Table 4

The σ factors of Rlv3841

Gene and name (if known)a

GC3s, quartopb

Closest homologsc


Species

Gene

BLAST e value


RL0422 (RpoN, used for N assimilation)

0.791 Y

S. meliloti

SMc01139

0.0

A. tumefaciens

AGR_C_581

0.0

M. loti

mll3196

2E-161

Brucella suis

BR0158

3E-156

RL0788

0.732 N

Pseudomonas fluorescens

Pflu02001224

9E-56

Erwinia carotovora

ECA2017

E-43

Burkholderia ambifaria

BambDRAFT_3017

9E-30

S. meliloti

SMa01432

2E-27

A.tumefaciens

AGR_C_2739

2E-16

M.loti

mlr77732

E-16

RL1138

0.714 N

Ralstonia eutropha

Reut_B3794

E-47

Bradyrhizobium japonicum

bll6484

2E-44

Silicibacter pomeroyi

SPO31254

E-29

M. loti

mlr7773

7E-29

A. tumefaciens

AGR_C_2739

2E-28

S. meliloti

SMc01419

9E-23

RL3020

0.749 Y

A. tumefaciens

AGR_C_4121

6E-56

B. suis

BRA0021

2E-32

Burkholderia fungorum

Bcep02004893

7E-32

Caulobacter crescentus

CC3253

2E-30

M. loti

mll3493

4E-25

S. meliloti

SMb20531

2E-18

RL3235

0.777 N

S. meliloti

SMc01419

E-48

A. tumefaciens

AGR_C_3679p

9E-44

Sphingopyxis alaskensis

SalaDRAFT_1954

5E-23

B. japonicum

bll2628

6E-23

M. loti

mlr04075

E-18

RL3402 (RpoD, 'housekeeping' σ)

0.823 Y

A. tumefaciens

AGR_C_3929p

0.0

S. meliloti

SMc01563

0.0

B. suis

BR1479

0.0

M. loti

mll2466

0.0

RL3509

0.758 N

S. meliloti

SMc02713

2E-38

S. alaskensis

SalaDRAFT_1954

4E-18

Burkholderia cepacia

Bcepa03005434

5E-18

Novosphingobium aromaticivorans

DSM 12444

2E-17

A. tumefaciens

AGR_C_3679

E-14

M. loti

mlr7773

5E-12

RL3703 (RpoZ)

0.790 Y

S. meliloti

SMc01506

5E-84

B. suis

BR1658

3E-80

Bartonella henselae

BH13830

5E-73

A. tumefaciens

AGR_L_1386p

5E-68

M. loti

mll3697

7E-68

RL3766 (RpoH, heat shock σ)

0.794 Y

A. tumefaciens

AGR_C_4439p

2E-155

S. meliloti

SMc00646

3E-148

M. loti

mlr3741

5E-138

B. suis

BR1650

E-133

RL4524

0.780 N

M. loti

mlr8088

5E-38

Rhodospirillum rubrum

Rrub02003750

3E-37

Rhodobacter sphaeroides

'rpoE'

3E-34

Magnetospirillum magnetotacticum

Magn03011107

E-33

S. meliloti

None listed in top 50 matches

A. tumefaciens

None listed in top 50 matches

RL4614 (RpoH2, heat shock σ)

0.771 N

S. meliloti

SMc03873

5E-118

M. loti

mlr3862

2E-98

B. suis

BR1763

5E-97

B. henselae

BH15210

3E-95

A. tumefaciens

AGR_C_4439pd

7E-58

pRL10385

0.720 N

M. loti

mll1224

2E-52

Microbulbifer degradans

Mdeg02003584

E-28

R. sphaeroides

Rsph03003515

E-27

Solibacter usitatus

AcidDRAFT_4778

6E-22

S. meliloti

None listed in top 50 matches

A. tumefaciens

None listed in top 50 matches

pRL11007 (EcfR)

0.778 N

M. loti

mlr0407

4E-57

R. sphaeroides

Rsph03002607

E-45

M. magnetotacticum

Magn03006880

8E-39

Bordetella parapertussis

BPP1584

4E-37

A. tumefaciens

AGR_L_1386p

3E-24

S. meliloti

SMa0143

2E-22

pRL110418

0.794 N

B. japonicum

blr7812

2E-83

Streptomyces avermitilis

SAV7424

7E-74

Nocardia farcina

nfa4970

3E-73

Frankia sp.

Francci3DRAFT_3517

7E-66

M. loti

mll6869

8E-33

S. meliloti

None listed in top 50 matches

A. tumefaciens

None listed in top 50 matches

pRL120319 (RpoI, iron uptake sigma)

0.640 N

Azotobacter vinelandii

AvinDRAFT_4065

4E-20

Pseudomonas aeruginosa

'pvdS'e

3E-18

S. meliloti

SMc04203

8E-09

A. tumefaciens

AGR_pAT_442

2E-08

pRL120580

0.587 N

Rhodopseudomonas palustris

RPA0550

4E-40

R. rubrum

Rrub02003750

8E-38

M. magnetotacticum

Magn03011107

5E-37

Pseudomonas syringae

PSPTO1043

3E-28

M. loti

mlr8088

4E-26

A. tumefaciens

AGR_C_3605

6E-14

S. meliloti

None listed in top 50 matches


aRhizobium leguminosarum biovar viciae 3841 (Rlv3841) locus tags are shown and, if the gene has been named in R. leguminosarum, this name is shown. bGC3s (G+C content of silent third positions of codons), member of quartop (yes [Y]/no [N]). cEach of the Rlv3841 sigma factors was used in BLASTP searches (maximum of 50 matches). The sequences and the locus tag numbers, together with the 'e' values, are shown for the top four matches. In those genera (Brucella, Pseudomonas, Streptomyces, Burkholderia) with more than one sequenced species, only one example is shown for each genus. In those cases in which one or more of the species used in the quartop analysis is not in the top four matches, these are also included. dA. tumefaciens has only one rpoH gene (AGR_C_4439p) whereas R. leguminosarum, M. loti, and S. meliloti have two. AGR_C_4439p is more closely related to Rlv3841 RpoH1 (RL3766) than to Rlv3841 RpoH2 (RL4614). eAlso known as PfrI in P. putida, and PbrA in P. fluorescens.

Young et al. Genome Biology 2006 7:R34   doi:10.1186/gb-2006-7-4-r34

Open Data