Eukaryotic type tRNA modification…
KEGG T03531: KR75_11080
Entry KR75_11080 CDS T03531 Name (GenBank) xylose isomerase KO K01805 xylose isomerase [EC:5.3.1.5] Organism kvd Klebsiella variicola DX120E Pathway kvd00040 Pentose and glucuronate interconversions kvd00051 Fructose and mannose metabolism kvd01100 Metabolic pathways Brite KEGG Orthology (KO) [BR:kvd00001] 09100 Metabolism 09101 Carbohydrate metabolism 00040 Pentose and glucuronate interconversions KR75_11080 00051 Fructose and mannose metabolism KR75_11080Enzymes [BR:kvd01000] 5. Isomerases 5.3 Intramolecular oxidoreductases 5.3.1 Interconverting aldoses and…
KEGG T01001: 1474
Entry 1474 CDS T01001 Symbol CST6, ECTD15 Name (RefSeq) cystatin E/M KO K13902 cystatin-M Organism hsa Homo sapiens (human) Disease H00651 Hypohidrotic ectodermal dysplasia Brite KEGG Orthology (KO) [BR:hsa00001] 09180 Brite Hierarchies 09181 Protein families: metabolism 01002 Peptidases and inhibitors [BR:hsa01002] 1474 (CST6)Peptidases and inhibitors [BR:hsa01002] Peptidase inhibitors Family I25: cystatin family 1474 (CST6) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…
KEGG T01001: 637
Entry 637 CDS T01001 Symbol BID, FP497 Name (RefSeq) BH3 interacting domain death agonist KO K04726 BH3 interacting domain death agonist Organism hsa Homo sapiens (human) Pathway hsa01524 Platinum drug resistance hsa04071 Sphingolipid signaling pathway hsa04115 p53 signaling pathway hsa04210 Apoptosis hsa04215 Apoptosis – multiple species hsa04217 Necroptosis hsa04650 Natural killer cell mediated…
The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids
Genome sequencing and assembly of R. tetraphylla After DNA extraction from young leaves and sequencing, the R. tetraphylla genome was first assembled into 1008 contigs with an N50 of 3.7 Mb. After haplotigs removal and a final pilon polishing, the 364,945,498 bp final assembly was distributed across 76 scaffolds with an N50…
Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis
Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article PubMed Google Scholar Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article PubMed Google Scholar Amborella Genome Project et al. The Amborella…
The Mla system of diderm Firmicute Veillonella parvula reveals an ancestral transenvelope bridge for phospholipid trafficking
Bacterial strains and growth conditions Veillonella parvula SKV38 was grown in SK medium (10 g/L tryptone [Difco], 10 g/L yeast extract [Difco], 0.4 g/L disodium phosphate, 2 g/L sodium chloride, and 10 ml/L 60% [wt/vol] sodium DL-lactate; described in ref. 51. Cultures were incubated at 37 °C in anaerobic conditions, either in anaerobic bags (GENbag anaero;…
Taxonomic and environmental distribution of bacterial amino acid auxotrophies
Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article ADS CAS PubMed Google Scholar Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….
KEGG T00046: PM0721
Entry PM0721 CDS T00046 Symbol ttrA Name (GenBank) TtrA KO K08357 tetrathionate reductase subunit A Organism pmu Pasteurella multocida subsp. multocida Pm70 Pathway pmu00920 Sulfur metabolism pmu01100 Metabolic pathways pmu01120 Microbial metabolism in diverse environments pmu02020 Two-component system Brite KEGG Orthology (KO) [BR:pmu00001] 09100 Metabolism 09102 Energy metabolism 00920 Sulfur metabolism PM0721 (ttrA) 09130 Environmental Information Processing 09132 Signal…
EMDB < EMD-14025
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
EMDB < EMD-16930
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
KEGG T06063: 106511269
Entry 106522761 CDS T06063 Symbol pak1 Name (RefSeq) serine/threonine-protein kinase PAK 1 KO K04409 p21-activated kinase 1 [EC:2.7.11.1] Organism alim Austrofundulus limnaeus (annual killifish) Pathway alim04010 MAPK signaling pathway alim04012 ErbB signaling pathway alim04510 Focal adhesion alim04625 C-type lectin receptor signaling pathway alim04810 Regulation of actin cytoskeleton alim05132 Salmonella infection Brite KEGG Orthology…
KEGG T00183: SAS2563
Entry SAS2563 CDS T00183 Name (GenBank) putative histidinol dehydrogenase KO K00013 histidinol dehydrogenase [EC:1.1.1.23] Organism sas Staphylococcus aureus subsp. aureus MSSA476 (MSSA) Pathway sas00340 Histidine metabolism sas01100 Metabolic pathways sas01110 Biosynthesis of secondary metabolites sas01230 Biosynthesis of amino acids Brite KEGG Orthology (KO) [BR:sas00001] 09100 Metabolism 09105 Amino acid metabolism 00340 Histidine metabolism SAS2563Enzymes [BR:sas01000] 1. Oxidoreductases 1.1 Acting on…
KEGG T00918: Mlut_12280
Entry Mlut_12280 CDS T00918 Name (GenBank) Undecaprenyl pyrophosphate synthetase KO K00806 undecaprenyl diphosphate synthase [EC:2.5.1.31] Organism mlu Micrococcus luteus Pathway mlu00550 Peptidoglycan biosynthesis mlu00900 Terpenoid backbone biosynthesis mlu01110 Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:mlu00001] 09100 Metabolism 09107 Glycan biosynthesis and metabolism 00550 Peptidoglycan biosynthesis Mlut_12280 09109 Metabolism of terpenoids and polyketides 00900 Terpenoid backbone biosynthesis Mlut_12280 09180 Brite…
Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2’-fucosyllactose utilization can be facilitated by coexisting species
Stewart, C. J. et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562, 583–588 (2018). Article CAS ADS PubMed PubMed Central Google Scholar Tamburini, S., Shen, N., Wu, H. C. & Clemente, J. C. The microbiome in early life: implications for health outcomes….
