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Authors: Pallavi Subhraveti Ron Caspi Quang Ong Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_900167095Cyc: Oceanospirillum multiglobuliferum ATCC 33336 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari phosphate thiamine phosphate ammonium ammonium cis-vaccenate cis-vaccenate cis-vaccenate cis-vaccenate (2-aminoethyl) phosphate phosphate diphosphate a 2,3,4-saturated fatty acid a 2,3,4-saturated fatty acid a 2,3,4-saturated fatty acid a 2,3,4-saturated fatty acid phosphonate predicted ABC RS10820 RS14810 RS15745 RS00205 RS00450 RS00210 RS01220 RS05530 transporter RS10840 RS11125 RS02005 of phosphate thiamine cis-vaccenoyl-CoA cis-vaccenoyl-CoA cis-vaccenoyl-CoA cis-vaccenoyl-CoA (2-aminoethyl) phosphate ammonium ammonium phosphate phosphate diphosphate a 2,3,4-saturated fatty acyl CoA a 2,3,4-saturated fatty acyl CoA a 2,3,4-saturated fatty acyl CoA a 2,3,4-saturated fatty acyl CoA phosphonate phosphate Fatty Acid and Cofactor, Prosthetic Group, Electron Carrier, and Vitamin Biosynthesis Lipid Degradation Macromolecule Modification protein S-nitrosylation 2-amino-6-[1-hydroxyethyl]- heptosyl- ADP-L-glycero-β- 6-methoxy-2-all- DNA combined a (3R)-3- a (3R)-3- a (3R,5Z)-3- a uracil 1498 a [protein]-L- and denitrosylation β a purine 3-(all-trans-heptaprenyl) a ribonucleoside superpathway of tetrahydrofolate biosynthesis fatty acid -oxidation I 7-methyl-7,8-dihydropterin Kdo -lipid A D-manno-heptose trans-octaprenyl- with exogenous hydroxyhexacosanoyl- hydroxydocosanoyl- hydroxydodec- in 16S rRNA β-alanine methionine ubiquinol-8 biosynthesis (prokaryotic) pyridoxal 5'-phosphate biosynthesis I lipoate biosynthesis thioredoxin pathway molybdenum cofactor biosynthesis tetrapyrrole biosynthesis 2 benzene-1,2-diol diphosphate dGDP NAD thiamine salvage I Cell Structure Biosynthesis a [protein]- 2-amino-4-hydroxy-6- ribonucleoside adenosylcobinamide lipopolysaccharide 1,4-benzoquinone bifunctional 3- DNA to form a [acp] [acp] 5-enoyl-[acp] 16S rRNA peptide- and incorporation I I (from glutamate) bifunctional 3-hydroxyacyl-[acyl- 3-hydroxyacyl-[acyl- 3-hydroxyacyl-[acyl- ribonucleoside- 4-aminobutyrate- all-trans- phosphorylation and L-cysteine a (3Z)-alk-3- hydroxymethyldihydropteridine 5'-triphosphate bifunctional heptosyltransferase demethylubiquinol 3- recombinational (uracil(1498)-N(3))- methionine (S)-S- ribonucleoside- D-erythrose demethylmenaquinone Holliday junction carrier-protein] carrier-protein] carrier-protein] diphosphate -2-oxoglutarate GTP 4-hydroxybenzoate octaprenyl an oxidized transhydrogenation thiamine peptidoglycan biosynthesis I (meso-diaminopimelate containing) enoyl-CoA diphosphokinase: adenosylcobinamide II: B5D26_RS09060 O-methyltransferase/ junction methyltransferase: oxide reductase: diphosphate 4-phosphate Glu methyltransferase/2- resolvase RuvX: dehydratase FabZ: dehydratase FabZ: dehydratase FabA: reductase transaminase: an octanoyl-[acp] thioredoxin + ATP Kdo transfer to lipid IV II reductase thiamine RS10815 thiamine 4-hydroxybenzoatediphosphate NAD A B5D26_RS11570 kinase/ lipopolysaccharide 2-polyprenyl-6- B5D26_RS11875 B5D26_RS07880 erythrose-4- glutamate--tRNA