Structured Review

Biotechnology Information open reading frame orf
Open Reading Frame Orf, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 89/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/open reading frame orf/product/Biotechnology Information
Average 89 stars, based on 1 article reviews
Price from $9.99 to $1999.99
open reading frame orf - by Bioz Stars, 2020-09
89/100 stars

Images

Related Articles

Sequencing:

Article Title: Cloning, expression, and characterization of a new Streptomyces sp. S27 xylanase for which xylobiose is the main hydrolysis product.
Article Snippet: .. A xylanase gene, xynBS27, was cloned from Streptomyces sp. S27 and consisted of 693 bp encoding a 230-residue protein, including a putative 41-residue signal peptide. .. A xylanase gene, xynBS27, was cloned from Streptomyces sp. S27 and consisted of 693 bp encoding a 230-residue protein, including a putative 41-residue signal peptide.

Article Title: A phylogenetic examination of the primary anthocyanin production pathway of the Plantae
Article Snippet: .. If protein sequences were not already available in the database accession, they were generated by first determining the correct reading frame of each Expressed Sequence Tag using the Open Reading Frame (ORF)-finding program at the National Center for Biotechnology Information ( http://www.ncbi.nlm.nih.gov/gorf/gorf.html ). .. All putative protein sequences were then “BLASTED” to ensure that they were indeed homologous to the sequence being analyzed— DFR, ANS, F3′H, F3′5′H, or F3GT.

Generated:

Article Title: A phylogenetic examination of the primary anthocyanin production pathway of the Plantae
Article Snippet: .. If protein sequences were not already available in the database accession, they were generated by first determining the correct reading frame of each Expressed Sequence Tag using the Open Reading Frame (ORF)-finding program at the National Center for Biotechnology Information ( http://www.ncbi.nlm.nih.gov/gorf/gorf.html ). .. All putative protein sequences were then “BLASTED” to ensure that they were indeed homologous to the sequence being analyzed— DFR, ANS, F3′H, F3′5′H, or F3GT.

other:

Article Title: Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia
Article Snippet: Consensus sequences covering the complete open reading frame (ORF) were submitted to the National Centre for Biotechnology Information (NCBI) GenBank and assigned accession numbers MT271025–MT271035.

Plasmid Preparation:

Article Title: Cloning, expression, and characterization of a new Streptomyces sp. S27 xylanase for which xylobiose is the main hydrolysis product.
Article Snippet: .. A xylanase gene, xynBS27, was cloned from Streptomyces sp. S27 and consisted of 693 bp encoding a 230-residue protein, including a putative 41-residue signal peptide. .. A xylanase gene, xynBS27, was cloned from Streptomyces sp. S27 and consisted of 693 bp encoding a 230-residue protein, including a putative 41-residue signal peptide.

Software:

Article Title: Cloning, expression, and characterization of a new Streptomyces sp. S27 xylanase for which xylobiose is the main hydrolysis product.
Article Snippet: .. A xylanase gene, xynBS27, was cloned from Streptomyces sp. S27 and consisted of 693 bp encoding a 230-residue protein, including a putative 41-residue signal peptide. .. A xylanase gene, xynBS27, was cloned from Streptomyces sp. S27 and consisted of 693 bp encoding a 230-residue protein, including a putative 41-residue signal peptide.

