gloeobacter violaceus strain pcc 7421  (ATCC)


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    ATCC gloeobacter violaceus strain pcc 7421
    Gloeobacter Violaceus Strain Pcc 7421, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    gloeobacter violaceus pcc 7421  (ATCC)


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    ATCC gloeobacter violaceus pcc 7421
    Origin of the 24 cyanobacterial genome sequences that were used to perform the bioinformatic evaluation of the presence of L-arginine-degrading pathways in cyanobacteria.
    Gloeobacter Violaceus Pcc 7421, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803"

    Article Title: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-8-437

    Origin of the 24 cyanobacterial genome sequences that were used to perform the bioinformatic evaluation of the presence of L-arginine-degrading pathways in cyanobacteria.
    Figure Legend Snippet: Origin of the 24 cyanobacterial genome sequences that were used to perform the bioinformatic evaluation of the presence of L-arginine-degrading pathways in cyanobacteria.

    Techniques Used:

    Presence of genes encoding enzymes of the L-arginine-degrading pathways in the genomes of selected marine and freshwater cyanobacteria.
    Figure Legend Snippet: Presence of genes encoding enzymes of the L-arginine-degrading pathways in the genomes of selected marine and freshwater cyanobacteria.

    Techniques Used:

    Presence of genes encoding enzymes of the L-arginine-degrading pathways in the genomes of selected marine and freshwater cyanobacteria.
    Figure Legend Snippet: Presence of genes encoding enzymes of the L-arginine-degrading pathways in the genomes of selected marine and freshwater cyanobacteria.

    Techniques Used:

    Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine decarboxylases (A1), agmatinases (A2.1), agmatine deiminases (A2.2), N -carbamoylputrescine hydrolases (A2.3), putrescine oxidases or putrescine transaminases (A3), and 4-aminobutyraldehyde dehydrogenases (A4) of the L-arginine decarboxylase pathway.
    Figure Legend Snippet: Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine decarboxylases (A1), agmatinases (A2.1), agmatine deiminases (A2.2), N -carbamoylputrescine hydrolases (A2.3), putrescine oxidases or putrescine transaminases (A3), and 4-aminobutyraldehyde dehydrogenases (A4) of the L-arginine decarboxylase pathway.

    Techniques Used:

    Database entries of genes from 24 cyanobacterial genomes encoding putative arginases (B1), L-ornithine transaminases (C2), and Δ 1 pyrroline-5-carboxylate dehydrogenases (C3) of the arginase pathway.
    Figure Legend Snippet: Database entries of genes from 24 cyanobacterial genomes encoding putative arginases (B1), L-ornithine transaminases (C2), and Δ 1 pyrroline-5-carboxylate dehydrogenases (C3) of the arginase pathway.

    Techniques Used:

    Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine amidinotransferases (C1), L-ornithine transaminases (C2), and Δ 1 pyrroline-5-carboxylate dehydrogenases (C3) of the L-arginine amidinotransferase pathway.
    Figure Legend Snippet: Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine amidinotransferases (C1), L-ornithine transaminases (C2), and Δ 1 pyrroline-5-carboxylate dehydrogenases (C3) of the L-arginine amidinotransferase pathway.

    Techniques Used:

    Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine deiminases (D1), L-ornithine transcarbamoylases (D2), carbamate kinases (D3), L-ornithine transaminases (D4), and Δ 1 pyrroline-5-carboxylate dehydrogenases (D5) of the L-arginine deiminase pathway.
    Figure Legend Snippet: Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine deiminases (D1), L-ornithine transcarbamoylases (D2), carbamate kinases (D3), L-ornithine transaminases (D4), and Δ 1 pyrroline-5-carboxylate dehydrogenases (D5) of the L-arginine deiminase pathway.

    Techniques Used:

    Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine oxidase/dehydrogenase (E1), 4-guanidino butyrase (E2), 4-aminobutyrate transaminase (E3), and succinate semialdehyde dehydrogenase (E4) of the L-arginine oxidase/dehydrogenase pathway.
    Figure Legend Snippet: Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine oxidase/dehydrogenase (E1), 4-guanidino butyrase (E2), 4-aminobutyrate transaminase (E3), and succinate semialdehyde dehydrogenase (E4) of the L-arginine oxidase/dehydrogenase pathway.

    Techniques Used:

    Genes encoding ureohydrolases in the investigated cyanobacterial marine and freshwater cyanobacteria.
    Figure Legend Snippet: Genes encoding ureohydrolases in the investigated cyanobacterial marine and freshwater cyanobacteria.

    Techniques Used:

    Comparison of cyanobacterial putative L-arginine deiminases or L-arginine amidinotransferases to selected prokaryotic sequences and a sequence of a primitive eukaryote*.
    Figure Legend Snippet: Comparison of cyanobacterial putative L-arginine deiminases or L-arginine amidinotransferases to selected prokaryotic sequences and a sequence of a primitive eukaryote*.