UDP-N-acetyl- methoxy-6-polyprenyl-1,4- B5D26_RS13170 B5D26_RS12730 B5D26_RS12730 B5D26_RS09765 subunit alpha: B5D26_RS08970 polyprenyltransferase: octanoyltransferase: cys 2-amino-4-hydroxy-6- adenosylcobinamide- heptosyltransferase hydroxyphenol 16S rRNA peptide- subunit alpha: GTP phosphate NAD kinase: GTP ligase: α-D-glucosamine a [protein] 3- benzoquinol methylase: crossover junction 3-hydroxyacyl-[acyl- 3-hydroxyacyl-[acyl- 3-hydroxyacyl-[acyl- B5D26_RS09265 B5D26_RS06325 B5D26_RS05025 molybdopterin- thiamine CMP-Kdo lipid IV hydroxymethyldihydropteridine phosphate II: B5D26_RS14135 methylase: (uracil(1498)-N(3))- 4-aminobutyrate- methionine (S)-S- B5D26_RS09265 cyclohydrolase 3-octaprenyl-4- a [lipoyl-carrier B5D26_RS02215 A nitrosothio- a (2E)-2- B5D26_RS13450 dehydrogenase: thioredoxin- synthase phosphate an L-glutamyl-B5D26_RS06695 UDP-N-acetylglucosamine guanylyltransferase: 3-methyl-6-methoxy- resolution of endodeoxyribonuclease carrier-protein] carrier-protein] carrier-protein] ribonucleotide- -2-oxoglutarate I FolE: protein] N 6 - NADP + L-cysteine:[protein 3-deoxy-D-manno- L-alanine long-chain fatty diphosphokinase: B5D26_RS12525 methyltransferase: oxide reductase: ribonucleotide- guanine RS05130 guanine hydroxybenzoate gapA Glu enoyl-CoA (heptosyl) - 2-octaprenyl-1,4- RuvC: B5D26_RS12445 dehydratase FabA: dehydratase FabA: dehydratase FabZ: diphosphate disulfide reductase: adenylyltransferase cysteine] GTP 3',8'-cyclase: [tRNA ] 1-carboxyvinyltransferase: octulosonic acid a 2,3,4-saturated acid--CoA ligase: B5D26_RS08630 B5D26_RS02580 ADP 2 2-methoxy-6-(all-trans recombinational B5D26_RS13190 transaminase: B5D26_RS09950 diphosphate B5D26_RS01305 octanoyl-L-lysine thiamine- a purine adenosyl- Kdo -lipid A 3 3-octaprenyl-4- 4-phospho- B5D26_RS01035 coenzyme A 3-hydroxybutyryl- a 2,3,4- [1-(2-amino-7-methyl-4-oxo- 2 benzoquinone junction B5D26_RS09765 B5D26_RS09765 B5D26_RS12730 reductase an N - B5D26_RS08720 a protein-L- 7,8- B5D26_RS13325 NAD(P)(+) MoeB: sulfurtransferase: B5D26_RS10925 phosphate kinase: transferase: fatty acid B5D26_RS00205 acyl-CoA -heptaprenyl)phenol reductase hydroxybenzoate D-erythronate lipoyl synthase: glutamyl-tRNA α CoA epimerase: saturated (3R)-3- 7,8-dihydro-3H-pteridin- ribonucleoside cobinamide a (2E)-hexacos- a (2E)-docos- a (2E,5Z)-dodeca- subunit beta: methyluracil 1498 methionine- dihydroneopterin transhydrogenase: B5D26_RS02040 B5D26_RS03090(8S)-3',8-cyclo-7,8- UDP-N-acetyl- - B5D26_RS06065 [+ 3 isozymes] dehydrogenase: formation of two 3-oxopropanoate subunit beta: decarboxylase: B5D26_RS05030 B5D26_RS13560 reductase: B5D26_RS10785 hydroxyacyl-CoA 6-yl)]ethyl diphosphate 5'-diphosphate phosphate 2-enoyl-[acp] 2-enoyl-[acp] 3,5-dienoyl-[acp] B5D26_RS09270 in 16S rRNA (S)-S-oxide a sugar RS13090 a sugar 3'-triphosphate 4-phosphoerythronate B5D26_RS05345 a carboxy-adenylated an [L-cysteine dihydroguanosine D-glucosamine- α-Kdo-(2->6)-lipid IV B5D26_RS09065 intact strands a 2'- B5D26_RS09270 B5D26_RS08930 a [lipoyl-carrier thiamine B5D26_RS02060 A a [protein]- dehydrogenase: a reduced [small subunit of desulfurase]-S- 5'-triphosphate enolpyruvate S-nitrosoglutathione [+ 8 isozymes] a 2,3,4- deoxyribonucleoside protein]-N 6 - diphosphate (S)-4-amino-5- 3-deoxy-D-manno- L-cysteine a 2,3,4-saturated GDP B5D26_RS00465 thioredoxin NADPH molybdopterin synthase] sulfanyl-L-cysteine UDP-N- saturated (3S)-3- 5'-diphosphate 2-octaprenylphenol lipoyl-L-lysine cyclic pyranopterin oxopentanoate octulosonic fatty acyl CoA (3R)-3-hydroxy-2-oxo- monophosphate acetylenolpyruvoylglucosamine S-(hydroxymethyl) Aldehyde Degradation hydroxyacyl-CoA Mo 2+ RS14250 Mo 2+ 7,8- acid kinase: 4 phosphooxybutanoate glutamate-1- reductase: B5D26_RS10600 glutathione dihydroneopterin synthase: B5D26_RS06075 3-hydroxyacyl-CoA semialdehyde- ala UDP-N-acetyl- dehydrogenase/ a (2R)-2-hydroxy a peptide with a (3R)-3- a 3-(all-trans a (3R)-3- a (3R,11Z)-3- 3'-phosphate phosphoserine B5D26_RS10915 α methylglyoxal degradation I dehydrogenase: undecaprenyl- a nascent a reduced (2R,3S)-3- a [protein]-L- a thiocarboxylated 2,1-aminomutase: α-D-muramate 4-O-phospho- - class III alcohol a peptidoglycan even numbered an N-terminal hydroxytetracosanoyl- -polyprenyl) hydroxyglutaryl- hydroxyoctadec- 3-(all-trans transaminase: cyclic pyranopterin B5D26_RS10785 diphospho-N- peptidoglycan electron-transfer UQ ATP H O dITP isopropylmalate methionine dADP + + [small subunit of B5D26_RS11510 Kdo-(2->6)-lipid IV dehydrogenase: acetyl-CoA C- with (L-alanyl- 2 K RS06405 K -octaprenyl) B5D26_RS00745 A acetylmuramoyl- UDP-N-acetyl- with (L-alanyl- straight chain flavoprotein Xaa-L-prolineXaa-Pro [acp] benzene-1,2-diol [acp] methyl ester 11-enoyl-[acp] 3-isopropylmalate peptide- phosphate B5D26_RS13115 methylglyoxal a 2,3,4-saturated acyltransferase a 2,3,4-saturated γ-D-glutamyl- electron transfer type I secretion 3-hydroxyacyl-[acyl- bifunctional 3- 3-hydroxyacyl-[acyl- 3-hydroxyacyl-[acyl- benzene-1,2-diol superpathway of thiamine diphosphate biosynthesis II molybdopterin synthase] UDP-N- L-alanyl-γ-D- α-D-glucosamine γ-D-glutamyl- 2,3,4-saturated aminopeptidase: non-canonical purine dehydratase methionine (R)-S- ribonucleoside- 4-phosphooxy- 5-aminolevulinate lactoylglutathione fatty acyl CoA FadA: 3-oxoacyl-CoA meso-2,6- long-chain fatty flavoprotein- system permease/ carrier-protein] demethylubiquinol 3- carrier-protein] carrier-protein] 7,8- bifunctional 3- acetylmuramate-- S-(hydroxysulfenamide) glutamyl-L-lysyl- undecaprenyldiphospho- meso-2,6- fatty acid B5D26_RS14680 NTP pyrophosphatase, small subunit: oxide reductase: diphosphate L-threonine molybdopterin lyase: B5D26_RS10790 diaminopimeloyl- acid--CoA ligase: ubiquinone ATPase: dehydratase FabZ: O-methyltransferase/ dehydratase FabA: dehydratase FabZ: dihydroneopterin demethylubiquinol 3- delta-aminolevulinic L-alanine ligase: -glutathione D-alanyl-D-alanine muramoylpentapeptide beta-N- diaminopimeloyl- RdgB/HAM1
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    Proc. Nati. Acad. Sci. USA Vol. 74, No. 3, pp. 984-988, March 1977 Biochemistry Nucleotide sequence surrounding a ribonuclease III processing site in bacteriophage T7 RNA (intercistronic region/polycistronic mRNA precursor/hairpin structure/endoribonuclease III) MARTIN ROSENBERG* AND RICHARD A. KRAMERt f * Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20014; and t Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305 Communicated