KEGG T00139: BP3287
Entry BP3287 CDS T00139 Symbol atpG Name (GenBank) ATP synthase gamma chain KO K02115 F-type H+-transporting ATPase subunit gamma Organism bpe Bordetella pertussis Tohama I Pathway bpe00190 Oxidative phosphorylation bpe01100 Metabolic pathways Module bpe_M00157 F-type ATPase, prokaryotes and chloroplasts Brite KEGG Orthology (KO) [BR:bpe00001] 09100 Metabolism 09102 Energy metabolism 00190 Oxidative phosphorylation BP3287 (atpG) 09180 Brite Hierarchies 09181 Protein…
KEGG T01028: 706234
Entry 706234 CDS T01028 Symbol TRAP1 Name (RefSeq) heat shock protein 75 kDa, mitochondrial KO K09488 TNF receptor-associated protein 1 Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc05012 Parkinson disease mcc05022 Pathways of neurodegeneration – multiple diseases Brite KEGG Orthology (KO) [BR:mcc00001] 09160 Human Diseases 09164 Neurodegenerative disease 05012 Parkinson disease 706234 (TRAP1) 05022 Pathways of neurodegeneration –…
KEGG T03271: 103675060
Entry 103675060 CDS T03271 Symbol APPL1 Name (RefSeq) DCC-interacting protein 13-alpha KO K08733 DCC-interacting protein 13 alpha Organism umr Ursus maritimus (polar bear) Pathway umr04211 Longevity regulating pathway umr05200 Pathways in cancer umr05210 Colorectal cancer Brite KEGG Orthology (KO) [BR:umr00001] 09150 Organismal Systems 09149 Aging 04211 Longevity regulating pathway 103675060 (APPL1) 09160 Human Diseases 09161 Cancer: overview 05200 Pathways in…
Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years
Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article CAS PubMed Google Scholar Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…
KEGG T01001: 257194
Entry 257194 CDS T01001 Symbol NEGR1, DMML2433, IGLON4, KILON, Ntra Name (RefSeq) neuronal growth regulator 1 KO K06775 neuronal growth regulator 1 Organism hsa Homo sapiens (human) Pathway hsa04514 Cell adhesion molecules Brite KEGG Orthology (KO) [BR:hsa00001] 09130 Environmental Information Processing 09133 Signaling molecules and interaction 04514 Cell adhesion molecules 257194 (NEGR1) 09180 Brite Hierarchies 09183 Protein families: signaling…
KEGG T08541: 104528229
Entry 104528229 CDS T08541 Symbol SLC15A4 Name (RefSeq) solute carrier family 15 member 4 KO K14638 solute carrier family 15 (peptide/histidine transporter), member 3/4 Organism acar Antrostomus carolinensis (chuck-will’s-widow) Brite KEGG Orthology (KO) [BR:acar00001] 09180 Brite Hierarchies 09183 Protein families: signaling and cellular processes 02000 Transporters [BR:acar02000] 104528229 (SLC15A4)Transporters [BR:acar02000] Solute carrier family (SLC) SLC15: Proton oligopeptide cotransporter 104528229 (SLC15A4)…
KEGG T01011: 100038077
Entry 100038077 CDS T01011 Symbol nkx2-2 Name (RefSeq) homeobox protein Nkx-2.2 isoform X1 KO K08029 homeobox protein Nkx-2.2 Organism xtr Xenopus tropicalis (tropical clawed frog) Brite KEGG Orthology (KO) [BR:xtr00001] 09180 Brite Hierarchies 09182 Protein families: genetic information processing 03000 Transcription factors [BR:xtr03000] 100038077 (nkx2-2)Transcription factors [BR:xtr03000] Eukaryotic type Helix-turn-helix Homeo domain ANTP: NKL 100038077 (nkx2-2) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT…
KEGG T09424: 118385109
Entry 118385109 CDS T09424 Name (RefSeq) adenylosuccinate synthetase isozyme 2-like KO K01939 adenylosuccinate synthase [EC:6.3.4.4] Organism oke Oncorhynchus keta (chum salmon) Pathway oke00230 Purine metabolism oke00250 Alanine, aspartate and glutamate metabolism oke01100 Metabolic pathways oke01232 Nucleotide metabolism oke01240 Biosynthesis of cofactors Module oke_M00049 Adenine ribonucleotide biosynthesis, IMP => ADP,ATP Brite KEGG Orthology (KO)…
KEGG T08782: 127423656
Entry 127423656 CDS T08782 Name (RefSeq) heparan sulfate glucosamine 3-O-sulfotransferase 3B1-like KO K07809 [heparan sulfate]-glucosamine 3-sulfotransferase 3 [EC:2.8.2.30] Organism masi Myxocyprinus asiaticus (Chinese sucker) Pathway masi00534 Glycosaminoglycan biosynthesis – heparan sulfate / heparin Brite KEGG Orthology (KO) [BR:masi00001] 09100 Metabolism 09107 Glycan biosynthesis and metabolism 00534 Glycosaminoglycan biosynthesis – heparan sulfate / heparin 127423656 09180 Brite Hierarchies 09181 Protein…
When will RNA get its AlphaFold moment? | Nucleic Acids Research
Abstract The protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there has been considerable excitement to build off the success of AlphaFold and predict the 3D structures of RNAs. RNA prediction methods use a variety of techniques, from physics-based to machine learning approaches….
