Table 2 MIPS functional catalog category classification of all the genes specifically down-regulated in the pkaA deletion strain

01 Metabolism

 01.01 amino acid metabolism

 01.01.03 assim. ammonia, metab. glutamate group

 01.01.03.05 metabolism of arginine

 01.01.03.05.01 biosynthesis of arginine

 01.01.05 metab. urea cycle, creatine and polyamines

 01.01.06.01 metabolism of aspartate

 01.01.06.01.02 degradation of aspartate

 01.01.06.04 metabolism of threonine

 01.01.06.04.01 biosynthesis of threonine

 01.01.06.05 metabolism of methionine

 01.01.06.05.01 biosynthesis of methionine

 01.01.06.05.01.01 biosynthesis of homocysteine

 01.01.09 metabolism of the cysteine - aromatic group

 01.01.11.01 metabolism of alanine

 01.01.11.02 metabolism of isoleucine

 01.01.11.02.01 biosynthesis of isoleucine

 01.01.11.02.02 degradation of isoleucine

 01.01.11.03 metabolism of valine

 01.01.11.03.01 biosynthesis of valine

 01.01.11.03.02 degradation of valine

 01.03.01 purin nucleot/nucleoside/nucleobase metab.

 01.03.07 deoxyribonucleotide metabolism

 01.03.16 polynucleotide degradation

 01.03.16.01 RNA degradation

 01.05.13 transfer of activated C-1 groups

 01.05.13.03 tetrahydrofolate-dependent C-1-transfer

 01.06.06 isoprenoid metabolism

 01.06.06.11 tetracyclic and pentacyclic triterpenes (cholesterin, steroids and hopanoids) metabolism

 01.07 metab. vitamins, cofactors, and prosthetic groups

 01.07.01 biosyn. vitam, cofactors, prosthetic groups

 01.20.19 metabolism of secondary products derived from glycine, l-serine and l-alanine

 01.20.19.01 metabolism of porphyrins

02 Energy

 02.07.01 pentose-phosphate pathway oxidative branch

 02.08 pyruvate dehydrogenase complex

 02.10 (citrate cycle, Krebs cycle, TCA cycle)

 02.13 respiration

 02.13.01 anaerobic respiration

 02.13.03 aerobic respiration

10 Cell cycle and DNA processing

 10.01.03 DNA synthesis and replication

 10.01.03.03 ori recognition, priming complex formation

11 Transcription

 11.02.01 rRNA synthesis

 11.04.01 rRNA processing

 11.04.03 mRNA processing (splicing, 5^-, 3^-end)

 11.04.03.01 splicing

 11.06.01 rRNA modification

12 Protein synthesis

 12.01 ribosome biogenesis

 12.01.01 ribosomal proteins

 12.04 translation

 12.04.02 translation elongation

 12.04.03 translation termination

 12.07 translational control

 12.10 aminoacyl-tRNA-synthetases

14 Protein fate (folding, modification, destination)

 14.01 protein folding and stabilization

 14.04 protein targeting, sorting and translocation

 14.10 assembly of protein complexes

16 Protein binding function or cofactor required (structural or catalytic)

 16.03.01 DNA binding

 16.07 structural protein binding

 16.19.05 GTP binding

 16.21 complex cofactor/cosubstrate/vitamin binding

 16.21.05 FAD/FMN binding

 16.21.17 pyridoxal phosphate binding

20 Cel. transp., transp. facilities and transp. routes

 20.01.01.01.01 heavy metal ion transport (Cu + , Fe3 +)

 20.01.03.03 C4-transport (malate, succinate, fumarate)

 20.01.21 RNA transport

 20.09.01 nuclear transport

 20.09.04 mitochondrial transport

 20.09.16.05 Type V protein secretion system

42 Biogenesis of cellular components

 42.10.05 nuclear membrane

 42.10.07 nucleolus

 42.16 mitochondrion