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 94
    Biotechnology Information genbank
    (A) Phylogenetic analysis of the ORF 5 in Korean type 2 PRRSVs. The phylogenetic tree was constructed with 198 Korean PRRSV isolates and 57 PRRSV strains isolated from around the world. The LV was used as the outgroup. Gray boxes and bundle lines indicate genetic clusters (I, II, III, and IV) of Korean isolates. Bootstrap values greater than 500 of 1,000 replicates are indicated PRRSV strains are denoted as follows: name of PRRSV <t>strain/GenBank</t> accession no./country name/collection time, year published, or vaccine. Korean isolates are denoted by serial numbers ( Table 7 ). (B) Korean type 2 PRRSV isolates between 2005 and 2009 belonging to cluster I. (C) Korean type 2 PRRSV isolates collected from 2005 to 2009 belonging to cluster II. (D) Korean type 2 PRRSV isolates obtained from 2005 to 2009 belonging to cluster III. (E) Korean type 2 PRRSV isolates acquired from 2005 to 2009 belonging to cluster IV.
    Genbank, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 94/100, based on 436 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/genbank/product/Biotechnology Information
    Average 94 stars, based on 436 article reviews
    Price from $9.99 to $1999.99
    genbank - by Bioz Stars, 2020-09
    94/100 stars
      Buy from Supplier

    85
    Biotechnology Information 689 o bayeri putative orfs
    Variation in gene density across the O. <t>bayeri</t> genome . (a) Identification and distribution of <t>ORFs</t> (of at least 100 amino acids) among the largest O. bayeri contigs. Only the 100 largest contigs are shown here for convenience. Yellow dots represent contigs in which no ORF could be annotated. Blue and red arrows and dots represent contigs harboring two or one ORF, respectively. (b) Two cases of gene order conservation between O. bayeri and Enc. cuniculi .
    689 O Bayeri Putative Orfs, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/689 o bayeri putative orfs/product/Biotechnology Information
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    689 o bayeri putative orfs - by Bioz Stars, 2020-09
    85/100 stars
      Buy from Supplier

    86
    Biotechnology Information hypothetical un reviewed aox protein sequence
    Nucleotide and deduced amino acid sequence of <t>AOx</t> from <t>A.terreus</t> MTCC6324. Double stranded primer walking confirmed an ORF of 2001(−) denotes a stop codon. The N-terminal conserved amino acids taking part in Rossmann fold architecture (GXGXXG motif) are underlined in black with its residues in bold. The full length cDNA is submitted to NCBI GenBank with accession no: JX139751.
    Hypothetical Un Reviewed Aox Protein Sequence, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hypothetical un reviewed aox protein sequence/product/Biotechnology Information
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    hypothetical un reviewed aox protein sequence - by Bioz Stars, 2020-09
    86/100 stars
      Buy from Supplier

    85
    Biotechnology Information ormdl1 orf
    Gene organization of human <t>ORMDL1,</t> ORMDL2, ORMDL3, ORMDL1 , ORMDL2, and Drosophila ORMDL . Exon numbers of ORMDL1 are shown above the bars. Coding exons are shown in color and their sizes (in nucleotides) are: exon 3, 181 (orange); exon 4, 152 (yellow); exon 5, 133 (green). The intron sizes in kilobases are shown in-between the bars. The numbers below the bars denote the amino-acid positions for the exon-intron boundaries, and for the end of the <t>ORF.</t> The dotted appearance of the bar representing exon 2 of ORMDL1 indicates that it is alternatively spliced. The structure of the two human pseudogenes is also shown. The chromosomal location of each gene or pseudogene is indicated to the right.
    Ormdl1 Orf, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ormdl1 orf/product/Biotechnology Information
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ormdl1 orf - by Bioz Stars, 2020-09
    85/100 stars
      Buy from Supplier

    Image Search Results


    (A) Phylogenetic analysis of the ORF 5 in Korean type 2 PRRSVs. The phylogenetic tree was constructed with 198 Korean PRRSV isolates and 57 PRRSV strains isolated from around the world. The LV was used as the outgroup. Gray boxes and bundle lines indicate genetic clusters (I, II, III, and IV) of Korean isolates. Bootstrap values greater than 500 of 1,000 replicates are indicated PRRSV strains are denoted as follows: name of PRRSV strain/GenBank accession no./country name/collection time, year published, or vaccine. Korean isolates are denoted by serial numbers ( Table 7 ). (B) Korean type 2 PRRSV isolates between 2005 and 2009 belonging to cluster I. (C) Korean type 2 PRRSV isolates collected from 2005 to 2009 belonging to cluster II. (D) Korean type 2 PRRSV isolates obtained from 2005 to 2009 belonging to cluster III. (E) Korean type 2 PRRSV isolates acquired from 2005 to 2009 belonging to cluster IV.