    Techniques Used: Sequencing

    gloeobacter violaceus strain pcc 7421  (ATCC)


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    ATCC gloeobacter violaceus strain pcc 7421
    Gloeobacter Violaceus Strain Pcc 7421, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    gloeobacter violaceus strain pcc 7421  (ATCC)


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    ATCC gloeobacter violaceus strain pcc 7421
    Gloeobacter Violaceus Strain Pcc 7421, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    gloeobacter violaceus  (ATCC)


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    ATCC gloeobacter violaceus
    CbbR-like genes in Synechococcus sp. strain PCC 7002. (A) Phylogenetic tree of proteins with >27% amino acid identity to Rhodobacter sphaeroides CbbR from cyanobacteria representing diverse habitats. Proteins were aligned by using CLUSTAL W and the dendrogram generated in the TREEVIEW program. Species name abbreviations: alr/all, Nostoc sp. strain PCC 7120; Avar, Anabaena variabilis ATCC 29413; Cwat, Crocosphaera watsonii WH8501; gll/glr, <t>Gloeobacter</t> <t>violaceus</t> (strain PCC 7421); Npun, Nostoc punctiforme ATCC 29133; PMM, Prochlorococcus marinus (subsp. pastoris, strain CCMP 1378/MED4); Selo, Synechococcus sp. strain PCC 7942 (elongatus); slr/sll, Synechocystis sp. strain PCC 6803; SynW8102, Synechococcus sp. strain WH8102; 7002, Synechococcus sp. strain PCC 7002; tlr/tll, Thermosynechococcus elongatus strain BP-1; Tery, Trichodesmium erythraeum IMS101; YSA′ and YSB′, Synechococcus sp. strain Yellowstone A-Prime and B-Prime. Locus tags are given for the Anabaena, Synechocystis strain PCC 6803, and Gloeobacter violaceus genes. GOIs from the Integrated Microbial Genomes database (DOE, Joint Genome Institute; http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) are used elsewhere except for the Yellowstone species, for which the GenBank accession numbers are given. (B) Physiological phenotype of the group 2 “ccmR” deletion mutant. Rates of Ci-dependent O2 evolution for wild-type (WT) and ΔccmR cells grown continuously with 2% (vol/vol) CO2 in air (two replicates are shown). (C) Structure of the ccmR genomic region in Synechococcus sp. strain PCC 7002. Possible cotranscribed regions are indicated with arrows (dashed lines represent the range of 5′ and 3′ delimits for each mRNA as indicated by RT-PCR; see Table ​Table5).5). Predicted stem and loop structures are shown. ndhF3/D3, NAD(P)H-dehydrogenase (NDH-13) subunit genes; chpY/cupA, gene for putative CO2 hydration protein associated with NDH-1; orf133, conserved gene of unknown function associated with NDH-1 genes; cytP450, cytochrome p450 (PFAM00067); DSBA, DSBA thioredoxin (PFAM 03123).
    Gloeobacter Violaceus, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Transcriptional Regulation of the CO 2 -Concentrating Mechanism in a Euryhaline, Coastal Marine Cyanobacterium, Synechococcus sp. Strain PCC 7002: Role of NdhR/CcmR"

    Article Title: Transcriptional Regulation of the CO 2 -Concentrating Mechanism in a Euryhaline, Coastal Marine Cyanobacterium, Synechococcus sp. Strain PCC 7002: Role of NdhR/CcmR

    Journal:

    doi: 10.1128/JB.01745-06

    CbbR-like genes in Synechococcus sp. strain PCC 7002. (A) Phylogenetic tree of proteins with >27% amino acid identity to Rhodobacter sphaeroides CbbR from cyanobacteria representing diverse habitats. Proteins were aligned by using CLUSTAL W and the dendrogram generated in the TREEVIEW program. Species name abbreviations: alr/all, Nostoc sp. strain PCC 7120; Avar, Anabaena variabilis ATCC 29413; Cwat, Crocosphaera watsonii WH8501; gll/glr, Gloeobacter violaceus (strain PCC 7421); Npun, Nostoc punctiforme ATCC 29133; PMM, Prochlorococcus marinus (subsp. pastoris, strain CCMP 1378/MED4); Selo, Synechococcus sp. strain PCC 7942 (elongatus); slr/sll, Synechocystis sp. strain PCC 6803; SynW8102, Synechococcus sp. strain WH8102; 7002, Synechococcus sp. strain PCC 7002; tlr/tll, Thermosynechococcus elongatus strain BP-1; Tery, Trichodesmium erythraeum IMS101; YSA′ and YSB′, Synechococcus sp. strain Yellowstone A-Prime and B-Prime. Locus tags are given for the Anabaena, Synechocystis strain PCC 6803, and Gloeobacter violaceus genes. GOIs from the Integrated Microbial Genomes database (DOE, Joint Genome Institute; http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) are used elsewhere except for the Yellowstone species, for which the GenBank accession numbers are given. (B) Physiological phenotype of the group 2 “ccmR” deletion mutant. Rates of Ci-dependent O2 evolution for wild-type (WT) and ΔccmR cells grown continuously with 2% (vol/vol) CO2 in air (two replicates are shown). (C) Structure of the ccmR genomic region in Synechococcus sp. strain PCC 7002. Possible cotranscribed regions are indicated with arrows (dashed lines represent the range of 5′ and 3′ delimits for each mRNA as indicated by RT-PCR; see Table ​Table5).5). Predicted stem and loop structures are shown. ndhF3/D3, NAD(P)H-dehydrogenase (NDH-13) subunit genes; chpY/cupA, gene for putative CO2 hydration protein associated with NDH-1; orf133, conserved gene of unknown function associated with NDH-1 genes; cytP450, cytochrome p450 (PFAM00067); DSBA, DSBA thioredoxin (PFAM 03123).
    Figure Legend Snippet: CbbR-like genes in Synechococcus sp. strain PCC 7002. (A) Phylogenetic tree of proteins with >27% amino acid identity to Rhodobacter sphaeroides CbbR from cyanobacteria representing diverse habitats. Proteins were aligned by using CLUSTAL W and the dendrogram generated in the TREEVIEW program. Species name abbreviations: alr/all, Nostoc sp. strain PCC 7120; Avar, Anabaena variabilis ATCC 29413; Cwat, Crocosphaera watsonii WH8501; gll/glr, Gloeobacter violaceus (strain PCC 7421); Npun, Nostoc punctiforme ATCC 29133; PMM, Prochlorococcus marinus (subsp. pastoris, strain CCMP 1378/MED4); Selo, Synechococcus sp. strain PCC 7942 (elongatus); slr/sll, Synechocystis sp. strain PCC 6803; SynW8102, Synechococcus sp. strain WH8102; 7002, Synechococcus sp. strain PCC 7002; tlr/tll, Thermosynechococcus elongatus strain BP-1; Tery, Trichodesmium erythraeum IMS101; YSA′ and YSB′, Synechococcus sp. strain Yellowstone A-Prime and B-Prime. Locus tags are given for the Anabaena, Synechocystis strain PCC 6803, and Gloeobacter violaceus genes. GOIs from the Integrated Microbial Genomes database (DOE, Joint Genome Institute; http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) are used elsewhere except for the Yellowstone species, for which the GenBank accession numbers are given. (B) Physiological phenotype of the group 2 “ccmR” deletion mutant. Rates of Ci-dependent O2 evolution for wild-type (WT) and ΔccmR cells grown continuously with 2% (vol/vol) CO2 in air (two replicates are shown). (C) Structure of the ccmR genomic region in Synechococcus sp. strain PCC 7002. Possible cotranscribed regions are indicated with arrows (dashed lines represent the range of 5′ and 3′ delimits for each mRNA as indicated by RT-PCR; see Table ​Table5).5). Predicted stem and loop structures are shown. ndhF3/D3, NAD(P)H-dehydrogenase (NDH-13) subunit genes; chpY/cupA, gene for putative CO2 hydration protein associated with NDH-1; orf133, conserved gene of unknown function associated with NDH-1 genes; cytP450, cytochrome p450 (PFAM00067); DSBA, DSBA thioredoxin (PFAM 03123).

    Techniques Used: Generated, Mutagenesis, Reverse Transcription Polymerase Chain Reaction

    gloeobacter violaceus  (ATCC)


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    ATCC gloeobacter violaceus
    CbbR-like genes in Synechococcus sp. strain PCC 7002. (A) Phylogenetic tree of proteins with >27% amino acid identity to Rhodobacter sphaeroides CbbR from cyanobacteria representing diverse habitats. Proteins were aligned by using CLUSTAL W and the dendrogram generated in the TREEVIEW program. Species name abbreviations: alr/all, Nostoc sp. strain PCC 7120; Avar, Anabaena variabilis ATCC 29413; Cwat, Crocosphaera watsonii WH8501; gll/glr, <t>Gloeobacter</t> <t>violaceus</t> (strain PCC 7421); Npun, Nostoc punctiforme ATCC 29133; PMM, Prochlorococcus marinus (subsp. pastoris, strain CCMP 1378/MED4); Selo, Synechococcus sp. strain PCC 7942 (elongatus); slr/sll, Synechocystis sp. strain PCC 6803; SynW8102, Synechococcus sp. strain WH8102; 7002, Synechococcus sp. strain PCC 7002; tlr/tll, Thermosynechococcus elongatus strain BP-1; Tery, Trichodesmium erythraeum IMS101; YSA′ and YSB′, Synechococcus sp. strain Yellowstone A-Prime and B-Prime. Locus tags are given for the Anabaena, Synechocystis strain PCC 6803, and Gloeobacter violaceus genes. GOIs from the Integrated Microbial Genomes database (DOE, Joint Genome Institute; http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) are used elsewhere except for the Yellowstone species, for which the GenBank accession numbers are given. (B) Physiological phenotype of the group 2 “ccmR” deletion mutant. Rates of Ci-dependent O2 evolution for wild-type (WT) and ΔccmR cells grown continuously with 2% (vol/vol) CO2 in air (two replicates are shown). (C) Structure of the ccmR genomic region in Synechococcus sp. strain PCC 7002. Possible cotranscribed regions are indicated with arrows (dashed lines represent the range of 5′ and 3′ delimits for each mRNA as indicated by RT-PCR; see Table ​Table5).5). Predicted stem and loop structures are shown. ndhF3/D3, NAD(P)H-dehydrogenase (NDH-13) subunit genes; chpY/cupA, gene for putative CO2 hydration protein associated with NDH-1; orf133, conserved gene of unknown function associated with NDH-1 genes; cytP450, cytochrome p450 (PFAM00067); DSBA, DSBA thioredoxin (PFAM 03123).
    Gloeobacter Violaceus, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gloeobacter violaceus/product/ATCC
    Average 93 stars, based on 1 article reviews
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    gloeobacter violaceus - by Bioz Stars, 2024-05
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    Images

