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ppis  (ATCC)


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    Structured Review

    ATCC ppis
    Dockerin and cohesin domain sequence pairs were used as input to AlphaFold3 for 3D structure and interaction predictions. The resulting PDB files were input to FoldDock to calculate the pDockQ scores. Scores larger than 0.3 are shown. ( A ) Protein-protein interactions <t>(PPIs)</t> are predicted between cohesins (rows) and dockerins (columns) in GHs of C. perfringens ATCC 13124. “+” and “-“ indicate the presence and absence of experimentally characterized PPIs . ( B ) PPIs are predicted between cohesins in scaffoldins (rows) and dockerins in GHs (columns) of ET540. ( C ) A conceptual model is proposed illustrating the protein organization in the mucinolysome of ET540. ( D ) Predicted PPI interface between cSca1-Doc <t>and</t> <t>cSca5-Coh.</t> Hydrogen-bond contacts are shown as red dashed lines with corresponding distance < 3.5 Å between atoms. Sequences of cSca1-Doc and cSca5-Coh are shown beside the PPI interface structure with residues highlighted corresponding to residues in the hydrogen-bond contact interface. ( E ) Sequence alignment of cSca1-Doc against dockerin sequences in four ATCC 13124 proteins. Key residues involved in hydrogen-bonding (#) and van der Waals (*) contacts are indicated. Residues for cSca1-Doc are predicted, while residues for ATCC 13124 proteins were published previously . The two EF hand motifs are indicated. ( F ) Sequence alignment of cSca5-Coh against cohesin sequences in five published ATCC 13124 proteins .
    Ppis, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1310 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Mucinolysome in gut microbiomes of farm animals and humans"

    Article Title: Mucinolysome in gut microbiomes of farm animals and humans

    Journal: bioRxiv

    doi: 10.1101/2025.10.14.682383

    Dockerin and cohesin domain sequence pairs were used as input to AlphaFold3 for 3D structure and interaction predictions. The resulting PDB files were input to FoldDock to calculate the pDockQ scores. Scores larger than 0.3 are shown. ( A ) Protein-protein interactions (PPIs) are predicted between cohesins (rows) and dockerins (columns) in GHs of C. perfringens ATCC 13124. “+” and “-“ indicate the presence and absence of experimentally characterized PPIs . ( B ) PPIs are predicted between cohesins in scaffoldins (rows) and dockerins in GHs (columns) of ET540. ( C ) A conceptual model is proposed illustrating the protein organization in the mucinolysome of ET540. ( D ) Predicted PPI interface between cSca1-Doc and cSca5-Coh. Hydrogen-bond contacts are shown as red dashed lines with corresponding distance < 3.5 Å between atoms. Sequences of cSca1-Doc and cSca5-Coh are shown beside the PPI interface structure with residues highlighted corresponding to residues in the hydrogen-bond contact interface. ( E ) Sequence alignment of cSca1-Doc against dockerin sequences in four ATCC 13124 proteins. Key residues involved in hydrogen-bonding (#) and van der Waals (*) contacts are indicated. Residues for cSca1-Doc are predicted, while residues for ATCC 13124 proteins were published previously . The two EF hand motifs are indicated. ( F ) Sequence alignment of cSca5-Coh against cohesin sequences in five published ATCC 13124 proteins .
    Figure Legend Snippet: Dockerin and cohesin domain sequence pairs were used as input to AlphaFold3 for 3D structure and interaction predictions. The resulting PDB files were input to FoldDock to calculate the pDockQ scores. Scores larger than 0.3 are shown. ( A ) Protein-protein interactions (PPIs) are predicted between cohesins (rows) and dockerins (columns) in GHs of C. perfringens ATCC 13124. “+” and “-“ indicate the presence and absence of experimentally characterized PPIs . ( B ) PPIs are predicted between cohesins in scaffoldins (rows) and dockerins in GHs (columns) of ET540. ( C ) A conceptual model is proposed illustrating the protein organization in the mucinolysome of ET540. ( D ) Predicted PPI interface between cSca1-Doc and cSca5-Coh. Hydrogen-bond contacts are shown as red dashed lines with corresponding distance < 3.5 Å between atoms. Sequences of cSca1-Doc and cSca5-Coh are shown beside the PPI interface structure with residues highlighted corresponding to residues in the hydrogen-bond contact interface. ( E ) Sequence alignment of cSca1-Doc against dockerin sequences in four ATCC 13124 proteins. Key residues involved in hydrogen-bonding (#) and van der Waals (*) contacts are indicated. Residues for cSca1-Doc are predicted, while residues for ATCC 13124 proteins were published previously . The two EF hand motifs are indicated. ( F ) Sequence alignment of cSca5-Coh against cohesin sequences in five published ATCC 13124 proteins .