    Journal: Journal of Veterinary Science

    Article Title: Genetic diversity of porcine reproductive and respiratory syndrome virus in Korea

    doi: 10.4142/jvs.2013.14.2.115

    Figure Lengend Snippet: (A) Phylogenetic analysis of the ORF 5 in Korean type 2 PRRSVs. The phylogenetic tree was constructed with 198 Korean PRRSV isolates and 57 PRRSV strains isolated from around the world. The LV was used as the outgroup. Gray boxes and bundle lines indicate genetic clusters (I, II, III, and IV) of Korean isolates. Bootstrap values greater than 500 of 1,000 replicates are indicated PRRSV strains are denoted as follows: name of PRRSV strain/GenBank accession no./country name/collection time, year published, or vaccine. Korean isolates are denoted by serial numbers ( Table 7 ). (B) Korean type 2 PRRSV isolates between 2005 and 2009 belonging to cluster I. (C) Korean type 2 PRRSV isolates collected from 2005 to 2009 belonging to cluster II. (D) Korean type 2 PRRSV isolates obtained from 2005 to 2009 belonging to cluster III. (E) Korean type 2 PRRSV isolates acquired from 2005 to 2009 belonging to cluster IV.

    Article Snippet: Phylogenetic analysis of the ORF 5 gene in type 1 PRRSV isolates A phylogenetic analysis was conducted using sequences of the ORF 5 gene from reference PRRSVs deposited in GenBank (National Center for Biotechnology Information, USA).

    Techniques: Construct, Isolation

    (A) Phylogenetic analysis of the open reading frame (ORF) 5 in Korean type 1 porcine reproductive and respiratory syndrome viruses (PRRSVs). The phylogenetic tree was constructed with 117 PRRSV isolates from Korea and 46 PRRSV strains isolated from around the world. The VR-2332 strain was used as the outgroup. Gray boxes and bundle lines indicate genetic clusters (I, II, and III) of Korean isolates. Bootstrap values greater than 500 of 1,000 replicates are indicated. PRRSV strains are denoted as follows: name of the PRRSV strain/GenBank accession no./country name/collection time, year published, or vaccine. Isolates are denoted by serial numbers ( Table 6 ). (B) Korean type 1 PRRSV isolates collected from 2007 to 2009 belonging to cluster I.

    Journal: Journal of Veterinary Science

    Article Title: Genetic diversity of porcine reproductive and respiratory syndrome virus in Korea

    doi: 10.4142/jvs.2013.14.2.115

    Figure Lengend Snippet: (A) Phylogenetic analysis of the open reading frame (ORF) 5 in Korean type 1 porcine reproductive and respiratory syndrome viruses (PRRSVs). The phylogenetic tree was constructed with 117 PRRSV isolates from Korea and 46 PRRSV strains isolated from around the world. The VR-2332 strain was used as the outgroup. Gray boxes and bundle lines indicate genetic clusters (I, II, and III) of Korean isolates. Bootstrap values greater than 500 of 1,000 replicates are indicated. PRRSV strains are denoted as follows: name of the PRRSV strain/GenBank accession no./country name/collection time, year published, or vaccine. Isolates are denoted by serial numbers ( Table 6 ). (B) Korean type 1 PRRSV isolates collected from 2007 to 2009 belonging to cluster I.

    Article Snippet: Phylogenetic analysis of the ORF 5 gene in type 1 PRRSV isolates A phylogenetic analysis was conducted using sequences of the ORF 5 gene from reference PRRSVs deposited in GenBank (National Center for Biotechnology Information, USA).