KEGG T00186: ECA0055
Entry ECA0055 CDS T00186 Symbol prlC Name (GenBank) oligopeptidase A KO K01414 oligopeptidase A [EC:3.4.24.70] Organism eca Pectobacterium atrosepticum SCRI1043 Brite KEGG Orthology (KO) [BR:eca00001] 09180 Brite Hierarchies 09181 Protein families: metabolism 01002 Peptidases and inhibitors [BR:eca01002] ECA0055 (prlC)Enzymes [BR:eca01000] 3. Hydrolases 3.4 Acting on peptide bonds (peptidases) 3.4.24 Metalloendopeptidases 3.4.24.70 oligopeptidase A ECA0055 (prlC)Peptidases and inhibitors [BR:eca01002] Metallo peptidases Family M3 ECA0055 (prlC) BRITE hierarchy SSDB OrthologParalogGene…
KEGG T00644: APJL_0327
Entry APJL_0327 CDS T00644 Symbol rumA Name (GenBank) 23S rRNA (Uracil-5-)-methyltransferase KO K03215 23S rRNA (uracil1939-C5)-methyltransferase [EC:2.1.1.190] Organism apj Actinobacillus pleuropneumoniae JL03 (serotype 3) Brite KEGG Orthology (KO) [BR:apj00001] 09180 Brite Hierarchies 09182 Protein families: genetic information processing 03009 Ribosome biogenesis [BR:apj03009] APJL_0327 (rumA)Enzymes [BR:apj01000] 2. Transferases 2.1 Transferring one-carbon groups 2.1.1 Methyltransferases 2.1.1.190 23S rRNA (uracil1939-C5)-methyltransferase APJL_0327 (rumA)Ribosome biogenesis [BR:apj03009] Prokaryotic type rRNA modification factors 23S rRNA…
Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae
Sheridan, P. O. et al. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat. Commun. 11, 1–12 (2020). Article Google Scholar Sheridan, P. O., Meng, Y., Williams, T. A. & Gubry-Rangin, C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat. Commun. 13, 1–13…
KEGG T00186: ECA2422
Entry ECA2422 CDS T00186 Symbol thrS Name (GenBank) threonyl-tRNA synthetase KO K01868 threonyl-tRNA synthetase [EC:6.1.1.3] Organism eca Pectobacterium atrosepticum SCRI1043 Pathway eca00970 Aminoacyl-tRNA biosynthesis Brite KEGG Orthology (KO) [BR:eca00001] 09120 Genetic Information Processing 09122 Translation 00970 Aminoacyl-tRNA biosynthesis ECA2422 (thrS) 09180 Brite Hierarchies 09181 Protein families: metabolism 01007 Amino acid related enzymes [BR:eca01007] ECA2422 (thrS) 09182 Protein families: genetic information processing 03016 Transfer…
KEGG T01028: 701915
Entry 701915 CDS T01028 Symbol KRT25 Name (RefSeq) keratin, type I cytoskeletal 25 KO K07604 type I keratin, acidic Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc04915 Estrogen signaling pathway mcc05150 Staphylococcus aureus infection Brite KEGG Orthology (KO) [BR:mcc00001] 09150 Organismal Systems 09152 Endocrine system 04915 Estrogen signaling pathway 701915 (KRT25) 09160 Human Diseases 09171 Infectious disease: bacterial 05150 Staphylococcus…
KEGG T05390: C3V38_02785
Entry C3V38_14330 CDS T05390 Name (GenBank) GTP pyrophosphokinase KO K01139 GTP diphosphokinase / guanosine-3′,5′-bis(diphosphate) 3′-diphosphatase [EC:2.7.6.5 3.1.7.2] Organism dit Dietzia sp. oral taxon 368 Pathway dit00230 Purine metabolism dit01100 Metabolic pathways Brite KEGG Orthology (KO) [BR:dit00001] 09100 Metabolism 09104 Nucleotide metabolism 00230 Purine metabolism C3V38_14330 09180 Brite Hierarchies 09182 Protein families: genetic information processing 03009 Ribosome biogenesis [BR:dit03009] C3V38_14330Enzymes [BR:dit01000] 2. Transferases 2.7 Transferring…
KEGG T01028: 698365
Entry 698365 CDS T01028 Symbol AMACR Name (RefSeq) alpha-methylacyl-CoA racemase KO K01796 alpha-methylacyl-CoA racemase [EC:5.1.99.4] Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc00120 Primary bile acid biosynthesis mcc01100 Metabolic pathways mcc04146 Peroxisome Module mcc_M00104 Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism 09103 Lipid metabolism 00120 Primary bile acid biosynthesis 698365 (AMACR) 09140…
EMDB < Search results
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
KEGG T01028: 703937
