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• W2123953670 abstract "Assignment of all transcription factors (TFs) from genome sequence data is not a straightforward task due to the wide variation in TFs among different species. A DNA binding domain (DBD) and a contiguous non-DBD with a characteristic SCOP or Pfam domain combination are observed in most members of TF families. We found that most of the experimentally verified TFs in prokaryotes are detectable by a combination of SCOP or Pfam domains assigned to DBDs and non-DBDs. Based on this finding, we set up rules to detect TFs and classify them into 52 TF families. Application of the rules to 154 entirely sequenced prokaryotic genomes detected >18 000 TFs classified into families, which have been made publicly available from the ‘GTOP_TF’ database. Despite the rough proportionality of the number of TFs per genome with genome size, species with reduced genomes, i.e. obligatory parasites and symbionts, have only a few if any TFs, reflecting a nearly complete loss. Also the number of TFs is significantly lower in archaea than in bacteria. In addition, all but 1 of the 19 TF families present in archaea is present in bacteria, whereas 33 TF families are found exclusively in bacteria. This observation indicates that a number of new TF families have evolved in bacteria, making the transcription regulatory system more divergent in bacteria than in archaea." @default.
• W2123953670 created "2016-06-24" @default.
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• W2123953670 date "2006-01-09" @default.
• W2123953670 modified "2023-10-06" @default.
• W2123953670 title "Genome-Wide Survey of Transcription Factors in Prokaryotes Reveals Many Bacteria-Specific Families Not Found in Archaea" @default.
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• W2123953670 doi "https://doi.org/10.1093/dnares/dsi016" @default.
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