Dataset Information

PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families.

ABSTRACT: PROtein Domain Organization and Comparison (PRODOC) comprises several programs that enable convenient comparison of proteins as a sequence of domains. The in-built dataset currently consists of approximately 698 000 proteins from 192 organisms with complete genomic data, and all the SWISSPROT proteins obtained from the Pfam database. All the entries in PRODOC are represented as a sequence of functional domains, assigned using hidden Markov models, instead of as a sequence of amino acids. On average 69% of the proteins in the proteomes and 49% of the residues are covered by functional domain assignments. Software tools allow the user to query the dataset with a sequence of domains and identify proteins with the same or a jumbled or circularly permuted arrangement of domains. As it is proposed that proteins with jumbled or the same domain sequences have similar functions, this search tool is useful in assigning the overall function of a multi-domain protein. Unique features of PRODOC include the generation of alignments between multi-domain proteins on the basis of the sequence of domains and in-built information on distantly related domain families forming superfamilies. It is also possible using PRODOC to identify domain sharing and gene fusion events across organisms. An exhaustive genome-genome comparison tool in PRODOC also enables the detection of successive domain sharing and domain fusion events across two organisms. The tool permits the identification of gene clusters involved in similar biological processes in two closely related organisms. The URL for PRODOC is http://hodgkin.mbu.iisc.ernet.in/~prodoc.

SUBMITTER: Krishnadev O

PROVIDER: S-EPMC1160235 | biostudies-literature | 2005 Jul

REPOSITORIES: biostudies-literature

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PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families.

Krishnadev O O Rekha N N Pandit S B SB Abhiman S S Mohanty S S Swapna L S LS Gore S S Srinivasan N N

Nucleic acids research 20050701 Web Server issue

PROtein Domain Organization and Comparison (PRODOC) comprises several programs that enable convenient comparison of proteins as a sequence of domains. The in-built dataset currently consists of approximately 698 000 proteins from 192 organisms with complete genomic data, and all the SWISSPROT proteins obtained from the Pfam database. All the entries in PRODOC are represented as a sequence of functional domains, assigned using hidden Markov models, instead of as a sequence of amino acids. On aver ...[more]

PMID: 15980440

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Project description:BACKGROUND: Serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. While studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. Current analysis is aimed at understanding the distribution and probable biological functions of the select serine proteases encoded in representative prokaryotic organisms. RESULTS: A total of 966 putative serine proteases, belonging to five families, were identified in the 91 prokaryotic genomes using various sensitive sequence search techniques. Phylogenetic analysis reveals several species-specific clusters of serine proteases suggesting their possible involvement in organism-specific functions. Atypical phylogenetic associations suggest an important role for lateral gene transfer events in facilitating the widespread distribution of the serine proteases in the prokaryotes. Domain organisations of the gene products were analysed, employing sensitive sequence search methods, to infer their probable biological functions. Trypsin, subtilisin and Lon protease families account for a significant proportion of the multi-domain representatives, while the D-Ala-D-Ala carboxypeptidase and the Clp protease families are mostly single-domain polypeptides in prokaryotes. Regulatory domains for protein interaction, signalling, pathogenesis, cell adhesion etc. were found tethered to the serine protease domains. Some domain combinations (such as S1-PDZ; LON-AAA-S16 etc.) were found to be widespread in the prokaryotic lineages suggesting a critical role in prokaryotes. CONCLUSION: Domain architectures of many serine proteases and their homologues identified in prokaryotes are very different from those observed in eukaryotes, suggesting distinct roles for serine proteases in prokaryotes. Many domain combinations were found unique to specific prokaryotic species, suggesting functional specialisation in various cellular and physiological processes.

Project description:Mapping urban features/human built-settlement extents at the annual time step has a wide variety of applications in demography, public health, sustainable development, and many other fields. Recently, while more multitemporal urban features/human built-settlement datasets have become available, issues still exist in remotely-sensed imagery due to spatial and temporal coverage, adverse atmospheric conditions, and expenses involved in producing such datasets. Remotely-sensed annual time-series of urban/built-settlement extents therefore do not yet exist and cover more than specific local areas or city-based regions. Moreover, while a few high-resolution global datasets of urban/built-settlement extents exist for key years, the observed date often deviates many years from the assigned one. These challenges make it difficult to increase temporal coverage while maintaining high fidelity in the spatial resolution. Here we describe an interpolative and flexible modelling framework for producing annual built-settlement extents. We use a combined technique of random forest and spatio-temporal dasymetric modelling with open source subnational data to produce annual 100 m × 100 m resolution binary built-settlement datasets in four test countries located in varying environmental and developmental contexts for test periods of five-year gaps. We find that in the majority of years, across all study areas, the model correctly identified between 85 and 99% of pixels that transition to built-settlement. Additionally, with few exceptions, the model substantially out performed a model that gave every pixel equal chance of transitioning to built-settlement in each year. This modelling framework shows strong promise for filling gaps in cross-sectional urban features/built-settlement datasets derived from remotely-sensed imagery, provides a base upon which to create urban future/built-settlement extent projections, and enables further exploration of the relationships between urban/built-settlement area and population dynamics.

Dataset Information

PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families.

Publications

PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families.

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