Table 5. Top 30 PHX genes from genomes of α-proteobacteria

Gene

E

(g)

CAUCR

SINME

MESLO

AGRTU

BRUME

Ribosomal proteins

Ribosomal protein L1 (rplA)

1.92

1.42

1.77

1.78

1.75

Ribosomal protein L2 (rplB)

1.81

1.37

1.90

1.88

1.85

Ribosomal protein L4 (rplD)

1.75

1.44

1.31

1.48

1.45

Ribosomal protein L9 (rplI)

1.61

1.71

1.41

1.70

1.66

Ribosomal protein L11 (rplK)

1.46

1.75

1.46

1.48

1.72

Ribosomal protein L15 (rplO)

1.66

1.69

1.44

1.48

1.75

Ribosomal protein L17 (rplQ)

1.86

1.33

1.67

1.62

1.34

Ribosomal protein L19 (rplS)

1.83

1.48

1.42

1.75

1.48

Ribosomal protein L20 (rplT)

1.59

1.62

1.51

1.62

1.73

Ribosomal protein L25 (rplY or ctc)

1.76

1.60

1.30

1.68

1.18

Ribosomal protein S1 (rpsA)

2.06

1.81

1.58

2.27†

1.96

Ribosomal protein S2 (rpsB)

2.07

1.41

1.52

1.92

1.49

Ribosomal protein S3 (rpsC)

1.30

1.37

1.46

1.97

1.53

Ribosomal protein S4 (rpsD)

1.75

1.92

1.72

1.80

1.67

Ribosomal protein S5 (rpsE)

1.66

1.52

1.53

1.43

1.77

Ribosomal protein S6 (rpsF)

1.38

1.58

(1.02)

-

1.58

Ribosomal protein S7 (rpsG)

1.60

1.39

1.37

2.15

1.36

Ribosomal protein S9 (rpsI)

1.69

1.51

1.53

1.66

1.71

Ribosomal protein S12 (rpsL)

1.39

1.46

1.44

1.82

1.38

Ribosomal protein S16 (rpsP)

1.87

1.47

1.37

1.76

1.51

Ribosomal protein S18 (rpsR)

1.52

1.51

1.59

-

1.56

Translation and transcription processing factors

Translation elongation factor G (fus)

2.26

1.93

1.84

2.26

2.39

Translation elongation factor Tu (tuf)

1.64

1.64

1.59

1.59

1.50

1.43

1.64

1.61

1.73

1.68

Translation elongation factor EF-Ts (tsf)

1.90

1.44

1.31

1.62

1.77

GTP-binding protein TypA (typA)

1.51

1.27

1.79

1.71

1.53

Translation initiation factor 2 (infB)

1.40

1.39

1.67

1.67

2.02

RNA polymerase, β' subunit (

rpoC)

2.39

1.80

2.05

2.24

2.01

RNA polymerase, β subunit (

rpoB)

2.38

1.78

1.86

2.10

2.29

RNA polymerase, α subunit (

rpoA)

1.86

1.64

1.79

2.03

1.91

Chaperones and degradation

HSP60 (groEL)

1.78

1.67†

1.66

1.13†

(0.66)†

(0.60)

2.03†

1.96

1.87

1.73

1.51

2.07

1.81†

Chaperone (groES)

1.35

1.58†

1.50

1.29

1.26†

1.19

1.07

1.06

1.30

1.48†

HSP70 (dnaK)

1.41

1.62

1.69

1.76

2.09

Trigger factor (tig)

2.28

1.40

1.64

1.85

2.35

Endopeptidase Clp ATP-binding chain A (clpA)

1.03

(0.68)

1.78

(0.75)

(0.76)

Polyribonucleotide nucleotidyltransferase (pnp)

2.01

1.80

1.85

2.21

1.95

Energy metabolism - respiration

ATP synthase α

subunit (atpA)

1.67

1.67

1.66

2.08

1.94

ATP synthase β subunit (

atpD)

2.04

1.72

1.56

1.91

1.92

NADH-quinone oxidoreductase chain G (nuoG)

1.21

(0.81)

0.96)

(0.97)

1.82

Cytochrome c oxidase subunit I (ctaD)

1.66

1.43

1.79

1.37

1.56

Electron transfer flavoprotein, α subunit (

etfA)

1.85

1.23

1.21†

1.60

(0.85)†

1.17

Energy metabolism – TCA cycle

Dihydrolipoamide succinyltransferase component (E2) of 2-oxoglutarate dehydrogenase complex (sucB)

1.81

1.34

1.13

1.62

1.91

Succi

nyl-CoA synthetase, α subunit (sucD)