    Techniques: Construct, Isolation

    Variation in gene density across the O. bayeri genome . (a) Identification and distribution of ORFs (of at least 100 amino acids) among the largest O. bayeri contigs. Only the 100 largest contigs are shown here for convenience. Yellow dots represent contigs in which no ORF could be annotated. Blue and red arrows and dots represent contigs harboring two or one ORF, respectively. (b) Two cases of gene order conservation between O. bayeri and Enc. cuniculi .

    Journal: Genome Biology

    Article Title: Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions

    doi: 10.1186/gb-2009-10-10-r106

    Figure Lengend Snippet: Variation in gene density across the O. bayeri genome . (a) Identification and distribution of ORFs (of at least 100 amino acids) among the largest O. bayeri contigs. Only the 100 largest contigs are shown here for convenience. Yellow dots represent contigs in which no ORF could be annotated. Blue and red arrows and dots represent contigs harboring two or one ORF, respectively. (b) Two cases of gene order conservation between O. bayeri and Enc. cuniculi .

    Article Snippet: The remaining 689 O. bayeri putative ORFs (of at least 200 amino acids) returned no significant hits in BLAST homology searches against the National Center for Biotechnology Information (NCBI) non-redundant database.

    Techniques:

    Distribution of O. bayeri (blue), Enc. cuniculi (yellow) and Ent. bieneusi (red) proteins among functional categories . The ordinate represents the number of ORFs assigned to the corresponding category. Each of the O. bayeri proteins was assigned to only one of eleven functional categories listed in [ 25 , 33 ]. The corresponding gene list is presented in the online version of this manuscript (Additional data file 3). *Based on a 4× sequence coverage [ 33 ].

    Journal: Genome Biology

    Article Title: Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions

    doi: 10.1186/gb-2009-10-10-r106

    Figure Lengend Snippet: Distribution of O. bayeri (blue), Enc. cuniculi (yellow) and Ent. bieneusi (red) proteins among functional categories . The ordinate represents the number of ORFs assigned to the corresponding category. Each of the O. bayeri proteins was assigned to only one of eleven functional categories listed in [ 25 , 33 ]. The corresponding gene list is presented in the online version of this manuscript (Additional data file 3). *Based on a 4× sequence coverage [ 33 ].

    Article Snippet: The remaining 689 O. bayeri putative ORFs (of at least 200 amino acids) returned no significant hits in BLAST homology searches against the National Center for Biotechnology Information (NCBI) non-redundant database.

    Techniques: Functional Assay, Sequencing

    Nucleotide and deduced amino acid sequence of AOx from A.terreus MTCC6324. Double stranded primer walking confirmed an ORF of 2001(−) denotes a stop codon. The N-terminal conserved amino acids taking part in Rossmann fold architecture (GXGXXG motif) are underlined in black with its residues in bold. The full length cDNA is submitted to NCBI GenBank with accession no: JX139751.

    Journal: PLoS ONE

    Article Title: Molecular Characterization and Expression of a Novel Alcohol Oxidase from Aspergillus terreus MTCC6324

    doi: 10.1371/journal.pone.0095368

    Figure Lengend Snippet: Nucleotide and deduced amino acid sequence of AOx from A.terreus MTCC6324. Double stranded primer walking confirmed an ORF of 2001(−) denotes a stop codon. The N-terminal conserved amino acids taking part in Rossmann fold architecture (GXGXXG motif) are underlined in black with its residues in bold. The full length cDNA is submitted to NCBI GenBank with accession no: JX139751.

    Article Snippet: Hypothetical un-reviewed AOx protein sequence from A.terreus NIH2624 (GI: 115437438) available in National Center for Biotechnology Information (NCBI) was used as an input parameter to generate theoretical peptide masses for comparison with those obtained from the pmf peak list.