    Techniques Used: Sequencing, Protein-Protein interactions



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    Dockerin and cohesin domain sequence pairs were used as input to AlphaFold3 for 3D structure and interaction predictions. The resulting PDB files were input to FoldDock to calculate the pDockQ scores. Scores larger than 0.3 are shown. ( A ) Protein-protein interactions <t>(PPIs)</t> are predicted between cohesins (rows) and dockerins (columns) in GHs of C. perfringens ATCC 13124. “+” and “-“ indicate the presence and absence of experimentally characterized PPIs . ( B ) PPIs are predicted between cohesins in scaffoldins (rows) and dockerins in GHs (columns) of ET540. ( C ) A conceptual model is proposed illustrating the protein organization in the mucinolysome of ET540. ( D ) Predicted PPI interface between cSca1-Doc <t>and</t> <t>cSca5-Coh.</t> Hydrogen-bond contacts are shown as red dashed lines with corresponding distance < 3.5 Å between atoms. Sequences of cSca1-Doc and cSca5-Coh are shown beside the PPI interface structure with residues highlighted corresponding to residues in the hydrogen-bond contact interface. ( E ) Sequence alignment of cSca1-Doc against dockerin sequences in four ATCC 13124 proteins. Key residues involved in hydrogen-bonding (#) and van der Waals (*) contacts are indicated. Residues for cSca1-Doc are predicted, while residues for ATCC 13124 proteins were published previously . The two EF hand motifs are indicated. ( F ) Sequence alignment of cSca5-Coh against cohesin sequences in five published ATCC 13124 proteins .
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    Dockerin and cohesin domain sequence pairs were used as input to AlphaFold3 for 3D structure and interaction predictions. The resulting PDB files were input to FoldDock to calculate the pDockQ scores. Scores larger than 0.3 are shown. ( A ) Protein-protein interactions <t>(PPIs)</t> are predicted between cohesins (rows) and dockerins (columns) in GHs of C. perfringens ATCC 13124. “+” and “-“ indicate the presence and absence of experimentally characterized PPIs . ( B ) PPIs are predicted between cohesins in scaffoldins (rows) and dockerins in GHs (columns) of ET540. ( C ) A conceptual model is proposed illustrating the protein organization in the mucinolysome of ET540. ( D ) Predicted PPI interface between cSca1-Doc <t>and</t> <t>cSca5-Coh.</t> Hydrogen-bond contacts are shown as red dashed lines with corresponding distance < 3.5 Å between atoms. Sequences of cSca1-Doc and cSca5-Coh are shown beside the PPI interface structure with residues highlighted corresponding to residues in the hydrogen-bond contact interface. ( E ) Sequence alignment of cSca1-Doc against dockerin sequences in four ATCC 13124 proteins. Key residues involved in hydrogen-bonding (#) and van der Waals (*) contacts are indicated. Residues for cSca1-Doc are predicted, while residues for ATCC 13124 proteins were published previously . The two EF hand motifs are indicated. ( F ) Sequence alignment of cSca5-Coh against cohesin sequences in five published ATCC 13124 proteins .
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    Dockerin and cohesin domain sequence pairs were used as input to AlphaFold3 for 3D structure and interaction predictions. The resulting PDB files were input to FoldDock to calculate the pDockQ scores. Scores larger than 0.3 are shown. ( A ) Protein-protein interactions <t>(PPIs)</t> are predicted between cohesins (rows) and dockerins (columns) in GHs of C. perfringens ATCC 13124. “+” and “-“ indicate the presence and absence of experimentally characterized PPIs . ( B ) PPIs are predicted between cohesins in scaffoldins (rows) and dockerins in GHs (columns) of ET540. ( C ) A conceptual model is proposed illustrating the protein organization in the mucinolysome of ET540. ( D ) Predicted PPI interface between cSca1-Doc <t>and</t> <t>cSca5-Coh.