Table 3

List of previously unknown genes that can be annotated using GPPP

E. coli gene name (Genbank id)

Previous annotation

Predicted function by GPPP

Additional evidences from BLAST/Pfam/COG

b1681 (1787971)

Hypothetical protein

Transport system, membrane protein

COG0719: predicted membrane components of ABC-transporter SufB

b1683 (1787973)

Hypothetical protein

Transport system, membrane protein

b2608 (1788960)

Hypothetical protein

RNA processing

Pfam domain: RimM. RimM is essential for processing of 16S rRNA.

b2766 (1789125)

Hypothetical protein

Flavorprotein, electron transport

COG0644:dehydrogenase/flavoprotein

b0407 (1786608)

Hypothetical protein

Protein secretion

Pfam domain: DUF219, (uncharacterized secreted protein)

b1395 (1787661)

Putative enzyme

Part of fad operon

BLAST: 3-hydroxyacyl-CoA dehydrogenase

b2341 (1788682)

Putative enzyme

Part of fad operon

BLAST: 3-hydroxyacyl-CoA dehydrogenase; enoyl-CoA isomerase/hydrotase

b0284 (1786478)

Hypothetical protein

Neighboring with xanthine dehydrogenase gene (b0286)

BLAST: Putative oxidoreductase

b2866 (1789230)

Hypothetical protein

Neighboring with xanthine dehydrogenase (b2868)

BLAST: Probable aldehyde oxidase and xanthine dehydrogenase family protein

b1674 (1787963)

Hypothetical protein

Oxidoreductase

BLAST: Aldehyde ferredoxin oxidoreductase

b2371 (1788714)

Hypothetical protein

Enzyme in carnitine metabolism

Pfam domain: CAIB-BAIF, domain involved in carnite metabolism

b2374 (1788717)

Hypothetical protein

Enzyme in carnitine metabolism

Pfam domain: CAIB-BAIF, domain involved in carnite metabolism

b2125 (2367130)

Hypothetical protein

Response regulator in 2-component system

Pfam domains: response-reg, REC probable cheY receiver domain

b0936 (1787167)

Hypothetical protein

Transport system

Pfam domain: PBPb, transport system related

b2075 (1788390)

Hypothetical protein

Integral transmembrane protein

Pfam: ACR_tran, SecD_SecF, Patched, transmembrane domain related

b2076 (1788391)

Hypothetical protein

Integral transmembrane protein

Pfam: ACR_tran

b1086 (1787327)

Hypothetical protein

RNA processing

BLAST: RNA pseudouridylate synthase

Zheng et al. Genome Biology 2002 3:research0060.1   doi:10.1186/gb-2002-3-11-research0060