Swiss-Prot/TrEMBL, KEGG, and COG groups. tRNAs were annotated using tRNAscan-SE (v1.23). rRNAs were annotated using a combination of BLASTN and an rRNA-specific database. The srpRNA was located using the SRPscan website. The rnpB and tmRNA were located using the Rfam database and Infernal. Riboswitches and other noncoding RNAs predicted in the G. sulfurreducens genome [GenBank:NC00293] were retrieved from the Rfam database [123] and used
to annotate the corresponding sequences in G. metallireducens. Operon organization was predicted using the commercial version of the FGENESB software (V. Solovyev and A. Salamov, unpublished; Softberry, Inc; 2003–2007), with sequence Liproxstatin-1 parameters estimated separately from the G. sulfurreducens and G. metallireducens genomes. Default parameters were used in operon prediction, including minimum ORF length of 100 bp. Binding sites of the global regulator ModE (consensus ATCGCTATATANNNNNNTATATAACGAT) were predicted using ScanACE software [41, 42] using the algorithm of Berg and von Hippel [124] and the footprinted matrix of E. coli ModE-regulated sites from the Regulon DB database v 4.0 [125]. Functional annotations of transport
proteins were evaluated by referring to TCDB http://www.tcdb.org, and PORES http://garlic.mefos.hr/pores was used to
annotate porins. Transposase families were assigned ISGme numbers for inclusion in the ISFinder database http://www-is.biotoul.fr. PF-573228 Manual curation The automated genome annotation of G. metallireducens was queried with the protein BLAST algorithm [126] using all predicted proteins in the automated annotation of the G. sulfurreducens genome [12] to identify conserved genes that aligned over their full lengths. The coordinates of numerous genes in both genomes were adjusted according to the criteria of full-length alignment, plausible ribosome-binding sites, and minimal overlap between genes on opposite DNA strands. The annotations of Thiamet G all other genes in G. metallireducens were checked by BLAST searches of NR. Discrepancies in functional annotation of conserved genes between the two genomes were also resolved by BLAST of NR and of the Swiss-Prot database. All hypothetical proteins were checked for similarity to previously identified domains, conservation among other Geobacteraceae, and absence from species other than Geobacteraceae. Genes that had no protein-level homologs in NR were checked (together with flanking intergenic sequences) by translated nucleotide BLAST in all six reading frames, and by nucleotide BLAST to ensure that conserved protein-coding or nucleotide features had not been missed.