    1) Product Images from "Transcriptional Regulation of the CO 2 -Concentrating Mechanism in a Euryhaline, Coastal Marine Cyanobacterium, Synechococcus sp. Strain PCC 7002: Role of NdhR/CcmR "

    Article Title: Transcriptional Regulation of the CO 2 -Concentrating Mechanism in a Euryhaline, Coastal Marine Cyanobacterium, Synechococcus sp. Strain PCC 7002: Role of NdhR/CcmR

    Journal:

    doi: 10.1128/JB.01745-06

    CbbR-like genes in Synechococcus sp. strain PCC 7002. (A) Phylogenetic tree of proteins with >27% amino acid identity to Rhodobacter sphaeroides CbbR from cyanobacteria representing diverse habitats. Proteins were aligned by using CLUSTAL W and the dendrogram generated in the TREEVIEW program. Species name abbreviations: alr/all, Nostoc sp. strain PCC 7120; Avar, Anabaena variabilis ATCC 29413; Cwat, Crocosphaera watsonii WH8501; gll/glr, Gloeobacter violaceus (strain PCC 7421); Npun, Nostoc punctiforme ATCC 29133; PMM, Prochlorococcus marinus (subsp. pastoris, strain CCMP 1378/MED4); Selo, Synechococcus sp. strain PCC 7942 (elongatus); slr/sll, Synechocystis sp. strain PCC 6803; SynW8102, Synechococcus sp. strain WH8102; 7002, Synechococcus sp. strain PCC 7002; tlr/tll, Thermosynechococcus elongatus strain BP-1; Tery, Trichodesmium erythraeum IMS101; YSA′ and YSB′, Synechococcus sp. strain Yellowstone A-Prime and B-Prime. Locus tags are given for the Anabaena, Synechocystis strain PCC 6803, and Gloeobacter violaceus genes. GOIs from the Integrated Microbial Genomes database (DOE, Joint Genome Institute; http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) are used elsewhere except for the Yellowstone species, for which the GenBank accession numbers are given. (B) Physiological phenotype of the group 2 “ccmR” deletion mutant. Rates of Ci-dependent O2 evolution for wild-type (WT) and ΔccmR cells grown continuously with 2% (vol/vol) CO2 in air (two replicates are shown). (C) Structure of the ccmR genomic region in Synechococcus sp. strain PCC 7002. Possible cotranscribed regions are indicated with arrows (dashed lines represent the range of 5′ and 3′ delimits for each mRNA as indicated by RT-PCR; see Table ​Table5).5). Predicted stem and loop structures are shown. ndhF3/D3, NAD(P)H-dehydrogenase (NDH-13) subunit genes; chpY/cupA, gene for putative CO2 hydration protein associated with NDH-1; orf133, conserved gene of unknown function associated with NDH-1 genes; cytP450, cytochrome p450 (PFAM00067); DSBA, DSBA thioredoxin (PFAM 03123).
    Figure Legend Snippet: CbbR-like genes in Synechococcus sp. strain PCC 7002. (A) Phylogenetic tree of proteins with >27% amino acid identity to Rhodobacter sphaeroides CbbR from cyanobacteria representing diverse habitats. Proteins were aligned by using CLUSTAL W and the dendrogram generated in the TREEVIEW program. Species name abbreviations: alr/all, Nostoc sp. strain PCC 7120; Avar, Anabaena variabilis ATCC 29413; Cwat, Crocosphaera watsonii WH8501; gll/glr, Gloeobacter violaceus (strain PCC 7421); Npun, Nostoc punctiforme ATCC 29133; PMM, Prochlorococcus marinus (subsp. pastoris, strain CCMP 1378/MED4); Selo, Synechococcus sp. strain PCC 7942 (elongatus); slr/sll, Synechocystis sp. strain PCC 6803; SynW8102, Synechococcus sp. strain WH8102; 7002, Synechococcus sp. strain PCC 7002; tlr/tll, Thermosynechococcus elongatus strain BP-1; Tery, Trichodesmium erythraeum IMS101; YSA′ and YSB′, Synechococcus sp. strain Yellowstone A-Prime and B-Prime. Locus tags are given for the Anabaena, Synechocystis strain PCC 6803, and Gloeobacter violaceus genes. GOIs from the Integrated Microbial Genomes database (DOE, Joint Genome Institute; http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) are used elsewhere except for the Yellowstone species, for which the GenBank accession numbers are given. (B) Physiological phenotype of the group 2 “ccmR” deletion mutant. Rates of Ci-dependent O2 evolution for wild-type (WT) and ΔccmR cells grown continuously with 2% (vol/vol) CO2 in air (two replicates are shown). (C) Structure of the ccmR genomic region in Synechococcus sp. strain PCC 7002. Possible cotranscribed regions are indicated with arrows (dashed lines represent the range of 5′ and 3′ delimits for each mRNA as indicated by RT-PCR; see Table ​Table5).5). Predicted stem and loop structures are shown. ndhF3/D3, NAD(P)H-dehydrogenase (NDH-13) subunit genes; chpY/cupA, gene for putative CO2 hydration protein associated with NDH-1; orf133, conserved gene of unknown function associated with NDH-1 genes; cytP450, cytochrome p450 (PFAM00067); DSBA, DSBA thioredoxin (PFAM 03123).

