The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total ∼58 000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein–protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/).

The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.

InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (), and for download by anonymous FTP (). The InterProScan search tool is now also available via a web service at .

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

Significance The isolation of an active formate hydrogenlyase is a breakthrough in understanding the molecular basis of bacterial hydrogen production. For over 100 years, Escherichia coli has been known to evolve H 2 when cultured under fermentative conditions. Glucose is metabolized to formate, which is then oxidized to CO 2 with the concomitant reduction of protons to H 2 by a single complex called formate hydrogenlyase, which had been genetically, but never biochemically, characterized. In this study, innovative molecular biology and electrochemical experiments reveal a hydrogenase enzyme with the unique ability to sustain H 2 production even under high partial pressures of H 2 . Harnessing bacterial H 2 production offers the prospect of a source of fully renewable H 2 energy, freed from any dependence on fossil fuel.

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A total of 30 Megasphaera elsdenii strains, selectively isolated from the feces of organically raised swine by using Me109 M medium, and one bovine strain were analyzed for tetracycline resistance genotypic and phenotypic traits. Tetracycline-resistant strains carried tet(O), tet(W), or a tet gene mosaic of tet(O) and tet(W). M. elsdenii strains carrying tet(OWO) genes exhibited the highest tetracycline MICs (128 to >256 g/ml), suggesting that tet(O)-tet(W) mosaic genes provide the selective advantage of greater tetracycline resistance for this species. Seven tet genotypes are now known for M. elsdenii, an archetype commensal anaerobe and model for tet gene evolution in the mammalian intestinal tract.Megasphaera elsdenii is a commensal (mutualist) species in the gastrointestinal tracts of ruminant and nonruminant mammals, including humans (7,25,26). This anaerobic bacterium contributes to the overall metabolism that takes place in those microbial ecosystems (2,5,13,15). M. elsdenii has been the focus of both prebiotic and probiotic applications for improving animal health (10,12,19,27).In a recent study of intestinal bacteria resistant to tetracycline, we detected resistant M. elsdenii strains at high population levels (approximately 10 7 CFU/g) in cecal samples from healthy swine (24). Eight strains were isolated and characterized. The M. elsdenii strains are highly resistant to chlortetracycline (MIC ϭ 256 to Ͼ256 g/ml) and carry one of two "tet(OWO)" genes for tetracycline resistance. [Throughout the manuscript, "tet(OW)" and "tet(OWO)" are used as convenient, practical terms for describing M. elsdenii recombinant tet genes and genotypes. As noted previously (24), these designations are not recognized under present tet classification guidelines (14). It is our hope that future guidelines will be developed to accommodate these novel interclass hybrid genes.] These tet genes are interclass mosaic genes apparently formed by doublecrossover recombinations between tet(O) and tet(W) genes.Our previous study used a nutritionally complex medium with high concentrations of chlortetracycline and, thus, was biased to select tetracycline-resistant M. elsdenii strains. In this study, Me109M medium was developed and used to select M. elsdenii strains without using chlortetracycline. The goals were twofold: first, to obtain tetracycline-sensitive strains of M. elsdenii useful both for investigating tet gene transfer and for probiotic applications, and second, to discover whether or not M. elsdenii strains have additional tet genotypes.Selective isolation of M. elsdenii-Me109M medium. On the basis of previous studies (4-6, 9, 14, 16, 17, 19-21) and preliminary experiments in our laboratory, Me109M medium was developed to selectively culture M. elsdenii. Me109M contained (per liter): tryptone-peptone, 4 g; yeast extract, 2 g; salts solution A (6 g of K 2 HPO 4 /liter of water), 40 ml; salts solution B [6 g of KH 2 PO 4 , 12 g of (NH 4 ) 2 SO 4 , 12 g of NaCl, 1.2 g of MgSO 4 -7H 2 O, 0.6 g of CaCl 2 /liter of water], 40 ml; ...