Table 2

The top 100 highly expressed coding ORFs predicted by RPKM values

3dNH41

Locus tag

RPKM2

3dN2

Locus tag

RPKM

5dNH4

Locus tag

RPKM


heat shock protein Hsp20

Francci3_1179

10755

heat shock protein Hsp20

Francci3_1179

3553

hypothetical protein

Francci3_1017

4967

aldehyde dehydrogenase

Francci3_2944

7165

aldehyde dehydrogenase

Francci3_2944

3152

heat shock protein Hsp20

Francci3_1179

2077

chaperonin GroEL

Francci3_4398

5923

hypothetical protein

Francci3_1545

2327

hypothetical protein

Francci3_3999

1926

    cold-shock DNA-binding

    Francci3_0260

    5495

transposase IS66

Francci3_1864

2261

transposase IS66

Francci3_1864

1801

    OsmC-like protein

    Francci3_4465

    5490

    hypothetical protein

    Francci3_2178

    1993

polysaccharide deacetylase

Francci3_0165

1616

    co-chaperonin GroES

    Francci3_0632

    5362

response regulator receiver

Francci3_0120

1823

hypothetical protein

Francci3_2101

1596

    Hemerythrin HHE cation

    Francci3_1066

    4392

    Hemerythrin HHE cation

    Francci3_1066

    1807

phage integrase

Francci3_4274

1451

hypothetical protein

Francci3_1545

4225

    hypothetical protein

    Francci3_1936

    1789

Radical SAM

Francci3_1753

1392

    NAD/NADP transhydrogenase

    Francci3_2947

    3226

    OsmC-like protein

    Francci3_4465

    1777

hypothetical protein

Francci3_2241

1333

UspA

Francci3_2760

3221

hypothetical protein

Francci3_3999

1614

hypothetical protein

Francci3_2890

1265

    hypothetical protein

    Francci3_3494

    3190

    cold-shock DNA-binding

    Francci3_0260

    1592

phosphoribosyl-ATPphosphatase

Francci3_4317

1245

    hypothetical protein

    Francci3_2178

    3071

    sigma 54 modulation

    Francci3_0764

    1574

hypothetical protein

Francci3_0159

1184

    sigma 54 modulation protein

    Francci3_0764

    3004

    cold-shock DNA-binding

    Francci3_4469

    1458

ribonucleaseHII

Francci3_3588

1161

    cold-shock DNA-binding

    Francci3_4469

    2949

    putative DNA-binding

    Francci3_1949

    1392

GDP-mannose 4,6-dehydratase

Francci3_1307

1134

    Alcohol dehydrogenase

    Francci3_2945

    2916

    LuxR family regulator

    Francci3_0765

    1361

hypothetical protein

Francci3_4023

1122

    putative Lsr2-like protein

    Francci3_3498

    2659

chaperoninGroEL

Francci3_4398

1199

major facilitator superfamily

Francci3_2289

1122

    hypothetical protein

    Francci3_1936

    2577

hypothetical protein

Francci3_4123

1176

RNA-directed DNA polymerase

Francci3_2318

1088

    hypothetical protein

    Francci3_2270

    2529

    hypothetical protein

    Francci3_3494

    1175

methionine-S-oxide reductase

Francci3_2268

1071

    thioredoxin-related

    Francci3_0447

    2355

    hypothetical protein

    Francci3_2269

    1174

HypA

Francci3_1937

1047

SsgA

Francci3_3418

2154

    transcriptional regulator

    Francci3_4255

    1167

acyltransferase 3

Francci3_2337

987

luciferase-like

Francci3_2761

2117

    co-chaperoninGroES

    Francci3_0632

    1150

hypothetical protein

Francci3_3302

982

    molecular chaperone DnaK

    Francci3_4352

    2036

hypothetical protein

Francci3_2442

1117

Serine acetyltransferase-like

Francci3_3842

970

    globin

    Francci3_2581

    1935

SsgA

Francci3_3418

1043

hypothetical protein

Francci3_0227

970

    LuxR family regulator

    Francci3_0765

    1934

    SecE subunit

    Francci3_0567

    1037

hypothetical protein

Francci3_1719

965

thioredoxin reductase

Francci3_4536

1913

    putative Lsr2-like protein

    Francci3_3498

    1022

hypothetical protein

Francci3_0238

957

Rhodanese-like

Francci3_0449

1881

    PEP phosphomutase

    Francci3_1533

    1005

hypothetical protein

Francci3_2200

947

    carbonic anhydrase

    Francci3_0708

    1859

    hypothetical protein

    Francci3_2270

    973

hypothetical protein

Francci3_1831

945

superfamily MFS_1

Francci3_2752

1811

chaperone hypC/hupF

Francci3_1946

954

serine/threonine kinase

Francci3_4051

938

hypothetical protein

Francci3_3250

1807

transposase, IS4

Francci3_3990

953

signal transduction kinase

Francci3_0085

938

    exodeoxyribonuclease III

    Francci3_1180

    1754

    thioredoxin-related

    Francci3_0447

    951

hypothetical protein

Francci3_4019

922

    PEP phosphomutase

    Francci3_1533

    1742

    ATP synthase F0

    Francci3_3713

    928

hypothetical protein

Francci3_0396

914

    STAS (anti-σ factor antagonist)