    Techniques Used: Generated, Mutagenesis, Reverse Transcription Polymerase Chain Reaction

    gloeobacter violaceus  (ATCC)


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    ATCC gloeobacter violaceus
    Gloeobacter Violaceus, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    gloeobacter violaceus strain pcc 7421  (ATCC)


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    ATCC gloeobacter violaceus strain pcc 7421
    Gloeobacter Violaceus Strain Pcc 7421, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATCC gloeobacter violaceus strain pcc 7421
    Gloeobacter Violaceus Strain Pcc 7421, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gloeobacter violaceus strain pcc 7421/product/ATCC
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    ATCC gloeobacter violaceus pcc 7421
    Origin of the 24 cyanobacterial genome sequences that were used to perform the bioinformatic evaluation of the presence of L-arginine-degrading pathways in cyanobacteria.
    Gloeobacter Violaceus Pcc 7421, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    ATCC gloeobacter violaceus
    CbbR-like genes in Synechococcus sp. strain PCC 7002. (A) Phylogenetic tree of proteins with >27% amino acid identity to Rhodobacter sphaeroides CbbR from cyanobacteria representing diverse habitats. Proteins were aligned by using CLUSTAL W and the dendrogram generated in the TREEVIEW program. Species name abbreviations: alr/all, Nostoc sp. strain PCC 7120; Avar, Anabaena variabilis ATCC 29413; Cwat, Crocosphaera watsonii WH8501; gll/glr, <t>Gloeobacter</t> <t>violaceus</t> (strain PCC 7421); Npun, Nostoc punctiforme ATCC 29133; PMM, Prochlorococcus marinus (subsp. pastoris, strain CCMP 1378/MED4); Selo, Synechococcus sp. strain PCC 7942 (elongatus); slr/sll, Synechocystis sp. strain PCC 6803; SynW8102, Synechococcus sp. strain WH8102; 7002, Synechococcus sp. strain PCC 7002; tlr/tll, Thermosynechococcus elongatus strain BP-1; Tery, Trichodesmium erythraeum IMS101; YSA′ and YSB′, Synechococcus sp. strain Yellowstone A-Prime and B-Prime. Locus tags are given for the Anabaena, Synechocystis strain PCC 6803, and Gloeobacter violaceus genes. GOIs from the Integrated Microbial Genomes database (DOE, Joint Genome Institute; http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) are used elsewhere except for the Yellowstone species, for which the GenBank accession numbers are given. (B) Physiological phenotype of the group 2 “ccmR” deletion mutant. Rates of Ci-dependent O2 evolution for wild-type (WT) and ΔccmR cells grown continuously with 2% (vol/vol) CO2 in air (two replicates are shown). (C) Structure of the ccmR genomic region in Synechococcus sp. strain PCC 7002. Possible cotranscribed regions are indicated with arrows (dashed lines represent the range of 5′ and 3′ delimits for each mRNA as indicated by RT-PCR; see Table ​Table5).5). Predicted stem and loop structures are shown. ndhF3/D3, NAD(P)H-dehydrogenase (NDH-13) subunit genes; chpY/cupA, gene for putative CO2 hydration protein associated with NDH-1; orf133, conserved gene of unknown function associated with NDH-1 genes; cytP450, cytochrome p450 (PFAM00067); DSBA, DSBA thioredoxin (PFAM 03123).
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    Origin of the 24 cyanobacterial genome sequences that were used to perform the bioinformatic evaluation of the presence of L-arginine-degrading pathways in cyanobacteria.