    Techniques: Sequencing, Chromosome Walking

    2D electrophoresis of microsomal membrane bound proteins and multiple sequence alignment of highly similar AOx proteins from filamentous fungi and yeast species showing the primers for overlapping PCR based on internal peptide fragments identified from pmf data of spot 6. ( A ). Mass spectrometry compatible silver stained 2D gel image of A.terreus MTCC6324 microsomal proteome. 150 µg of A.terreus microsomal protein having high AOx activity were resolved on 3–10 linear immobiline dry pH gradient strip as first dimension and subsequently run on 12% polyacrylamide resolving gel as second dimension. Seven spots (marked 1–7 along with arrow heads) showing the highest normalized volumes were analysed using MALDI-TOF-MS. ( B ). Internal peptide fragment 1 (GVATVPSKP) and fragment 2(NHITAGIQHGWSHP) shown in red bars, served as templates for designing overlapping PCR primers mapped as AOX-FP2 and AOX-RP1, respectively as an approach for characterizing full length AOx coding region. The gene identification numbers (GI) for the aligned amino acid sequences of AOxs are as follows: P.angusta (GI:113652); C.boidinii (GI:231528); A.terreus NIH2624 (GI:115437438); K.pastoris (GI: 2104963); C. Victoriae (GI: 13182929); P.fulva (GI: 9082281); P.chrysogenum (GI: 18028450). Sequences were aligned using CLUSTALW2 and viewed using GeneDock software. Forward and reverse primers are shown as black arrows with primer names mentioned above. Symbol ( // ) represents discontinuity in multiple sequence alignment. Highly conserved amino acid blocks are shaded in black.

    Journal: PLoS ONE

    Article Title: Molecular Characterization and Expression of a Novel Alcohol Oxidase from Aspergillus terreus MTCC6324

    doi: 10.1371/journal.pone.0095368

    Figure Lengend Snippet: 2D electrophoresis of microsomal membrane bound proteins and multiple sequence alignment of highly similar AOx proteins from filamentous fungi and yeast species showing the primers for overlapping PCR based on internal peptide fragments identified from pmf data of spot 6. ( A ). Mass spectrometry compatible silver stained 2D gel image of A.terreus MTCC6324 microsomal proteome. 150 µg of A.terreus microsomal protein having high AOx activity were resolved on 3–10 linear immobiline dry pH gradient strip as first dimension and subsequently run on 12% polyacrylamide resolving gel as second dimension. Seven spots (marked 1–7 along with arrow heads) showing the highest normalized volumes were analysed using MALDI-TOF-MS. ( B ). Internal peptide fragment 1 (GVATVPSKP) and fragment 2(NHITAGIQHGWSHP) shown in red bars, served as templates for designing overlapping PCR primers mapped as AOX-FP2 and AOX-RP1, respectively as an approach for characterizing full length AOx coding region. The gene identification numbers (GI) for the aligned amino acid sequences of AOxs are as follows: P.angusta (GI:113652); C.boidinii (GI:231528); A.terreus NIH2624 (GI:115437438); K.pastoris (GI: 2104963); C. Victoriae (GI: 13182929); P.fulva (GI: 9082281); P.chrysogenum (GI: 18028450). Sequences were aligned using CLUSTALW2 and viewed using GeneDock software. Forward and reverse primers are shown as black arrows with primer names mentioned above. Symbol ( // ) represents discontinuity in multiple sequence alignment. Highly conserved amino acid blocks are shaded in black.

    Article Snippet: Hypothetical un-reviewed AOx protein sequence from A.terreus NIH2624 (GI: 115437438) available in National Center for Biotechnology Information (NCBI) was used as an input parameter to generate theoretical peptide masses for comparison with those obtained from the pmf peak list.

