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novPTMenzy: a database for enzymes involved in novel post-translational modifications.

Khater S, Mohanty D - Database (Oxford) (2015)

Bottom Line: Unlike well-known PTMs like phosphorylation, glycosylation, SUMOylation, no bioinformatics resources are available for enzymes associated with novel and unusual PTMs. Therefore, we have developed the novPTMenzy database which catalogs information on the sequence, structure, active site and genomic neighborhood of experimentally characterized enzymes involved in five novel PTMs, namely AMPylation, Eliminylation, Sulfation, Hydroxylation and Deamidation.It also has a specialized analysis interface for some PTMs like AMPylation and Eliminylation.The novPTMenzy database is a unique resource that can aid in discovery of unusual PTM catalyzing enzymes in newly sequenced genomes.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Centre, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.

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Screenshots depicting typical analysis using search interface and comparative sequence analysis tools of novPTMenzy database. Panel 1: The Search interface used sequence to HMM profile alignment to identify AMPylation domain in query sequence and classified it as Fic type from among Fic, Doc, AvrB and AnkX subfamilies. It also depicts putative active site residues identified in the Fic type AMPylation domain, provides links to experimentally characterized homologs and also structural homologs. Panel 2: Structural homologs of the Fic domain in the query sequence. Panel 3: Alignment with the closest structural homolog obtained by clicking the button labeled ‘Str Ali’ in the structural homolog cell in Panel 1. Panel 4: Tree button in Panel 1 builds a phylogenetic tree of the PTM catalyzing domain in the query sequence along with seed sequences for the corresponding domain stored in novPTMenzy. It could be either visualized by clicking ‘view tree’ button or downloaded for further analysis. Panel 5: Identification of a Doc domain in a different query sequence using the search interface of novPTMenzy.
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bav039-F4: Screenshots depicting typical analysis using search interface and comparative sequence analysis tools of novPTMenzy database. Panel 1: The Search interface used sequence to HMM profile alignment to identify AMPylation domain in query sequence and classified it as Fic type from among Fic, Doc, AvrB and AnkX subfamilies. It also depicts putative active site residues identified in the Fic type AMPylation domain, provides links to experimentally characterized homologs and also structural homologs. Panel 2: Structural homologs of the Fic domain in the query sequence. Panel 3: Alignment with the closest structural homolog obtained by clicking the button labeled ‘Str Ali’ in the structural homolog cell in Panel 1. Panel 4: Tree button in Panel 1 builds a phylogenetic tree of the PTM catalyzing domain in the query sequence along with seed sequences for the corresponding domain stored in novPTMenzy. It could be either visualized by clicking ‘view tree’ button or downloaded for further analysis. Panel 5: Identification of a Doc domain in a different query sequence using the search interface of novPTMenzy.

Mentions: Given a query sequence (fasta formatted or bare sequence) or an accession number, the search interface of novPTMenzy matches it to profiles of different PTM catalyzing enzymes using HMMER (53) tool. Details of the hit are provided as a table and a color-coded alignment of the sequence with profile is displayed below it (panel 1 in Figure 4). Alignment colors vary from green to red based on the quality of alignment. It also annotates the putative active site residues in the query sequence by highlighting them in the alignment and also displaying them in tabular form (panel 2 in Figure 4). novPTMenzy also provides interfaces for alignment of the query protein sequence with other homologous sequences which have been experimentally characterized as well as with structural homologs present in PDB (panel 3 in Figure 4). A local version of the NCBI BLAST program is used to search for the closest neighbors in the sequence database of experimentally characterized enzymes and enzymes with 3D structures. The accession numbers of closest neighbors displayed in the table are linked back to our database for active site pocket visualization and more annotation. This interface also allows construction of phylogenetic tree and its visualization using a url-based link to the PhyloWidget (54) program (panel 4 in Figure 4). Seed sequences for each PTM catalyzing domains are stored in the novPTMenzy database and are used for construction of the phylogenetic tree using the ClustalW (55) program. Users have an option to download the phylogenetic tree for future offline analyses.Figure 4.


novPTMenzy: a database for enzymes involved in novel post-translational modifications.

Khater S, Mohanty D - Database (Oxford) (2015)

Screenshots depicting typical analysis using search interface and comparative sequence analysis tools of novPTMenzy database. Panel 1: The Search interface used sequence to HMM profile alignment to identify AMPylation domain in query sequence and classified it as Fic type from among Fic, Doc, AvrB and AnkX subfamilies. It also depicts putative active site residues identified in the Fic type AMPylation domain, provides links to experimentally characterized homologs and also structural homologs. Panel 2: Structural homologs of the Fic domain in the query sequence. Panel 3: Alignment with the closest structural homolog obtained by clicking the button labeled ‘Str Ali’ in the structural homolog cell in Panel 1. Panel 4: Tree button in Panel 1 builds a phylogenetic tree of the PTM catalyzing domain in the query sequence along with seed sequences for the corresponding domain stored in novPTMenzy. It could be either visualized by clicking ‘view tree’ button or downloaded for further analysis. Panel 5: Identification of a Doc domain in a different query sequence using the search interface of novPTMenzy.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414956&req=5

bav039-F4: Screenshots depicting typical analysis using search interface and comparative sequence analysis tools of novPTMenzy database. Panel 1: The Search interface used sequence to HMM profile alignment to identify AMPylation domain in query sequence and classified it as Fic type from among Fic, Doc, AvrB and AnkX subfamilies. It also depicts putative active site residues identified in the Fic type AMPylation domain, provides links to experimentally characterized homologs and also structural homologs. Panel 2: Structural homologs of the Fic domain in the query sequence. Panel 3: Alignment with the closest structural homolog obtained by clicking the button labeled ‘Str Ali’ in the structural homolog cell in Panel 1. Panel 4: Tree button in Panel 1 builds a phylogenetic tree of the PTM catalyzing domain in the query sequence along with seed sequences for the corresponding domain stored in novPTMenzy. It could be either visualized by clicking ‘view tree’ button or downloaded for further analysis. Panel 5: Identification of a Doc domain in a different query sequence using the search interface of novPTMenzy.
Mentions: Given a query sequence (fasta formatted or bare sequence) or an accession number, the search interface of novPTMenzy matches it to profiles of different PTM catalyzing enzymes using HMMER (53) tool. Details of the hit are provided as a table and a color-coded alignment of the sequence with profile is displayed below it (panel 1 in Figure 4). Alignment colors vary from green to red based on the quality of alignment. It also annotates the putative active site residues in the query sequence by highlighting them in the alignment and also displaying them in tabular form (panel 2 in Figure 4). novPTMenzy also provides interfaces for alignment of the query protein sequence with other homologous sequences which have been experimentally characterized as well as with structural homologs present in PDB (panel 3 in Figure 4). A local version of the NCBI BLAST program is used to search for the closest neighbors in the sequence database of experimentally characterized enzymes and enzymes with 3D structures. The accession numbers of closest neighbors displayed in the table are linked back to our database for active site pocket visualization and more annotation. This interface also allows construction of phylogenetic tree and its visualization using a url-based link to the PhyloWidget (54) program (panel 4 in Figure 4). Seed sequences for each PTM catalyzing domains are stored in the novPTMenzy database and are used for construction of the phylogenetic tree using the ClustalW (55) program. Users have an option to download the phylogenetic tree for future offline analyses.Figure 4.

Bottom Line: Unlike well-known PTMs like phosphorylation, glycosylation, SUMOylation, no bioinformatics resources are available for enzymes associated with novel and unusual PTMs. Therefore, we have developed the novPTMenzy database which catalogs information on the sequence, structure, active site and genomic neighborhood of experimentally characterized enzymes involved in five novel PTMs, namely AMPylation, Eliminylation, Sulfation, Hydroxylation and Deamidation.It also has a specialized analysis interface for some PTMs like AMPylation and Eliminylation.The novPTMenzy database is a unique resource that can aid in discovery of unusual PTM catalyzing enzymes in newly sequenced genomes.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Centre, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.

Show MeSH