Entry 703937 CDS T01028 Symbol PTPRG Name (RefSeq) receptor-type tyrosine-protein phosphatase gamma isoform X2 KO K16667 receptor-type tyrosine-protein phosphatase gamma [EC:3.1.3.48] Organism mcc Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies 09181 Protein families: metabolism 01009 Protein phosphatases and associated proteins [BR:mcc01009] 703937 (PTPRG)Enzymes [BR:mcc01000] 3. Hydrolases 3.1 Acting on ester bonds 3.1.3 Phosphoric-monoester hydrolases 3.1.3.48 protein-tyrosine-phosphatase 703937 (PTPRG)Protein phosphatases and…
KEGG T07278: 119316072
Entry 119322531 CDS T07278 Name (RefSeq) porphobilinogen deaminase, chloroplastic-like KO K01749 hydroxymethylbilane synthase [EC:2.5.1.61] Organism tdc Triticum dicoccoides (wild emmer wheat) Pathway tdc00860 Porphyrin metabolism tdc01100 Metabolic pathways tdc01110 Biosynthesis of secondary metabolites tdc01240 Biosynthesis of cofactors Module tdc_M00121 Heme biosynthesis, plants and bacteria, glutamate => heme Brite KEGG Orthology (KO) [BR:tdc00001] 09100 Metabolism 09108…
KEGG T01028: 704242
Entry 704242 CDS T01028 Symbol CYP39A1 Name (RefSeq) 24-hydroxycholesterol 7-alpha-hydroxylase KO K07439 24-hydroxycholesterol 7alpha-hydroxylase [EC:1.14.14.26] Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc00120 Primary bile acid biosynthesis Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism 09103 Lipid metabolism 00120 Primary bile acid biosynthesis 704242 (CYP39A1) 09180 Brite Hierarchies 09181 Protein families: metabolism 00199 Cytochrome P450 [BR:mcc00199] 704242 (CYP39A1)Enzymes [BR:mcc01000] 1. Oxidoreductases 1.14 Acting on paired…
UniProt: A0A8U0V2F9_MUSPF
ID A0A8U0V2F9_MUSPF Unreviewed; 413 AA. AC A0A8U0V2F9; DT 12-OCT-2022, integrated into UniProtKB/TrEMBL. DT 12-OCT-2022, sequence version 1. DT 03-MAY-2023, entry version 4. DE SubName: Full=Protein C-ets-1 isoform X5 {ECO:0000313|RefSeq:XP_044936298.1}; GN Name=ETS1 {ECO:0000313|RefSeq:XP_044936298.1}; OS Mustela putorius furo (European domestic ferret) (Mustela furo). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC…
KEGG T01028: 694719
Entry 694719 CDS T01028 Symbol RPL23 Name (RefSeq) 60S ribosomal protein L23 KO K02894 large subunit ribosomal protein L23e Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc03010 Ribosome mcc05171 Coronavirus disease – COVID-19 Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing 09122 Translation 03010 Ribosome 694719 (RPL23) 09160 Human Diseases 09172 Infectious disease: viral 05171 Coronavirus disease – COVID-19 694719…
Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis
Identification of CH cases from WGS in ISL and UKB We used WGS from 45,510 Icelanders and 130,709 British ancestry participants from the UKB17,18. Average sequencing depth was 33× for UKB and 38× for ISL. Participants with prior diagnoses of hematological disorders or grossly abnormal hematology measurements on entry were…
KEGG T08540: 104459063
Entry 104463828 CDS T08540 Symbol ACOX3 Name (RefSeq) peroxisomal acyl-coenzyme A oxidase 3 KO K00232 acyl-CoA oxidase [EC:1.3.3.6] Organism pguu Pterocles gutturalis (yellow-throated sandgrouse) Pathway pguu00071 Fatty acid degradation pguu00410 beta-Alanine metabolism pguu00592 alpha-Linolenic acid metabolism pguu00640 Propanoate metabolism pguu01040 Biosynthesis of unsaturated fatty acids pguu01100 Metabolic pathways pguu01200 Carbon metabolism pguu01212 Fatty…
KEGG T01028: 704366
Entry 704366 CDS T01028 Symbol ZDHHC15 Name (RefSeq) palmitoyltransferase ZDHHC15 KO K20028 palmitoyltransferase ZDHHC2/15/20 [EC:2.3.1.225] Organism mcc Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies 09182 Protein families: genetic information processing 04131 Membrane trafficking [BR:mcc04131] 704366 (ZDHHC15)Enzymes [BR:mcc01000] 2. Transferases 2.3 Acyltransferases 2.3.1 Transferring groups other than aminoacyl groups 2.3.1.225 protein S-acyltransferase 704366 (ZDHHC15)Membrane trafficking [BR:mcc04131] SNARE SNARE associated proteins Palmitoyltransferases 704366 (ZDHHC15) BRITE hierarchy…