</t> Hydrogen-bond contacts are shown as red dashed lines with corresponding distance < 3.5 Å between atoms. Sequences of cSca1-Doc and cSca5-Coh are shown beside the PPI interface structure with residues highlighted corresponding to residues in the hydrogen-bond contact interface. ( E ) Sequence alignment of cSca1-Doc against dockerin sequences in four ATCC 13124 proteins. Key residues involved in hydrogen-bonding (#) and van der Waals (*) contacts are indicated. Residues for cSca1-Doc are predicted, while residues for ATCC 13124 proteins were published previously . The two EF hand motifs are indicated. ( F ) Sequence alignment of cSca5-Coh against cohesin sequences in five published ATCC 13124 proteins .
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    Dockerin and cohesin domain sequence pairs were used as input to AlphaFold3 for 3D structure and interaction predictions. The resulting PDB files were input to FoldDock to calculate the pDockQ scores. Scores larger than 0.3 are shown. ( A ) Protein-protein interactions <t>(PPIs)</t> are predicted between cohesins (rows) and dockerins (columns) in GHs of C. perfringens ATCC 13124. “+” and “-“ indicate the presence and absence of experimentally characterized PPIs . ( B ) PPIs are predicted between cohesins in scaffoldins (rows) and dockerins in GHs (columns) of ET540. ( C ) A conceptual model is proposed illustrating the protein organization in the mucinolysome of ET540. ( D ) Predicted PPI interface between cSca1-Doc <t>and</t> <t>cSca5-Coh.</t> Hydrogen-bond contacts are shown as red dashed lines with corresponding distance < 3.5 Å between atoms. Sequences of cSca1-Doc and cSca5-Coh are shown beside the PPI interface structure with residues highlighted corresponding to residues in the hydrogen-bond contact interface. ( E ) Sequence alignment of cSca1-Doc against dockerin sequences in four ATCC 13124 proteins. Key residues involved in hydrogen-bonding (#) and van der Waals (*) contacts are indicated. Residues for cSca1-Doc are predicted, while residues for ATCC 13124 proteins were published previously . The two EF hand motifs are indicated. ( F ) Sequence alignment of cSca5-Coh against cohesin sequences in five published ATCC 13124 proteins .
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    Dockerin and cohesin domain sequence pairs were used as input to AlphaFold3 for 3D structure and interaction predictions. The resulting PDB files were input to FoldDock to calculate the pDockQ scores. Scores larger than 0.3 are shown. ( A ) Protein-protein interactions <t>(PPIs)</t> are predicted between cohesins (rows) and dockerins (columns) in GHs of C. perfringens ATCC 13124. “+” and “-“ indicate the presence and absence of experimentally characterized PPIs . ( B ) PPIs are predicted between cohesins in scaffoldins (rows) and dockerins in GHs (columns) of ET540. ( C ) A conceptual model is proposed illustrating the protein organization in the mucinolysome of ET540. ( D ) Predicted PPI interface between cSca1-Doc <t>and</t> <t>cSca5-Coh.</t> Hydrogen-bond contacts are shown as red dashed lines with corresponding distance < 3.5 Å between atoms. Sequences of cSca1-Doc and cSca5-Coh are shown beside the PPI interface structure with residues highlighted corresponding to residues in the hydrogen-bond contact interface. ( E ) Sequence alignment of cSca1-Doc against dockerin sequences in four ATCC 13124 proteins. Key residues involved in hydrogen-bonding (#) and van der Waals (*) contacts are indicated. Residues for cSca1-Doc are predicted, while residues for ATCC 13124 proteins were published previously . The two EF hand motifs are indicated. ( F ) Sequence alignment of cSca5-Coh against cohesin sequences in five published ATCC 13124 proteins .
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    Image Search Results