1.70

1.24

1.36

1.18

1.79

1.70

Energy metabolism - glycolysis

Glyceraldehyde 3-phosphate dehydrogenase (gap)

1.54

1.66

1.75

1.83†

1.90

Detoxification

Alkyl hydroperoxide reductase, subunit c (ahpC)

1.91

(0.99)†

(0.88)

(0.71)

1.45†

Superoxide dismutase (Mn, Fe) (sodB)

1.31

(0.66)

1.36

1.25

2.06

(0.75)†

(0.58)†

1.11

Amino acid and nucletide biosynthesis

Glutamine synthetase I

2.08

1.48

1.89

1.69

1.31

Glutamine synthetase II

-

1.27†

1.82

1.92

-

Ketol-acid reductoisomerase protein (ilvC)

1.43

1.54

1.63

1.79

1.40

Nucleoside diphosphate kinase (ndk)

1.91

1.54

1.40

1.54

1.48

Cell division

Cell division protein (ftsZ)

1.34

1.33

(0.88)

1.82

(0.99)

2.07

(0.55)†

2.04

Flagella

Flagellin (fla)

1.62

1.58

1.20

1.16

(0.74)

1.41

1.32

(0.95)

(0.79)

1.55

1.26

1.85

1.56

1.08

(0.70)

1.64†

Cell wall

Penicillin-binding protein (mrcA)

(0.48)

(0.60)†

(0.57)

1.75

(0.83)

(0.65)

Outer membrane proteins

Porin (BMEI1305, BMEI1306)

-

-

1.51

1.48

1.36

1.28

(0.87)‡

-

1.80

1.72

Outer membrane protein A2 (SMc02396, AGR_L_373)

-

1.53

1.25

-

1.91†

1.71

1.54

-

Outer membrane protein (ropB)

-

1.57

1.20

(0.83)

1.51

(0.76)

1.56

1.49†

1.44

1.33

1.16

1.14

Transport

Sugar-binding periplasmic receptor (chvE)

-

1.36†

1.58

2.14

1.13†

Secreted sugar-binding protein

-

(0.87)

1.79

-

1.25†

Glycerol-3-phosphate ABC transporter (ugpB)

-

(0.77)

1.66

2.03

(1.00)†

(0.89)†

1.34

Glycerol-3-phosphate ABC transporter

-

-

1.18

1.96

(0.96)

Sugar ABC transporter, maltose-binding component (mlr3050)

-

1.15

1.68

(0.76)

-

(1.07)†

Sugar ABC transporter, periplasmic sugar-binding protein (mll5706)

-

(0.95)

1.69

(0.80)†

-

Permease protein, sugar ABC transporter (mlr3338)

-

(0.84)

1.77

-

(0.65)

ABC transporter, dipeptide binding component (mll1660)

-

-

1.78

1.17

1.03

-

-

Periplasmic binding protein, Leu/Val/Ile-specific (livK)

-

1.37

1.68

1.85

1.14

Periplasmic phosphate binding protein (AGR_C_738)

1.18

1.45

-

1.92

1.64

Hypothetical protein (SMa0252), C4-dicarboxylate transport system (AGR_C_4976)

-

1.58†

(0.67)†

-

1.72

-

Ammonium transporter (amtB)

1.60

1.12

1.69

1.72

(0.68)

Rhizopine periplasmic transport protein (mocB)

-

(0.86)†

(0.74)†

1.77

(0.62)†

(0.59)†

-

ABC transporter, periplasmic binding protein (mll3069)

-

1.18

1.73

1.57

1.47†

Proton channel family protein (tolQ or exbB)

1.81

(1.00)

(0.85)

1.02

(0.86)†

(0.63)

(0.90)

(0.71)

Other

TonB-dependent receptor*

2.02

(0.87)

-

-

-

-

TonB-dependent receptor*

2.13

-

-

-

-

TonB-dependent receptor*

1.91

-

-

-

-

Acetyl-CoA synthase (acs)

(0.74)

(0.95)

1.81

(0.58)

(0.98)

Hypothetical protein (CC2257)

1.70

-

-

-

-

Included are all genes ranking among the top 30 PHX genes in any of the five genomes (underlined if among top 10) and their homologs in other genomes even if they are not among the top 30. Numbers in parentheses indicate the gene is not PHX; - indicates that the gene does not have a homolog in the genome.

*CAUCR contains 25 PHX genes annotated as TonB-dependent receptor or putative TonB-dependent receptor. However, the sequence similarity among these proteins is generally very low (<15%).

†

Gene located outside the largest chromosome.

‡

PA gene.