KEGG T05489: A6B45_00495
Entry A6B45_05465 CDS T05489 Name (GenBank) diacetyl reductase KO K03366 meso-butanediol dehydrogenase / (S,S)-butanediol dehydrogenase / diacetyl reductase [EC:1.1.1.- 1.1.1.76 1.1.1.304] Organism lsu Leuconostoc suionicum Pathway lsu00650 Butanoate metabolism lsu01110 Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:lsu00001] 09100 Metabolism 09101 Carbohydrate metabolism 00650 Butanoate metabolism A6B45_05465Enzymes [BR:lsu01000] 1. Oxidoreductases 1.1 Acting on the CH-OH group of donors 1.1.1 With NAD+…
KEGG T01028: 695442
Entry 695442 CDS T01028 Symbol RPLP1 Name (RefSeq) 60S acidic ribosomal protein P1 KO K02942 large subunit ribosomal protein LP1 Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc03010 Ribosome mcc05171 Coronavirus disease – COVID-19 Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing 09122 Translation 03010 Ribosome 695442 (RPLP1) 09160 Human Diseases 09172 Infectious disease: viral 05171 Coronavirus disease –…
KEGG T01028: 717682
Entry 717682 CDS T01028 Symbol SEPTIN2 Name (RefSeq) septin-2 isoform X1 KO K16942 septin 2 Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc05100 Bacterial invasion of epithelial cells Brite KEGG Orthology (KO) [BR:mcc00001] 09160 Human Diseases 09171 Infectious disease: bacterial 05100 Bacterial invasion of epithelial cells 717682 (SEPTIN2) 09180 Brite Hierarchies 09182 Protein families: genetic information processing 04131 Membrane trafficking…
KEGG T01028: 699325
Entry 699325 CDS T01028 Symbol OSBP Name (RefSeq) oxysterol-binding protein 1 KO K20456 oxysterol-binding protein 1 Organism mcc Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies 09182 Protein families: genetic information processing 04131 Membrane trafficking [BR:mcc04131] 699325 (OSBP)Membrane trafficking [BR:mcc04131] Endoplasmic reticulum (ER) – Golgi transport Others Oxysterol-binding proteins 699325 (OSBP) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…
KEGG T04128: 106346836
Entry 111199314 CDS T04128 Name (RefSeq) GDP-L-fucose synthase 1 isoform X2 KO K02377 GDP-L-fucose synthase [EC:1.1.1.271] Organism bna Brassica napus (rape) Pathway bna00051 Fructose and mannose metabolism bna00520 Amino sugar and nucleotide sugar metabolism bna01100 Metabolic pathways bna01250 Biosynthesis of nucleotide sugars Brite KEGG Orthology (KO) [BR:bna00001] 09100 Metabolism 09101 Carbohydrate metabolism 00051 Fructose and mannose…
KEGG T01028: 706713
Entry 706713 CDS T01028 Symbol HNMT Name (RefSeq) histamine N-methyltransferase KO K00546 histamine N-methyltransferase [EC:2.1.1.8] Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc00340 Histidine metabolism mcc01100 Metabolic pathways Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism 09105 Amino acid metabolism 00340 Histidine metabolism 706713 (HNMT) 09180 Brite Hierarchies 09183 Protein families: signaling and cellular processes 04147 Exosome [BR:mcc04147] 706713 (HNMT)Enzymes [BR:mcc01000] 2. Transferases 2.1 Transferring…
KEGG T01028: 694392
Entry 694392 CDS T01028 Symbol WEE2 Name (RefSeq) wee1-like protein kinase 2 KO K06632 wee1-like protein kinase [EC:2.7.11.1] Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc04110 Cell cycle mcc05170 Human immunodeficiency virus 1 infection Brite KEGG Orthology (KO) [BR:mcc00001] 09140 Cellular Processes 09143 Cell growth and death 04110 Cell cycle 694392 (WEE2) 09160 Human Diseases 09172 Infectious disease: viral 05170…
KEGG T02386: 101070831