    Francci3_0441

    1728

mannose 4,6-dehydratase

Francci3_1053

921

CRISPR-associated protein

Francci3_0021

899

    hypothetical protein

    Francci3_1935

    1687

phage integrase

Francci3_4338

919

hypothetical protein

Francci3_0038

899

sigma 38

Francci3_3505

1673

protein of unknown function

Francci3_3347

892

Recombinase

Francci3_3989

898

hypothetical protein

Francci3_0227

1665

transposase, IS4

Francci3_0391

878

aldo/keto reductase

Francci3_3416

890

hypothetical protein

Francci3_1615

1634

major facilitator MFS_1

Francci3_2752

865

transposase, IS4

Francci3_1873

875

    hypothetical protein

    Francci3_2943

    1629

    NAD/NADP transhydrogenase

    Francci3_2947

    863

Excisionase/Xis, DNA-binding

Francci3_0405

875

    hypothetical protein

    Francci3_0054

    1629

hypothetical protein

Francci3_4084

855

transposase, IS4

Francci3_0151

874

transposase IS66

Francci3_1864

1625

hypothetical protein

Francci3_2380

839

CRISPR-associated protein

Francci3_0020

869

    transcriptional regulator, CarD

    Francci3_4255

    1596

hypothetical protein

Francci3_4114

821

CRISPR-associated protein

Francci3_3345

863

alanine dehydrogenase/PNT-like

Francci3_2946

1532

    Alcohol dehydrogenase

    Francci3_2945

    796

glycosyl transferase

Francci3_3318

859

    serine phosphatase

    Francci3_3249

    1453

    hypothetical protein

    Francci3_3791

    782

metallophosphoesterase

Francci3_1990

839

chaperonin GroEL

Francci3_0633

1439

    acyl-CoA dehydrogenase

    Francci3_1000

    781

hypothetical protein

Francci3_3339

837

    hypothetical protein

    Francci3_0949

    1437

transcriptional regulator

Francci3_3081

780

transcriptional regulator

Francci3_3081

834

    transcription factor WhiB

    Francci3_3759

    1430

hypothetical protein

Francci3_0037

779

hypothetical protein

Francci3_3317

826

fatty acid desaturase, type 2

Francci3_0307

1430

Amino acid adenylation

Francci3_2461

777

hypothetical protein

Francci3_4072

824

STAS

Francci3_4302

1405

hypothetical protein

Francci3_1615

775

transcriptional regulator

Francci3_0908

816

Heavy metal transportprotein

Francci3_0489

1368

hypothetical protein

Francci3_2179

775

hypothetical protein

Francci3_4129

809

sigma-24

Francci3_3768

1353

    hypothetical protein

    Francci3_1534

    773

transposase, IS4

Francci3_4227

803

transcriptional regulator, TetR

Francci3_2758

1349

hypothetical protein

Francci3_2329

767

Antibiotic biosynthesis

Francci3_0875

800

    hypothetical protein

    Francci3_3417

    1343

    carbonic anhydrase

    Francci3_0708

    764

hypothetical protein

Francci3_3336

796

    SecE subunit

    Francci3_0567

    1339

    transcription factor WhiB

    Francci3_3759

    751

hypothetical protein

Francci3_2440

781

Excisionase/Xis, DNA-binding

Francci3_0099

1327

UspA

Francci3_2760

747

hypothetical protein

Francci3_4509

778

    hypothetical protein

    Francci3_3791

    1315

    exodeoxyribonuclease III

    Francci3_1180

    747

putative copper resistance

Francci3_2497

771

    ATP synthase F0, A subunit

    Francci3_3713

    1263

hypothetical protein

Francci3_1832

737

transcriptional regulator

Francci3_0210

765

