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Table 4 Forty unique GH-like contig hits by BLAST analysis of secretome mass data against transcriptome assemblya

From: Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses

Contig name

Putative GH family

Gene length

RPKMb

value

Accession number

Enzyme annotation [species name]

Mass spot hits (a: first batch; b: second batch; c: third batch)

(number: band ID on SDS-PAGE)

Contig18827

GH13

891

105.6

EEQ33998.1

1,4-α-glucan branching enzyme [Microsporum canis]

b9

Contig148

GH13

819

19.8

XP_963252.2

1,4-α-glucan branching enzyme [Neurospora crassa]

b9

Contig1907

GH1

882

757.2

CAC34952.1c

β-glucosidase [Piromyces sp. E2]

a3, a10, b4, b5, b6, b8, b9, b12

Contig11849

GH3

2,064

29.0

ZP_04746179.1

β-glucosidase [Roseburia intestinalis]

b5

Contig4463

GH1

522

2,290.4

AAP30745.1c

β-glucosidase Cel1C [Piromyces sp. E2]

a11, b2, b4, b5, b10, b12

Contig16557

GH1

1,959

1,612.4

AAP30745.1c

β-glucosidase Cel1C [Piromyces sp. E2]

a3, a10, a11, b1, b2, b4, b5, b8, b9, b10, b12

Contig7663

GH1

1,959

1,096.6

AAP30745.1 c

β-glucosidase Cel1C [Piromyces sp. E2]

a3, a10, a11, b1, b2, b4, b5, b8, b9, b10, b12

Contig19120

GH1

1,548

166.5

AAP30745.1 c

β-glucosidase Cel1C [Piromyces sp. E2]

b1, b2, b5, b6

Contig8008

GH3

2,277

408.1

AAO41704.1 c

β-glucosidase precursor [Piromyces sp. E2]

b2, b3, b4, b5, b6, b8, b12

Contig2687

GH6

552

241.0

AAR08200.1

CelA [Neocallimastix frontalis]

a11

Contig6374

GH6

1,854

24.7

AAM94167.1 c

Cellulosomal exoglucanase Cel6A [Piromyces equi]

b5

Contig12342

GH43

1,653

664.5

ZP_06201238.1

Conserved hypothetical protein [Bacteroides sp. D20]

b12

Contig19148

GH10

519

7.8

YP_001181173.1

Endo-1,4-β-xylanase [Caldicellulosiruptor saccharolyticus]

b4

Contig1253

GH43

2,103

236.9

ACZ98594.1

Endo-1,4-β-xylanase [Cellulosilyticum ruminicola]

a11

Contig15284

GH11

1,137

341.8

ACL68347.1

Endo-1,4-β-xylanase [Neocallimastix patriciarum]

b5

Contig8371

GH11

2,412

158.3

ACL68347.1

Endo-1,4-β-xylanase [Neocallimastix patriciarum]

b3, b9

Contig19624

GH45

696

60.0

CAB92325.1 c

Endoglucanase 45A [Piromyces equi]

b3

Contig14117

GH11

1,017

159.8

CAA57820.1

Endoxylanase [Neocallimastix frontalis]

b9

Contig18110

GH11

879

32.3

CAA57820.1

Endoxylanase [Neocallimastix frontalis]

b9

Contig10964

GH18

687

82.7

YP_001643260.1

GH family protein [Bacillus weihenstephanensis]

b4, b8

Contig6246

GH31

1,932

232.1

XP_002438844.1

Hypothetical protein [Sorghum bicolor]

b2

Contig13446

GH31

3,237

301.4

XP_002109215.1

Hypothetical protein [Trichoplax adhaerens]

a4

Contig2828

GH4

948

9,936.5

CAA76361.1

Malate dehydrogenase [Piromyces sp. E2]

b8

Contig9297

GH10

993

984.7

AAB30669.1

Xylanase B; XYLB [Neocallimastix patriciarum]

b2, b3, b4, b5, b10

Contig13211

GH10

819

352.0

AAB30669.1

Xylanase B; XYLB [Neocallimastix patriciarum]

b2, b3, b5

Contig13165

GH10

990

205.1

AAB30669.1

Xylanase B; XYLB [Neocallimastix patriciarum]

b3, b5, b10

Contig8421

GH10

1,998

138.5

AAB30669.1

Xylanase B; XYLB [Neocallimastix patriciarum]

b9

Contig2430

GH10

1,098

132.9

AAB30669.1

Xylanase B; XYLB [Neocallimastix patriciarum]

b10, b12

Contig3792

GH10

927

5.1

AAB30669.1

Xylanase B; XYLB [Neocallimastix patriciarum]

a5

Contig11636

GH43

510

966.2

BAC75546.1

Xylosidase [Penicillium herquei]

a1, c11

Contig8146

GH1

1,986

2,290.4

AAD45834.1 c

β-glucosidase [Orpinomyces sp. PC-2]

b2, b12

Contig13432

GH1

723

33.0

AAD45834.1 c

β-glucosidase [Orpinomyces sp. PC-2]

a8, a10, b5, b6

Contig13654

GH48

2,271

6,167.8

AAN76734.1 c

Cellulase Cel48A precursor [Piromyces sp. E2]

a2, a3, a10, a11, b10, b12

Contig4845

GH48

2,286

362.2

AAN76734.1 c

Cellulase Cel48A precursor [Piromyces sp. E2]

b10

Contig6576

GH48

1,896

351.4

AAN76734.1 c

Cellulase Cel48A precursor [Piromyces sp. E2]

a11

Contig69

GH48

1,179

141.9

AAN76734.1 c

Cellulase Cel48A precursor [Piromyces sp. E2]

a2, a3, b12

Contig2523

GH48

1,596

86.8

AAN76735.1 c

Cellulase Cel48A precursor [Piromyces equi]

a2, a11, b12

Contig6878

GH9

1,032

285.9

AAM81967.1

Cellulase Cel9A precursor [Piromyces sp. E2]

b9

Contig8960

GH9

2,037

154.1

AAM81967.1

Cellulase Cel9A precursor [Piromyces sp. E2]

b9

Contig7007

GH11

1,131

479.8

Q12667

Endo-1,4-β-xylanase A

b2, b3, b4, b5

  1. aGH: glycosyl hydrolase; RPKM: Reads Per Kilobase of exon model per million mapped reads. bRPKM is a method for estimating relative expression levels of a transcriptome by normalizing short-read expressed tags from deep sequencing over ORF length and total reads (RPKM) [35]. cOnline protein sequences hits by using only ESI-Trap LC-MS/MS data against MASCOT online database.
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