Entry 101070831 CDS T02386 Symbol cldn3d Name (RefSeq) claudin-4 KO K06087 claudin Organism tru Takifugu rubripes (torafugu) Pathway tru04514 Cell adhesion molecules tru04530 Tight junction Brite KEGG Orthology (KO) [BR:tru00001] 09130 Environmental Information Processing 09133 Signaling molecules and interaction 04514 Cell adhesion molecules 101070831 (cldn3d) 09140 Cellular Processes 09144 Cellular community – eukaryotes 04530 Tight junction 101070831 (cldn3d) 09180 Brite Hierarchies 09183 Protein…
KEGG T01028: 693999
Entry 693999 CDS T01028 Symbol POLI Name (RefSeq) DNA polymerase iota isoform X1 KO K03510 DNA polymerase iota [EC:2.7.7.7] Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc03460 Fanconi anemia pathway Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing 09124 Replication and repair 03460 Fanconi anemia pathway 693999 (POLI) 09180 Brite Hierarchies 09182 Protein families: genetic information processing 03400 DNA…
KEGG T02994: 18603710
Entry 18603710 CDS T02994 Name (RefSeq) gibberellin 2-beta-dioxygenase 2 KO K04125 gibberellin 2beta-dioxygenase [EC:1.14.11.13] Organism tcc Theobroma cacao (cacao) Pathway tcc00904 Diterpenoid biosynthesis tcc01110 Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:tcc00001] 09100 Metabolism 09109 Metabolism of terpenoids and polyketides 00904 Diterpenoid biosynthesis 18603710Enzymes [BR:tcc01000] 1. Oxidoreductases 1.14 Acting on paired donors, with incorporation or reduction of molecular oxygen 1.14.11 With…
KEGG T00186: ECA4130
Entry ECA4130 CDS T00186 Name (GenBank) alkaline phosphatase KO K01077 alkaline phosphatase [EC:3.1.3.1] Organism eca Pectobacterium atrosepticum SCRI1043 Pathway eca00730 Thiamine metabolism eca00790 Folate biosynthesis eca01100 Metabolic pathways eca01240 Biosynthesis of cofactors eca02020 Two-component system Module eca_M00126 Tetrahydrofolate biosynthesis, GTP => THF Brite KEGG Orthology (KO) [BR:eca00001] 09100 Metabolism 09108 Metabolism of cofactors and vitamins 00730…
KEGG T01028: 712850
Entry 712850 CDS T01028 Symbol PDE4A Name (RefSeq) cAMP-specific 3′,5′-cyclic phosphodiesterase 4A isoform X1 KO K13293 cAMP-specific phosphodiesterase 4 [EC:3.1.4.53] Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc00230 Purine metabolism mcc01100 Metabolic pathways mcc04024 cAMP signaling pathway mcc04928 Parathyroid hormone synthesis, secretion and action mcc05032 Morphine addiction Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism 09104…
KEGG T01892: HMPREF4655_20621
Entry HMPREF4655_20621 CDS T01892 Symbol pssA Name (GenBank) CDP-diacylglycerol-serine O-phosphatidyltransferase KO K17103 CDP-diacylglycerol—serine O-phosphatidyltransferase [EC:2.7.8.8] Organism hpo Helicobacter pylori 35A Pathway hpo00260 Glycine, serine and threonine metabolism hpo00564 Glycerophospholipid metabolism hpo01100 Metabolic pathways hpo01110 Biosynthesis of secondary metabolites Module hpo_M00093 Phosphatidylethanolamine (PE) biosynthesis, PA => PS => PE Brite KEGG Orthology (KO) [BR:hpo00001] 09100…
Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria
Isolation of phyllosphere isolates All bacterial strains were isolated in June 2021 from the flag leaves of four wheat cultivars (Sheriff, Heerup, Rembrandt and Kvium) grown in an experimental field in Høje Taastrup, near Copenhagen, Denmark. Wheat flag leaves were picked, pooled, and either washed or blended prior to dilution…
KEGG T01028: 701317
Entry 701317 CDS T01028 Symbol HIPK4 Name (RefSeq) homeodomain-interacting protein kinase 4 KO K08826 homeodomain interacting protein kinase [EC:2.7.11.1] Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc04218 Cellular senescence Brite KEGG Orthology (KO) [BR:mcc00001] 09140 Cellular Processes 09143 Cell growth and death 04218 Cellular senescence 701317 (HIPK4) 09180 Brite Hierarchies 09181 Protein families: metabolism 01001 Protein kinases [BR:mcc01001] 701317 (HIPK4)Enzymes [BR:mcc01000] 2….