30S ribosomal proteinS1

Francci3_1057

1256

    protein of unknown function

    Francci3_2628

    714

hypothetical protein

Francci3_1090

764

heat shock protein Hsp20

Francci3_2174

1241

hypothetical protein

Francci3_4509

714

hypothetical protein

Francci3_4156

760

NAD(P) transhydrogenase, beta

Francci3_2948

1231

hypothetical protein

Francci3_1650

709

RNA-binding S4

Francci3_3479

747

    putative transcriptional regulator

    Francci3_1674

    1218

    STAS

    Francci3_0441

    701

hypothetical protein

Francci3_1545

746

protein of unknown function

Francci3_0450

1215

    molecularchaperoneDnaK

    Francci3_4352

    694

hypothetical protein

Francci3_3238

746

    Alcohol dehydrogenase

    Francci3_1544

    1206

hypothetical protein

Francci3_0159

693

hypothetical protein

Francci3_3301

737

    putative DNA-binding protein

    Francci3_1949

    1203

    acyl transferase region

    Francci3_0991

    691

hypothetical protein

Francci3_1985

724

glutaredoxin 2

Francci3_0483

1202

regulatory protein GntR

Francci3_3218

690

    Rhodanese-like

    Francci3_2753

    721

translation elongation factor Tu

Francci3_0580

1179

CRISPR-associated protein

Francci3_3346

680

Thiolase

Francci3_2502

718

    thioredoxin

    Francci3_4537

    1165

hypothetical protein

Francci3_1874

678

response regulator receiver

Francci3_0120

715

cytochrome P450

Francci3_4464

1164

    hypothetical protein

    Francci3_1935

    672

hypothetical protein

Francci3_0498

705

hypothetical protein

Francci3_2582

1156

IS630 family transposase

Francci3_1872

670

DNApolymeraseIIIsubunitalpha

Francci3_4168

703

    hypothetical protein

    Francci3_1534

    1106

    globin

    Francci3_2581

    663

hypothetical protein

Francci3_0037

693

    protein of unknown function

    Francci3_1406

    1054

hypothetical protein

Francci3_4127

657

hypothetical protein

Francci3_3241

684

Vesicle-fusing ATPase

Francci3_2630

1041

    thioredoxin

    Francci3_4537

    653

30SribosomalproteinS6

Francci3_4522

683

HesB/YadR/YfhF

Francci3_3121

1032

hypothetical protein

Francci3_0066

644

putative hydrolase

Francci3_2567

682

hypothetical protein

Francci3_0532

1022

    Alcohol dehydrogenase

    Francci3_1544

    644

transposase IS116/IS110

Francci3_2124

681

    acyl transferase region

    Francci3_0991

    1015

hypothetical protein

Francci3_2440

642

hypothetical protein

Francci3_1807

675

Superoxide dismutase

Francci3_2817

1013

Tetratricopeptide TPR_4

Francci3_1951

639

hypothetical protein

Francci3_1805

675

hypothetical protein

Francci3_2185

1007

hypothetical protein

Francci3_0227

635

hypothetical protein

Francci3_2364

675

hypothetical protein

Francci3_4343

1006

hypothetical protein

Francci3_2315

634

hypothetical protein

Francci3_2380

671

    serine/threonine kinase

    Francci3_4051

    989

hypothetical protein

Francci3_4019

633

response regulator receiver

Francci3_4048

670

    acyl-CoA dehydrogenase

    Francci3_1000

    989

    hypothetical protein

    Francci3_0949

    633

putative O-methyltransferase

Francci3_0204

670

conserved hypothetical protein

Francci3_0096

986

    serine phosphatase

    Francci3_3249

    632

channel protein

Francci3_3898

669

