Table 2

Genes with highest GEI

Locus

Gene namea

EGD-e locusb

Description

10403S Average GEIc


LMRG_04519

ssrA

NL

transfer-messenger RNA (tmRNA)

8566.2

LMRG_04503

ssrS

NL

6S RNA

7921.4

Noncoding

lhrA

NL

Hfq-binding RNA

4532.3

Noncoding

sbrE

NL

putative ncRNA

2359.9

LMRG_01574d

lmo2257

lmo2257

hypothetical CDS

2066.3

LMRG_02041

fri

lmo0943

non-heme iron-binding ferritin

1572.6

LMRG_04515

NGN

NL

bacterial signal recognition particle RNA

1462.2

LMRG_02926e

NGN

NL

-

1407

LMRG_00994

lmo1847

lmo1847

similar to adhesion binding proteins and lipoproteins with multiple specificity for metal cations (ABC transporter)

1378.9

LMRG_00378

flaA

lmo0690

flagellin protein

1366.9

LMRG_04523

rnpB

NL

bacterial RNAse P class B

1243.8

LMRG_01165

cspB

lmo2016

similar to major cold-shock protein

1109.5

Noncoding

NGN

NL

T-box leader

1086.7

LMRG_00891

sod

lmo1439

superoxide dismutase

845.4

LMRG_00996

lmo1849

lmo1849

similar to metal cations ABC transporter, ATP-binding proteins

827.4

LMRG_01986

lmo2711

lmo2711

similar to hypothetical proteins

802.1

LMRG_00921

lmo1468

lmo1468

similar to unknown proteins

738.5

LMRG_02618

lmo0196

lmo0196

similar to B. subtilis SpoVG protein

702.9

LMRG_00814

cspL

lmo1364

similar to cold shock protein

679.4

LMRG_01081

hup

lmo1934

similar to non-specific DNA-binding protein HU

631.8

LMRG_00995

lmo1848

lmo1848

similar metal cations ABC transporter (permease protein)

621.2

LMRG_00922

rpsU

lmo1469

30S ribosomal protein S21

609

LMRG_02619

lmo0197

lmo0197

similar to B. subtilis SpoVG protein

577.3

Noncoding

NGN

NL

putative ncRNA

561.9

LMRG_00679

trxA

lmo1233

thioredoxin

516.5

LMRG_01674

lmo2158

lmo2158

similar to B. subtilis YwmG protein

509.2

LMRG_02633

ctc

lmo0211

similar to B. subtilis general stress protein

496.4

LMRG_01479

lmo2363

lmo2363

similar to glutamate decarboxylase

491

LMRG_00517

pdhD

lmo1055

highly similar to dihydrolipoamide dehydrogenase, E3 subunit of pyruvate dehydrogenase complex

483.5

LMRG_00703

lmo1254

lmo1254

similar to alpha,alpha-phosphotrehalase

395.9

LMRG_02718

lmo2373

lmo2373

similar to phosphotransferase system beta-glucoside-specific enzyme IIB component

378.5

LMRG_01737

lmo2511

lmo2511

similar to B. subtilis YvyD protein

377.1

LMRG_00515

pdhB

lmo1053

highly similar to pyruvate dehydrogenase (E1 beta subunit)

356.4

LMRG_00704

lmo1255

lmo1255

similar to PTS system trehalose-specific enzyme IIBC

353.6

LMRG_00516

pdhC

lmo1054

highly similar to pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit)

351.3

LMRG_01480

lmo2362

lmo2362

similar to amino acid antiporter (acid resistance)

351.1

LMRG_02239

lmo2692

lmo2692

unknown

344.1

LMRG_00875

lmo1423

lmo1423

unknown

341.2

LMRG_01835

lmo2413

lmo2413

similar to aminotransferase

333.1

LMRG_01429

lmo1541

lmo1541

similar to unknown protein

318.8


aNGN = No gene name given;

bNL = No EGDe locus;

cAverage normalized number of reads matching each of the σB-dependent genes in the two 10403S datasets divided by the length of the genes times 100 bp;

dThe high coverage of LMRG_01574 is restricted to the portion that overlaps with lhrA. LMRG_01574 may not be a valid coding gene;

eLMRG_02926 completely overlaps with the bacterial RNAse P class B noncoding gene. LMRG_02926 may not be a valid coding gene as no Pfam matches were found for the putative protein coded by this gene.

Oliver et al. BMC Genomics 2009 10:641   doi:10.1186/1471-2164-10-641

Open Data