KEGG T01028: 717212
Entry 717212 CDS T01028 Symbol PPT2 Name (RefSeq) lysosomal thioesterase PPT2 isoform X1 KO K01074 palmitoyl-protein thioesterase [EC:3.1.2.22] Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc00062 Fatty acid elongation mcc01100 Metabolic pathways mcc01212 Fatty acid metabolism mcc04142 Lysosome Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism 09103 Lipid metabolism 00062 Fatty acid elongation 717212 (PPT2) 09140 Cellular Processes 09141 Transport…
KEGG T01028: 715211
Entry 715211 CDS T01028 Symbol CYB5RL Name (RefSeq) NADH-cytochrome b5 reductase-like isoform X1 KO K00326 cytochrome-b5 reductase [EC:1.6.2.2] Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc00520 Amino sugar and nucleotide sugar metabolism Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism 09101 Carbohydrate metabolism 00520 Amino sugar and nucleotide sugar metabolism 715211 (CYB5RL)Enzymes [BR:mcc01000] 1. Oxidoreductases 1.6 Acting on NADH or NADPH 1.6.2 With…
KEGG T01028: 705628
Entry 705628 CDS T01028 Symbol NUP85 Name (RefSeq) nuclear pore complex protein Nup85 isoform X1 KO K14304 nuclear pore complex protein Nup85 Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc03013 Nucleocytoplasmic transport mcc05014 Amyotrophic lateral sclerosis Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing 09122 Translation 03013 Nucleocytoplasmic transport 705628 (NUP85) 09160 Human Diseases 09164 Neurodegenerative disease 05014 Amyotrophic…
KEGG T01028: 717394
Entry 717394 CDS T01028 Symbol VPS35 Name (RefSeq) vacuolar protein sorting-associated protein 35 isoform X1 KO K18468 vacuolar protein sorting-associated protein 35 Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc04144 Endocytosis Brite KEGG Orthology (KO) [BR:mcc00001] 09140 Cellular Processes 09141 Transport and catabolism 04144 Endocytosis 717394 (VPS35) 09180 Brite Hierarchies 09182 Protein families: genetic information processing 04131 Membrane trafficking [BR:mcc04131] 717394…
EMDB < EMD-40454
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Mouse mm10 chr4:22,481,383-22,489,763 UCSC Genome Browser v455
Custom Tracks Adiposehidedensesquishpackfull Cerebellumhidedensesquishpackfull Cortexhidedensesquishpackfull Liverhidedensesquishpackfull Lunghidedensesquishpackfull Sintesthidedensesquishpackfull Spleenhidedensesquishpackfull mouse_7_core ATAC Adipose Rep1hidedensefull ATAC Adipose Rep2hidedensefull ATAC Cerebellum Rep1hidedensefull ATAC Cerebellum Rep2hidedensefull ATAC Colon Rep1hidedensefull ATAC Colon Rep2hidedensefull ATAC Cortex Rep1hidedensefull ATAC Cortex Rep2hidedensefull ATAC Heart Rep1hidedensefull ATAC Heart Rep2hidedensefull ATAC Liver Rep1hidedensefull ATAC Liver Rep2hidedensefull ATAC…
The Age of Aquarius – RNA, the Epicenter of Genetic Information
The veil on genetic information was lifted by the advent of gene cloning and sequencing technologies in the 1970s. The discovery and purification of bacterial nucleases capable of cutting DNA at specific sequences and ligases capable of joining them enabled DNA from any species – or mRNAs converted to complementary…
EMDB < EMD-25228
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps
de Jonge, P. A., Nobrega, F. L., Brouns, S. J. J. & Dutilh, B. E. Molecular and evolutionary determinants of bacteriophage host range. Trends Microbiol. 27, 51–63 (2019). Article PubMed Google Scholar Cambillau, C. Bacteriophage module reshuffling results in adaptive host range as exemplified by the baseplate model of listerial…
Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans
Protein sequence and prediction analysis The amino acid sequence of FcR was deduced from the F. cylindrus genome sequence33. Protein alignments with characterized microbial rhodopsins were performed using the MUSCLE algorithm implemented in Geneious (v.5.6)69. Predictions of subcellular location were performed with SignalP v.4.0 and TargetP (v.1.1)70. Putative transmembrane domains…
EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets | BMC Bioinformatics
EasyCGTree was implemented in Perl programming languages (www.perl.org/) and was built using a collection of published reputable tools, including Clustal Omega version 1.2.4 [12]; consense from PHYLIP version 3.698 [13]; FastTree version 2.1 [14]; hmmbuild and hmmsearch from HMMER version 3.0 (hmmer.org/); IQ-TREE version 2.1.1 [15]; trimAl version 1.2 [16];…
Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos
Genes coding for endo-chitinases (EC 3.2.1.14), the enzymes that cleave chitin polymers into oligomers [16], were found on 32 of 42 Endozoicomonadaceae genomes (Fig. 1 and Table S1), including representatives of all formally described genera and all Candidatus Gorgonimonas MAGs. Several genomes harbored more than one endo-chitinase encoding gene, resulting in…
KEGG T00007: b1676
Entry b1676 CDS T00007 Symbol pykF Name (RefSeq) pyruvate kinase I KO K00873 pyruvate kinase [EC:2.7.1.40] Organism eco Escherichia coli K-12 MG1655 Pathway eco00010 Glycolysis / Gluconeogenesis eco00620 Pyruvate metabolism eco01100 Metabolic pathways eco01110 Biosynthesis of secondary metabolites eco01120 Microbial metabolism in diverse environments eco01200 Carbon metabolism eco01230 Biosynthesis of amino acids Module…