    Dockerin and cohesin domain sequence pairs were used as input to AlphaFold3 for 3D structure and interaction predictions. The resulting PDB files were input to FoldDock to calculate the pDockQ scores. Scores larger than 0.3 are shown. ( A ) Protein-protein interactions (PPIs) are predicted between cohesins (rows) and dockerins (columns) in GHs of C. perfringens ATCC 13124. “+” and “-“ indicate the presence and absence of experimentally characterized PPIs . ( B ) PPIs are predicted between cohesins in scaffoldins (rows) and dockerins in GHs (columns) of ET540. ( C ) A conceptual model is proposed illustrating the protein organization in the mucinolysome of ET540. ( D ) Predicted PPI interface between cSca1-Doc and cSca5-Coh. Hydrogen-bond contacts are shown as red dashed lines with corresponding distance < 3.5 Å between atoms. Sequences of cSca1-Doc and cSca5-Coh are shown beside the PPI interface structure with residues highlighted corresponding to residues in the hydrogen-bond contact interface. ( E ) Sequence alignment of cSca1-Doc against dockerin sequences in four ATCC 13124 proteins. Key residues involved in hydrogen-bonding (#) and van der Waals (*) contacts are indicated. Residues for cSca1-Doc are predicted, while residues for ATCC 13124 proteins were published previously . The two EF hand motifs are indicated. ( F ) Sequence alignment of cSca5-Coh against cohesin sequences in five published ATCC 13124 proteins .

    Journal: bioRxiv

    Article Title: Mucinolysome in gut microbiomes of farm animals and humans

    doi: 10.1101/2025.10.14.682383

    Figure Lengend Snippet: Dockerin and cohesin domain sequence pairs were used as input to AlphaFold3 for 3D structure and interaction predictions. The resulting PDB files were input to FoldDock to calculate the pDockQ scores. Scores larger than 0.3 are shown. ( A ) Protein-protein interactions (PPIs) are predicted between cohesins (rows) and dockerins (columns) in GHs of C. perfringens ATCC 13124. “+” and “-“ indicate the presence and absence of experimentally characterized PPIs . ( B ) PPIs are predicted between cohesins in scaffoldins (rows) and dockerins in GHs (columns) of ET540. ( C ) A conceptual model is proposed illustrating the protein organization in the mucinolysome of ET540. ( D ) Predicted PPI interface between cSca1-Doc and cSca5-Coh. Hydrogen-bond contacts are shown as red dashed lines with corresponding distance < 3.5 Å between atoms. Sequences of cSca1-Doc and cSca5-Coh are shown beside the PPI interface structure with residues highlighted corresponding to residues in the hydrogen-bond contact interface. ( E ) Sequence alignment of cSca1-Doc against dockerin sequences in four ATCC 13124 proteins. Key residues involved in hydrogen-bonding (#) and van der Waals (*) contacts are indicated. Residues for cSca1-Doc are predicted, while residues for ATCC 13124 proteins were published previously . The two EF hand motifs are indicated. ( F ) Sequence alignment of cSca5-Coh against cohesin sequences in five published ATCC 13124 proteins .

    Article Snippet: CAZymes in five genomes Table S4: PPIs predicted for Coh-Doc pairs in C. perfringens ATCC 13124 Table S5: PPIs predicted for Coh-Doc pairs in Lpuc ET540/kol109 Table S6: Chemically defined media composition Table S7: Gene expression of all genes in ET540 Table S8: All MAGs searched in this study Table S9: SRA samples of 65 genomes Table S10: 2,897 fecal samples of different animal hosts

    Techniques: Sequencing, Protein-Protein interactions