Table 4 Set of 100 COGs lost by obligate intracellular bacteria

COG2264

J

Ribosomal protein L11 methylase

COG1188

J

Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog)

COG2265

J

SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase

COG1595*

K

DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog

COG1508

K

DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog

COG1522

K

Transcriptional regulators

COG1167

KE

Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs

COG1974*

KT

SOS-response transcriptional repressors (RecA-mediated autopeptidases)

COG1643

L

HrpA-like helicases

COG0277*

C

FAD/FMN-containing dehydrogenases

COG0247*

C

Fe-S oxidoreductase

COG2225*

C

Malate synthase

COG1902

C

NADH:flavin oxidoreductases, Old Yellow Enzyme family

COG0778*

C

Nitroreductase

COG2352*

C

Phosphoenolpyruvate carboxylase

COG1600

C

Uncharacterized Fe-S protein

COG1062*

C

Zn-dependent alcohol dehydrogenases, class III

COG0239

D

Integral membrane protein possibly involved in chromosome condensation

COG0683

E

ABC-type branched-chain amino acid transport systems, periplasmic component

COG1176

E

ABC-type spermidine/putrescine transport system, permease component I

COG1177

E

ABC-type spermidine/putrescine transport system, permease component II

COG2049*

E

Allophanate hydrolase subunit 1

COG1984*

E

Allophanate hydrolase subunit 2

COG2303*

E

Choline dehydrogenase and related flavoproteins

COG0014*

E

Gamma-glutamyl phosphate reductase

COG0405

E

Gamma-glutamyltransferase

COG0263*

E

Glutamate 5-kinase

COG0665

E

Glycine/D-amino acid oxidases (deaminating)

COG0346*

E

Lactoylglutathione lyase and related lyases

COG2755*

E

Lysophospholipase L1 and related esterases

COG1410*

E

Methionine synthase I, cobalamin-binding domain

COG0347

E

Nitrogen regulatory protein PII

COG1280

E

Putative threonine efflux protein

COG2008

E

Threonine aldolase

COG1762

GT

Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type)

COG0315

H

Molybdenum cofactor biosynthesis enzyme

COG2896

H

Molybdenum cofactor biosynthesis enzyme

COG0303*

H

Molybdopterin biosynthesis enzyme

COG0521*

H

Molybdopterin biosynthesis enzymes

COG0314

H

Molybdopterin converting factor, large subunit

COG1977

H

Molybdopterin converting factor, small subunit

COG0746

H

Molybdopterin-guanine dinucleotide biosynthesis protein A

COG2267*

I

Lysophospholipase

COG0318

IQ

Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II

COG2230*

M

Cyclopropane fatty acid synthase and related methyltransferases

COG1596

M

Periplasmic protein involved in polysaccharide export

COG0810

M

Periplasmic protein TonB, links inner and outer membranes

COG1247

M

Sortase and related acyltransferases

COG2148

M

Sugar transferases involved in lipopolysaccharide synthesis

COG3206

M

Uncharacterized protein involved in exopolysaccharide biosynthesis

COG1580

N

Flagellar basal body-associated protein

COG1291

N

Flagellar motor component

COG1344

N

Flagellin and related hook-associated proteins

COG0643

NT

Chemotaxis protein histidine kinase and related kinases

COG2201

NT

Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain

COG0835

NT

Chemotaxis signal transduction protein

COG0840

NT

Methyl-accepting chemotaxis protein

COG1352

NT

Methylase of chemotaxis methyl-accepting proteins

COG0229

O

Conserved domain frequently associated with peptide methionine sulfoxide reductase

COG4235

O

Cytochrome c biogenesis factor

COG1281

O

Disulfide bond chaperones of the HSP33 family

COG0386

O

Glutathione peroxidase

COG2360

O

Leu/Phe-tRNA-protein transferase

COG0652*

O

Peptidyl-prolyl cis-trans isomerase (rotamase) – cyclophilin family

COG1764

O

Predicted redox protein, regulator of disulfide bond formation

COG2518

O

Protein-L-isoaspartate carboxylmethyltransferase

COG3118*

O

Thioredoxin domain-containing protein

COG2844

O

UTP:GlnB (protein PII) uridylyltransferase

COG1391*

OT

Glutamine synthetase adenylyltransferase

COG0725

P

ABC-type molybdate transport system, periplasmic component

COG0600

P

ABC-type nitrate/sulfonate/bicarbonate transport system, permease component

COG0004

P

Ammonia permease

COG1393*

P

Arsenate reductase and related proteins, glutaredoxin family

COG0704*

P

Phosphate uptake regulator

COG0855*

P

Polyphosphate kinase

COG2897*

P

Rhodanese-related sulfurtransferase

COG0659*

P

Sulfate permease and related transporters (MFS superfamily)

COG0179*

Q

2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)

COG3127

Q

Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component

COG0664*

T

cAMP-binding proteins – catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases

COG5001*

T

Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain

COG0394

T

Protein-tyrosine-phosphatase

COG3852

T

Signal transduction histidine kinase, nitrogen specific

COG1253

R

Hemolysins and related proteins containing CBS domains

COG0714*

R

MoxR-like ATPases

COG1741

R

Pirin-related protein

COG0388*

R

Predicted amidohydrolase

COG2081

R

Predicted flavoproteins

COG1694

R

Predicted pyrophosphatase

COG1611*

R

Predicted Rossmann fold nucleotide-binding protein

COG0523

R

Putative GTPases (G3E family)

COG2334

R

Putative homoserine kinase type II (protein kinase fold)

COG1540*

R

Uncharacterized proteins, homologs of lactam utilization protein B

COG0397

S

Uncharacterized conserved protein

COG1576

S

Uncharacterized conserved protein

COG2127*

S

Uncharacterized conserved protein

COG2606*

S

Uncharacterized conserved protein

COG2983

S

Uncharacterized conserved protein

COG1671

S

Uncharacterized protein conserved in bacteria

COG3024

S

Uncharacterized protein conserved in bacteria