    Journal: BMC Genomics

    Article Title: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

    doi: 10.1186/1471-2164-8-437

    Figure Lengend Snippet: Origin of the 24 cyanobacterial genome sequences that were used to perform the bioinformatic evaluation of the presence of L-arginine-degrading pathways in cyanobacteria.

    Article Snippet: Moreover, three heterocyst-forming N -fixing species Anabaena variabilis ATCC 29413, Nostoc sp. PCC 7120, and Nostoc punctiforme PCC 73102 as well as Gloeobacter violaceus PCC 7421, a strain which lacks thylakoid membranes, were investigated.

    Techniques:

    Presence of genes encoding enzymes of the L-arginine-degrading pathways in the genomes of selected marine and freshwater cyanobacteria.

    Journal: BMC Genomics

    Article Title: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

    doi: 10.1186/1471-2164-8-437

    Figure Lengend Snippet: Presence of genes encoding enzymes of the L-arginine-degrading pathways in the genomes of selected marine and freshwater cyanobacteria.

    Article Snippet: Moreover, three heterocyst-forming N -fixing species Anabaena variabilis ATCC 29413, Nostoc sp. PCC 7120, and Nostoc punctiforme PCC 73102 as well as Gloeobacter violaceus PCC 7421, a strain which lacks thylakoid membranes, were investigated.

    Techniques:

    Presence of genes encoding enzymes of the L-arginine-degrading pathways in the genomes of selected marine and freshwater cyanobacteria.

    Journal: BMC Genomics

    Article Title: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

    doi: 10.1186/1471-2164-8-437

    Figure Lengend Snippet: Presence of genes encoding enzymes of the L-arginine-degrading pathways in the genomes of selected marine and freshwater cyanobacteria.

    Article Snippet: Moreover, three heterocyst-forming N -fixing species Anabaena variabilis ATCC 29413, Nostoc sp. PCC 7120, and Nostoc punctiforme PCC 73102 as well as Gloeobacter violaceus PCC 7421, a strain which lacks thylakoid membranes, were investigated.

    Techniques:

    Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine decarboxylases (A1), agmatinases (A2.1), agmatine deiminases (A2.2), N -carbamoylputrescine hydrolases (A2.3), putrescine oxidases or putrescine transaminases (A3), and 4-aminobutyraldehyde dehydrogenases (A4) of the L-arginine decarboxylase pathway.

    Journal: BMC Genomics

    Article Title: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

    doi: 10.1186/1471-2164-8-437

    Figure Lengend Snippet: Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine decarboxylases (A1), agmatinases (A2.1), agmatine deiminases (A2.2), N -carbamoylputrescine hydrolases (A2.3), putrescine oxidases or putrescine transaminases (A3), and 4-aminobutyraldehyde dehydrogenases (A4) of the L-arginine decarboxylase pathway.

    Article Snippet: Moreover, three heterocyst-forming N -fixing species Anabaena variabilis ATCC 29413, Nostoc sp. PCC 7120, and Nostoc punctiforme PCC 73102 as well as Gloeobacter violaceus PCC 7421, a strain which lacks thylakoid membranes, were investigated.

    Techniques:

    Database entries of genes from 24 cyanobacterial genomes encoding putative arginases (B1), L-ornithine transaminases (C2), and Δ 1 pyrroline-5-carboxylate dehydrogenases (C3) of the arginase pathway.

    Journal: BMC Genomics

    Article Title: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

    doi: 10.1186/1471-2164-8-437

    Figure Lengend Snippet: Database entries of genes from 24 cyanobacterial genomes encoding putative arginases (B1), L-ornithine transaminases (C2), and Δ 1 pyrroline-5-carboxylate dehydrogenases (C3) of the arginase pathway.

    Article Snippet: Moreover, three heterocyst-forming N -fixing species Anabaena variabilis ATCC 29413, Nostoc sp. PCC 7120, and Nostoc punctiforme PCC 73102 as well as Gloeobacter violaceus PCC 7421, a strain which lacks thylakoid membranes, were investigated.

    Techniques:

    Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine amidinotransferases (C1), L-ornithine transaminases (C2), and Δ 1 pyrroline-5-carboxylate dehydrogenases (C3) of the L-arginine amidinotransferase pathway.

    Journal: BMC Genomics

    Article Title: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

    doi: 10.1186/1471-2164-8-437

    Figure Lengend Snippet: Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine amidinotransferases (C1), L-ornithine transaminases (C2), and Δ 1 pyrroline-5-carboxylate dehydrogenases (C3) of the L-arginine amidinotransferase pathway.