KEGG T01028: 717963
Entry 717963 CDS T01028 Symbol STIM1 Name (RefSeq) stromal interaction molecule 1 precursor KO K16059 stromal interaction molecule 1 Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc04020 Calcium signaling pathway mcc04611 Platelet activation Brite KEGG Orthology (KO) [BR:mcc00001] 09130 Environmental Information Processing 09132 Signal transduction 04020 Calcium signaling pathway 717963 (STIM1) 09150 Organismal Systems 09151 Immune system 04611 Platelet activation 717963…
KEGG T05149: 103473078
Entry 103473078 CDS T05149 Symbol ppt1 Name (RefSeq) palmitoyl-protein thioesterase 1 isoform X1 KO K01074 palmitoyl-protein thioesterase [EC:3.1.2.22] Organism pret Poecilia reticulata (guppy) Pathway pret00062 Fatty acid elongation pret01100 Metabolic pathways pret01212 Fatty acid metabolism pret04142 Lysosome Brite KEGG Orthology (KO) [BR:pret00001] 09100 Metabolism 09103 Lipid metabolism 00062 Fatty acid elongation 103473078 (ppt1) 09140 Cellular Processes 09141 Transport and…
KEGG T05897: 110480856
Entry 110480856 CDS T05897 Symbol AGA Name (RefSeq) N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase KO K01444 N4-(beta-N-acetylglucosaminyl)-L-asparaginase [EC:3.5.1.26] Organism lsr Lonchura striata domestica (Bengalese finch) Pathway lsr00511 Other glycan degradation lsr04142 Lysosome Brite KEGG Orthology (KO) [BR:lsr00001] 09100 Metabolism 09107 Glycan biosynthesis and metabolism 00511 Other glycan degradation 110480856 (AGA) 09140 Cellular Processes 09141 Transport and catabolism 04142 Lysosome 110480856 (AGA)Enzymes [BR:lsr01000] 3. Hydrolases 3.5 Acting on carbon-nitrogen bonds,…
KEGG T02867: BN877_I0744
Entry BN877_I0744 CDS T02867 Symbol coxB1 Name (GenBank) cytochrome c oxidase, subunit II KO K02275 cytochrome c oxidase subunit II [EC:7.1.1.9] Organism rir Agrobacterium pusense IRBG74 Pathway rir00190 Oxidative phosphorylation rir01100 Metabolic pathways Module rir_M00155 Cytochrome c oxidase, prokaryotes Brite KEGG Orthology (KO) [BR:rir00001] 09100 Metabolism 09102 Energy metabolism 00190 Oxidative phosphorylation BN877_I0744 (coxB1)Enzymes [BR:rir01000] 7. Translocases 7.1 Catalysing the…
KEGG T08832: 125909104
Entry 125925080 CDS T08832 Name (RefSeq) adenylosuccinate synthetase isozyme 2 isoform X1 KO K01939 adenylosuccinate synthase [EC:6.3.4.4] Organism puc Panthera uncia (snow leopard) Pathway puc00230 Purine metabolism puc00250 Alanine, aspartate and glutamate metabolism puc01100 Metabolic pathways puc01232 Nucleotide metabolism puc01240 Biosynthesis of cofactors Module puc_M00049 Adenine ribonucleotide biosynthesis, IMP => ADP,ATP Brite KEGG…
KEGG T00061: RC0581
Entry RC0582 CDS T00061 Symbol pheT Name (GenBank) phenylalanyl-tRNA synthetase beta chain KO K01890 phenylalanyl-tRNA synthetase beta chain [EC:6.1.1.20] Organism rco Rickettsia conorii Pathway rco00970 Aminoacyl-tRNA biosynthesis Brite KEGG Orthology (KO) [BR:rco00001] 09120 Genetic Information Processing 09122 Translation 00970 Aminoacyl-tRNA biosynthesis RC0582 (pheT) 09180 Brite Hierarchies 09181 Protein families: metabolism 01007 Amino acid related enzymes [BR:rco01007] RC0582 (pheT) 09182 Protein families: genetic…
KEGG T00123: EF1761
Entry EF1761 CDS T00123 Symbol ftsE Name (RefSeq) cell division ATP-binding protein FtsE KO K09812 cell division transport system ATP-binding protein Organism efa Enterococcus faecalis V583 Pathway efa02010 ABC transporters Brite KEGG Orthology (KO) [BR:efa00001] 09130 Environmental Information Processing 09131 Membrane transport 02010 ABC transporters EF1761 (ftsE) 09180 Brite Hierarchies 09182 Protein families: genetic information processing 03036 Chromosome and associated…
The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons
The genome assembly was performed with the pipeline v1.5 of the Vertebrate Genomes Project (VGP) and can be found under NCBI BioProject PRJNA558064, accession number GCA_009819655.1, for further details on the sample collection and assembly see Ishigohoka et al.9. In brief, a female blackcap from mainland Spain was caught to…
KEGG T00835: Ccel_0126
Entry Ccel_0126 CDS T00835 Name (GenBank) 3-isopropylmalate dehydratase, large subunit KO K01703 3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit [EC:4.2.1.33 4.2.1.35] Organism cce Ruminiclostridium cellulolyticum Pathway cce00290 Valine, leucine and isoleucine biosynthesis cce00660 C5-Branched dibasic acid metabolism cce01100 Metabolic pathways cce01110 Biosynthesis of secondary metabolites cce01210 2-Oxocarboxylic acid metabolism cce01230 Biosynthesis of amino acids Module cce_M00432 …
KEGG T01028: 713306
Entry 713306 CDS T01028 Symbol GATM Name (RefSeq) glycine amidinotransferase, mitochondrial KO K00613 glycine amidinotransferase [EC:2.1.4.1] Organism mcc Macaca mulatta (rhesus monkey) Pathway mcc00260 Glycine, serine and threonine metabolism mcc00330 Arginine and proline metabolism mcc01100 Metabolic pathways Module mcc_M00047 Creatine pathway Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism 09105 Amino acid metabolism 00260 Glycine, serine and…