hypothetical protein

Francci3_3886

983

Amino acid adenylation

Francci3_2459

632

hypothetical protein

Francci3_2032

667

    Rhodanese-like

    Francci3_2753

    982

transposase IS116/IS110

Francci3_2124

630

hypothetical protein

Francci3_1459

664

hypothetical protein

Francci3_4042

973

    hypothetical protein

    Francci3_3417

    628

flavoprotein

Francci3_1816

662

hypothetical protein

Francci3_3999

971

Antibiotic biosynthesis

Francci3_0875

626

hypothetical protein

Francci3_0160

660

    protein of unknown function

    Francci3_2628

    958

    protein of unknown function

    Francci3_1406

    621

AMP-dependent synthetase

Francci3_1806

659

    LuxR family regulator

    Francci3_3253

    958

hypothetical protein

Francci3_3247

621

serine/threonine protein kinase

Francci3_3395

659

50SribosomalproteinL24

Francci3_0593

944

    hypothetical protein

    Francci3_2943

    620

hypothetical protein

Francci3_4161

655

ribosomal protein S2

Francci3_3581

936

transcription factor WhiB

Francci3_3790

618

hypC/hupF

Francci3_1946

655

hypothetical protein

Francci3_2736

934

hypothetical protein

Francci3_3997

618

hypothetical protein

Francci3_0494

655

    hypothetical protein

    Francci3_2269

    932

transcriptional regulator

Francci3_4158

614

transcriptional regulator

Francci3_0985

654

hypothetical protein

Francci3_2809

929

hypothetical protein

Francci3_2184

610

Excisionase/Xis, DNA-binding

Francci3_1856

653

acyl-CoA dehydrogenase-like

Francci3_0053

915

    hypothetical protein

    Francci3_0054

    608

phosphohydrolase

Francci3_1134

648

Antibiotic biosynthesis

Francci3_0875

911

CRISPR-associated protein

Francci3_0023

608

SsgA

Francci3_3418

646

2-oxoacid oxidoreductase

Francci3_3248

906

Recombinase

Francci3_2373

607

major facilitator MFS_1

Francci3_2752

643

translationinitiationfactorIF-1

Francci3_0605

904

CRISPR-associated protein

Francci3_3345

606

Inorganic diphosphatase

Francci3_4310

636

electron transfer flavoprotein

Francci3_3659

889

hypothetical protein

Francci3_2219

606

hypothetical protein

Francci3_1032

636

hypothetical protein

Francci3_4326

884

hypothetical protein

Francci3_3299

605

DNA-directed RNA polymerase

Francci3_3194

635

50SribosomalproteinL33

Francci3_0563

880

    LuxR family regulator

    Francci3_3253

    604

chaperoninGroEL

Francci3_4398

635

hypothetical protein

Francci3_3625

856

hypothetical protein

Francci3_2101

604

UspA

Francci3_2760

633

Cytochrome-c oxidase

Francci3_2009

855

    transcriptional regulator

    Francci3_1674

    600

Aldehyde dehydrogenase

Francci3_2944

632

GrpE protein

Francci3_4353

846

transcriptional regulator

Francci3_0908

596

hypothetical protein

Francci3_1014

631


1 Gene annotations and locus tag numbers are colored based on their presence in all three samples (bold), in the 3dN2 and 5dNH4 samples (italic), in the 3dN2 and 3dNH4 samples (underscore), in the 3dNH4 and 5dNH4 samples (italic/underscore), and in one of the three samples (normal font).

2 RPKM (Reads per Kilobase Million) = (# reads per ORF)/(size of ORF in kilobases × millions of reads in the dataset).

Bickhart and Benson BMC Microbiology 2011 11:192   doi:10.1186/1471-2180-11-192

Open Data