    Article Snippet: Moreover, three heterocyst-forming N -fixing species Anabaena variabilis ATCC 29413, Nostoc sp. PCC 7120, and Nostoc punctiforme PCC 73102 as well as Gloeobacter violaceus PCC 7421, a strain which lacks thylakoid membranes, were investigated.

    Techniques:

    Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine deiminases (D1), L-ornithine transcarbamoylases (D2), carbamate kinases (D3), L-ornithine transaminases (D4), and Δ 1 pyrroline-5-carboxylate dehydrogenases (D5) of the L-arginine deiminase pathway.

    Journal: BMC Genomics

    Article Title: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

    doi: 10.1186/1471-2164-8-437

    Figure Lengend Snippet: Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine deiminases (D1), L-ornithine transcarbamoylases (D2), carbamate kinases (D3), L-ornithine transaminases (D4), and Δ 1 pyrroline-5-carboxylate dehydrogenases (D5) of the L-arginine deiminase pathway.

    Article Snippet: Moreover, three heterocyst-forming N -fixing species Anabaena variabilis ATCC 29413, Nostoc sp. PCC 7120, and Nostoc punctiforme PCC 73102 as well as Gloeobacter violaceus PCC 7421, a strain which lacks thylakoid membranes, were investigated.

    Techniques:

    Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine oxidase/dehydrogenase (E1), 4-guanidino butyrase (E2), 4-aminobutyrate transaminase (E3), and succinate semialdehyde dehydrogenase (E4) of the L-arginine oxidase/dehydrogenase pathway.

    Journal: BMC Genomics

    Article Title: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

    doi: 10.1186/1471-2164-8-437

    Figure Lengend Snippet: Database entries of genes from 24 cyanobacterial genomes encoding putative L-arginine oxidase/dehydrogenase (E1), 4-guanidino butyrase (E2), 4-aminobutyrate transaminase (E3), and succinate semialdehyde dehydrogenase (E4) of the L-arginine oxidase/dehydrogenase pathway.

    Article Snippet: Moreover, three heterocyst-forming N -fixing species Anabaena variabilis ATCC 29413, Nostoc sp. PCC 7120, and Nostoc punctiforme PCC 73102 as well as Gloeobacter violaceus PCC 7421, a strain which lacks thylakoid membranes, were investigated.

    Techniques:

    Genes encoding ureohydrolases in the investigated cyanobacterial marine and freshwater cyanobacteria.

    Journal: BMC Genomics

    Article Title: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

    doi: 10.1186/1471-2164-8-437

    Figure Lengend Snippet: Genes encoding ureohydrolases in the investigated cyanobacterial marine and freshwater cyanobacteria.

    Article Snippet: Moreover, three heterocyst-forming N -fixing species Anabaena variabilis ATCC 29413, Nostoc sp. PCC 7120, and Nostoc punctiforme PCC 73102 as well as Gloeobacter violaceus PCC 7421, a strain which lacks thylakoid membranes, were investigated.

    Techniques:

    Comparison of cyanobacterial putative L-arginine deiminases or L-arginine amidinotransferases to selected prokaryotic sequences and a sequence of a primitive eukaryote*.

    Journal: BMC Genomics

    Article Title: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

    doi: 10.1186/1471-2164-8-437

    Figure Lengend Snippet: Comparison of cyanobacterial putative L-arginine deiminases or L-arginine amidinotransferases to selected prokaryotic sequences and a sequence of a primitive eukaryote*.

    Article Snippet: Moreover, three heterocyst-forming N -fixing species Anabaena variabilis ATCC 29413, Nostoc sp. PCC 7120, and Nostoc punctiforme PCC 73102 as well as Gloeobacter violaceus PCC 7421, a strain which lacks thylakoid membranes, were investigated.