by Charles Yanofsky, January 3, 1977 ABSTRACT We have determined a nucleotide sequence of the 5' end of the gene 0.7 mRNAs, (ii) some fragments that 87 residues surrounding a ribonuclease III (endoribonuclease contain the RNase III cleavage site are not recognized and III; EC 3.1.4.24) processing site in the bacteriophage 17 inter- cistronic region between early genes 0.3 and 0.7. The structural cleaved by the enzyme; and (iii) the 3'-terminal oligoadenylate requirements necessary for proper recognition and cleavage by sequences found on the ends of the in vdvo T7 early mRNAs (11) RNase III are discussed. In addition, other structural features are not encoded by the genome, but presumably represent a characteristic of this intercistronic boundary are described. nontemplate-dependent post-transcriptional modification. Here, we report the complete nucleotide sequence of the gene When bacteriophage T7 infects Escherichia coli, the host RNA 0.3-0.7 intercistronic region of T7 and propose a specific role polymerase (RNA nucleotidyltransferase, EC 2.7.7.6) tran- for RNA secondary structure in substrate recognition and action scribes only the early region of the phage genome (i.e., leftmost of RNase III.
  • (10) Patent No.: US 8119385 B2

    (10) Patent No.: US 8119385 B2

    US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides.
  • Human Metabolome Technologies

    Human Metabolome Technologies

    Human Metabolome Human Metabolome Technologies Inc. (HMT) is a leading metabolomics service provider company established on July 2003 based on capillary electrophoresis mass spectrometry (CE-MS) technologies. Technologies The company was listed on the Mothers section of Tokyo Stock Exchange in December 2013. Our main Commissioned metabolome analysis services business is commissioned metabolomics analysis using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS): We have a time-tested track record in a number of different fields including medical sciences, pharmaceuticals, food products, fermentation, and cosmetics. With an aim of contributing in a wide range of fields, we will now set our sights on untapped areas such as the environment, energy, and chemical industries. History Jul 2003 Founded in Suehiromachi in Tsuruoka, Yamagata Prefecture with capital of 10 million yen. Jun 2004 Concluded a joint research agreement with Ajinomoto Co., Inc. May 2009 Commenced the “HMT Research Grant for Young Leaders” Aug 2012 Launched a cancer research specialized package, “C-SCOPE.” Oct 2012 Established a sales subsidiary, “Human Metabolome Technologies America, Inc.” in Massachusetts, USA Sep 2013 Registered the patent “The biomarker for depression, the measuring method for the biomarker of depression, and the program and storage for the diagnostic method” (patent number 5372213) in Japan Dec 2013 Listed on the Mothers section of the Tokyo Stock Exchange Jan 2016 Established a biomarker business company “HMT Biomedical Co., Ltd.” in Yokohama, Kanagawa, Japan May 2017 Established a sales subsidiary, “Human Metabolome Technologies Europe B.V.” in Leiden, Netherlands Apr 2018 Launched functional lipidomics specialized package “Mediator Scan” Human Metabolome Technologies Inc.