    Techniques: Two-Dimensional Gel Electrophoresis, Sequencing, Polymerase Chain Reaction, Peptide Mass Fingerprinting, Mass Spectrometry, Staining, Activity Assay, Stripping Membranes, Software

    Ligation of overlapping PCR products at common restriction site and the full length AOx cDNA clone confirmation in TA vector through restriction digestion and double stranded DNA sequencing by primer walking. ( A ). Amplified overlapping PCR amplicons using A.terreus MTCC 6324 cDNA as PCR template. Lane M represents wide range DNA marker, lane L1 represents PCR 1, a ∼1577 bp cDNA fragment of AOx from its start codon, lane L2 represents PCR 2, a ∼1278 bp overlapping cDNA fragment of AOx till the stop codon. Qualitative gel analysis was performed in 0.8% agarose concentration stained with ethidium bromide. ( B ). Restriction digestion pattern of ligated overlapping PCR fragments in TA vector with EcoR I restriction enzyme. The release of ∼2001 bp full length AOx fragment from TA vector backbone of ∼3015 bp was evident. Qualitative gel analysis was performed in 0.8% agarose concentration stained with ethidium bromide. ( C ). Pair-wise sequence alignment of primer walking DNA sequence with the un-reviewed AOx sequence information from A.terreus NIH strain at nucleotide and amino acid level shows a deletion of six contiguous nucleotide sequences (position 685–690) which codes for two serine residues at position 186 and 187. Corresponding sharp nucleotide chromatogram of the deleted region is highlighted, confirming the good quality of the sequencing data and ruling out any possible error in sequencing. Highly similar residues are highlighted in black. ( D ). Qualitative agarose gel for PCR amplification of full length AOx from TA vector. Lane M is a wide range DNA marker, lane L1, shows PCR amplicon of AOx at ∼20001 bp using forward and reverse primers with EcoR I and Hind III restriction sites, respectively.

    Journal: PLoS ONE

    Article Title: Molecular Characterization and Expression of a Novel Alcohol Oxidase from Aspergillus terreus MTCC6324

    doi: 10.1371/journal.pone.0095368

    Figure Lengend Snippet: Ligation of overlapping PCR products at common restriction site and the full length AOx cDNA clone confirmation in TA vector through restriction digestion and double stranded DNA sequencing by primer walking. ( A ). Amplified overlapping PCR amplicons using A.terreus MTCC 6324 cDNA as PCR template. Lane M represents wide range DNA marker, lane L1 represents PCR 1, a ∼1577 bp cDNA fragment of AOx from its start codon, lane L2 represents PCR 2, a ∼1278 bp overlapping cDNA fragment of AOx till the stop codon. Qualitative gel analysis was performed in 0.8% agarose concentration stained with ethidium bromide. ( B ). Restriction digestion pattern of ligated overlapping PCR fragments in TA vector with EcoR I restriction enzyme. The release of ∼2001 bp full length AOx fragment from TA vector backbone of ∼3015 bp was evident. Qualitative gel analysis was performed in 0.8% agarose concentration stained with ethidium bromide. ( C ). Pair-wise sequence alignment of primer walking DNA sequence with the un-reviewed AOx sequence information from A.terreus NIH strain at nucleotide and amino acid level shows a deletion of six contiguous nucleotide sequences (position 685–690) which codes for two serine residues at position 186 and 187. Corresponding sharp nucleotide chromatogram of the deleted region is highlighted, confirming the good quality of the sequencing data and ruling out any possible error in sequencing. Highly similar residues are highlighted in black. ( D ). Qualitative agarose gel for PCR amplification of full length AOx from TA vector. Lane M is a wide range DNA marker, lane L1, shows PCR amplicon of AOx at ∼20001 bp using forward and reverse primers with EcoR I and Hind III restriction sites, respectively.

    Article Snippet: Hypothetical un-reviewed AOx protein sequence from A.terreus NIH2624 (GI: 115437438) available in National Center for Biotechnology Information (NCBI) was used as an input parameter to generate theoretical peptide masses for comparison with those obtained from the pmf peak list.

