ProRule: a new database containing functional and structural information on PROSITE profiles

Motivation: Increase the discriminatory power of PROSITE profiles to facilitate function determination and provide biologically relevant information about domains detected by profiles for the annotation of proteins. Summary: We have created a new database, ProRule, which contains additional information about PROSITE profiles. ProRule contains notably the position of structurally and/or functionally critical amino acids, as well as the condition they must fulfill to play their biological role. These supplementary data should help function determination and annotation of the UniProt Swiss-Prot knowledgebase. ProRule also contains information about the domain detected by the profile in the Swiss-Prot line format. Hence, ProRule can be used to make Swiss-Prot annotation more homogeneous and consistent. The format of ProRule can be extended to provide information about combination of domains. Availability: ProRule can be accessed through ScanProsite at http://www.expasy.org/tools/scanprosite. A file containing the rules will be made available under the PROSITE copyright conditions on our ftp site (ftp://www.expasy.org/databases/prosite/) by the next PROSITE release. Contact: [email protected]

Recent improvements to the PROSITE database

The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. The PROSITE web page has been redesigned and several tools have been implemented to help the user discover new conserved regions in their own proteins and to visualize domain arrangements. We also introduced the facility to search PDB with a PROSITE entry or a user's pattern and visualize matched positions on 3D structures. The latest version of PROSITE (release 18.17 of November 30, 2003) contains 1676 entries. The database is accessible at http://www.expasy.org/prosit

Synthesis of Fluorescent Azafluorenones and Derivatives via a Ruthenium-Catalyzed [2 + 2 + 2] Cycloaddition

International audienc

Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert

International audienceTwo gamma-and UV-radiation-tolerant, Gram-negative, rod-shaped bacterial strains, VCD115 T and VCD117, were isolated from a mixture of sand samples collected in the Sahara Desert in Morocco and Tunisia, after exposure of the sand to 15 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequences and DNA–DNA hybridizations showed that VCD115 T and VCD117 are members of a novel species belonging to the genus Deinococcus, with Deinococcus grandis as its closest relative. The DNA G+C contents of VCD115 T and VCD117 are 59?8 and 60?6 mol%, respectively. The major fatty acids (straight-chain 15 : 1, 16 : 1, 17 : 1 and 16 : 0), polar lipids (dominated by phosphoglycolipids and glycolipids) and quinone type (MK-8) support the affiliation to the genus Deinococcus. The strains did not grow on rich medium such as trypticase soy broth (TSB), but did grow as whitish colonies on tenfold-diluted TSB. The genotypic and phenotypic properties allowed differentiation of VCD115 T and VCD117 from recognized Deinococcus species. Strains VCD115 T and VCD117 are therefore identified as representing a novel species, for which the name Deinococcus deserti sp. nov. is proposed, with the type strain VCD115 T (=DSM 17065 T =LMG 22923 T)

Functionally and structurally relevant residues in PROSITE motif descriptors

PROSITE is an annotated collection of biologically meaningful motif descriptors dedicated to the identification of protein families and domains. Its current release 18.43 (January 4, 2004) contains 1311 documentation entries describing 1775 motif descriptors, which are either patterns or profiles (Hulo et al, 2004; Sigrist et al, 2002). Both are derived from multiple alignments of homologous sequences, giving them the notable advantage of identifying distant relationships between sequences that would have passed unnoticed based solely on pairwise sequence alignment. PROSITE is also a member database of InterPro (Mulder et al, 2003) and a main contributor to the InterPro annotation. More information on PROSITE is available at http://www.expasy.org/prosite

ProRule: a new database containing functional and structural information on PROSITE profiles

Increase the discriminatory power of PROSITE profiles to facilitate function determination and provide biologically relevant information about domains detected by profiles for the annotation of proteins

Recent improvements to the PROSITE database

The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. The PROSITE web page has been redesigned and several tools have been implemented to help the user discover new conserved regions in their own proteins and to visualize domain arrangements. We also introduced the facility to search PDB with a PROSITE entry or a user’s pattern and visualize matched positions on 3D structures. The latest version of PROSITE (release 18.17 of November 30, 2003) contains 1676 entries. The database is accessible at http://www.expasy.org/prosite/