    Techniques: Sequencing

    CbbR-like genes in Synechococcus sp. strain PCC 7002. (A) Phylogenetic tree of proteins with >27% amino acid identity to Rhodobacter sphaeroides CbbR from cyanobacteria representing diverse habitats. Proteins were aligned by using CLUSTAL W and the dendrogram generated in the TREEVIEW program. Species name abbreviations: alr/all, Nostoc sp. strain PCC 7120; Avar, Anabaena variabilis ATCC 29413; Cwat, Crocosphaera watsonii WH8501; gll/glr, Gloeobacter violaceus (strain PCC 7421); Npun, Nostoc punctiforme ATCC 29133; PMM, Prochlorococcus marinus (subsp. pastoris, strain CCMP 1378/MED4); Selo, Synechococcus sp. strain PCC 7942 (elongatus); slr/sll, Synechocystis sp. strain PCC 6803; SynW8102, Synechococcus sp. strain WH8102; 7002, Synechococcus sp. strain PCC 7002; tlr/tll, Thermosynechococcus elongatus strain BP-1; Tery, Trichodesmium erythraeum IMS101; YSA′ and YSB′, Synechococcus sp. strain Yellowstone A-Prime and B-Prime. Locus tags are given for the Anabaena, Synechocystis strain PCC 6803, and Gloeobacter violaceus genes. GOIs from the Integrated Microbial Genomes database (DOE, Joint Genome Institute; http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) are used elsewhere except for the Yellowstone species, for which the GenBank accession numbers are given. (B) Physiological phenotype of the group 2 “ccmR” deletion mutant. Rates of Ci-dependent O2 evolution for wild-type (WT) and ΔccmR cells grown continuously with 2% (vol/vol) CO2 in air (two replicates are shown). (C) Structure of the ccmR genomic region in Synechococcus sp. strain PCC 7002. Possible cotranscribed regions are indicated with arrows (dashed lines represent the range of 5′ and 3′ delimits for each mRNA as indicated by RT-PCR; see Table ​Table5).5). Predicted stem and loop structures are shown. ndhF3/D3, NAD(P)H-dehydrogenase (NDH-13) subunit genes; chpY/cupA, gene for putative CO2 hydration protein associated with NDH-1; orf133, conserved gene of unknown function associated with NDH-1 genes; cytP450, cytochrome p450 (PFAM00067); DSBA, DSBA thioredoxin (PFAM 03123).

    Journal:

    Article Title: Transcriptional Regulation of the CO 2 -Concentrating Mechanism in a Euryhaline, Coastal Marine Cyanobacterium, Synechococcus sp. Strain PCC 7002: Role of NdhR/CcmR

    doi: 10.1128/JB.01745-06

    Figure Lengend Snippet: CbbR-like genes in Synechococcus sp. strain PCC 7002. (A) Phylogenetic tree of proteins with >27% amino acid identity to Rhodobacter sphaeroides CbbR from cyanobacteria representing diverse habitats. Proteins were aligned by using CLUSTAL W and the dendrogram generated in the TREEVIEW program. Species name abbreviations: alr/all, Nostoc sp. strain PCC 7120; Avar, Anabaena variabilis ATCC 29413; Cwat, Crocosphaera watsonii WH8501; gll/glr, Gloeobacter violaceus (strain PCC 7421); Npun, Nostoc punctiforme ATCC 29133; PMM, Prochlorococcus marinus (subsp. pastoris, strain CCMP 1378/MED4); Selo, Synechococcus sp. strain PCC 7942 (elongatus); slr/sll, Synechocystis sp. strain PCC 6803; SynW8102, Synechococcus sp. strain WH8102; 7002, Synechococcus sp. strain PCC 7002; tlr/tll, Thermosynechococcus elongatus strain BP-1; Tery, Trichodesmium erythraeum IMS101; YSA′ and YSB′, Synechococcus sp. strain Yellowstone A-Prime and B-Prime. Locus tags are given for the Anabaena, Synechocystis strain PCC 6803, and Gloeobacter violaceus genes. GOIs from the Integrated Microbial Genomes database (DOE, Joint Genome Institute; http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) are used elsewhere except for the Yellowstone species, for which the GenBank accession numbers are given. (B) Physiological phenotype of the group 2 “ccmR” deletion mutant. Rates of Ci-dependent O2 evolution for wild-type (WT) and ΔccmR cells grown continuously with 2% (vol/vol) CO2 in air (two replicates are shown). (C) Structure of the ccmR genomic region in Synechococcus sp. strain PCC 7002. Possible cotranscribed regions are indicated with arrows (dashed lines represent the range of 5′ and 3′ delimits for each mRNA as indicated by RT-PCR; see Table ​Table5).5). Predicted stem and loop structures are shown. ndhF3/D3, NAD(P)H-dehydrogenase (NDH-13) subunit genes; chpY/cupA, gene for putative CO2 hydration protein associated with NDH-1; orf133, conserved gene of unknown function associated with NDH-1 genes; cytP450, cytochrome p450 (PFAM00067); DSBA, DSBA thioredoxin (PFAM 03123).

    Article Snippet: Species name abbreviations: alr/all, Nostoc sp. strain PCC 7120; Avar, Anabaena variabilis ATCC 29413; Cwat, Crocosphaera watsonii WH8501; gll/glr, Gloeobacter violaceus (strain PCC 7421); Npun, Nostoc punctiforme ATCC 29133; PMM, Prochlorococcus marinus (subsp. pastoris , strain CCMP 1378/MED4); Selo, Synechococcus sp. strain PCC 7942 (elongatus); slr/sll, Synechocystis sp. strain PCC 6803; SynW8102, Synechococcus sp. strain WH8102; 7002, Synechococcus sp. strain PCC 7002; tlr/tll, Thermosynechococcus elongatus strain BP-1; Tery, Trichodesmium erythraeum IMS101; YSA′ and YSB′, Synechococcus sp. strain Yellowstone A-Prime and B-Prime.

    Techniques: Generated, Mutagenesis, Reverse Transcription Polymerase Chain Reaction