    Techniques: Ligation, Polymerase Chain Reaction, Plasmid Preparation, DNA Sequencing, Chromosome Walking, Amplification, Marker, Concentration Assay, Staining, Sequencing, Agarose Gel Electrophoresis

    3D superimposition of predicted rAOx holoenzyme model with that of the holoenzyme aryl alcohol oxidase crystal structure (PDB id: 3FIM). The 3D superimposition of our predicted FAD bound rAOx model (shown in yellow color ribbon structure) with the chain B of crystal structure of holoenzyme AOx (shown in green color ribbon structure) from P. eryngii (PDB id: 3FIM) using Molsoft ICM browser ( www.molsoft.com ). Both the FAD molecules from respective protein models and the ρ -methoxybenzyl alcohol as the docked substrate molecule to the model rAOx from A.terreus MTCC6324 are shown as Corey-Pauling-Koltun (CPK) model with its individual binding pockets highlighted in white scaffolds.

    Journal: PLoS ONE

    Article Title: Molecular Characterization and Expression of a Novel Alcohol Oxidase from Aspergillus terreus MTCC6324

    doi: 10.1371/journal.pone.0095368

    Figure Lengend Snippet: 3D superimposition of predicted rAOx holoenzyme model with that of the holoenzyme aryl alcohol oxidase crystal structure (PDB id: 3FIM). The 3D superimposition of our predicted FAD bound rAOx model (shown in yellow color ribbon structure) with the chain B of crystal structure of holoenzyme AOx (shown in green color ribbon structure) from P. eryngii (PDB id: 3FIM) using Molsoft ICM browser ( www.molsoft.com ). Both the FAD molecules from respective protein models and the ρ -methoxybenzyl alcohol as the docked substrate molecule to the model rAOx from A.terreus MTCC6324 are shown as Corey-Pauling-Koltun (CPK) model with its individual binding pockets highlighted in white scaffolds.

    Article Snippet: Hypothetical un-reviewed AOx protein sequence from A.terreus NIH2624 (GI: 115437438) available in National Center for Biotechnology Information (NCBI) was used as an input parameter to generate theoretical peptide masses for comparison with those obtained from the pmf peak list.

    Techniques: Binding Assay

    Gene organization of human ORMDL1, ORMDL2, ORMDL3, ORMDL1 , ORMDL2, and Drosophila ORMDL . Exon numbers of ORMDL1 are shown above the bars. Coding exons are shown in color and their sizes (in nucleotides) are: exon 3, 181 (orange); exon 4, 152 (yellow); exon 5, 133 (green). The intron sizes in kilobases are shown in-between the bars. The numbers below the bars denote the amino-acid positions for the exon-intron boundaries, and for the end of the ORF. The dotted appearance of the bar representing exon 2 of ORMDL1 indicates that it is alternatively spliced. The structure of the two human pseudogenes is also shown. The chromosomal location of each gene or pseudogene is indicated to the right.

    Journal: Genome Biology

    Article Title: ORMDL proteins are a conserved new family of endoplasmic reticulum membrane proteins

    doi:

    Figure Lengend Snippet: Gene organization of human ORMDL1, ORMDL2, ORMDL3, ORMDL1 , ORMDL2, and Drosophila ORMDL . Exon numbers of ORMDL1 are shown above the bars. Coding exons are shown in color and their sizes (in nucleotides) are: exon 3, 181 (orange); exon 4, 152 (yellow); exon 5, 133 (green). The intron sizes in kilobases are shown in-between the bars. The numbers below the bars denote the amino-acid positions for the exon-intron boundaries, and for the end of the ORF. The dotted appearance of the bar representing exon 2 of ORMDL1 indicates that it is alternatively spliced. The structure of the two human pseudogenes is also shown. The chromosomal location of each gene or pseudogene is indicated to the right.

    Article Snippet: ORMDL1 belongs to an evolutionarily conserved gene family The ORMDL1 ORF was used for database sequence comparisons using the National Center for Biotechnology Information (NCBI) BLAST server [ , ] (tBLASTN against nucleotide databases, and BLASTP, PSI-BLAST and PHI-BLAST against the non-redundant protein database).

    Techniques: