Table 2

Functional categories (putative functions) of proteins deduced from the obtained cDNAs (116 unigenes) after subtraction of waxy rice (GM077) with its wild-type (BP034)
Clone ID Number of clones Top-matched molecule in Genbank on Blastx (accession number) Top-matched molecule in Genbank on Blastx (species) Protein name and/or putative function e-Value COGs
INFORMATION STORAGE AND PROCESSING (13)
[J] Translation, ribosomal structure and biogenesis (3)
D06 1 P49608.1 Cucurbita maxima Aconitate hydratase, cytoplasmic 7.00E-52 KOG0452
C46 6 ACM79935.1 Populus deltoides Eukaryotic translation, initiation factor 5A 7.00E-14 KOG3271
2B05 1 NP_001148134.1 Zea mays Arginyl-tRNA synthetase 7.00E-62 KOG4426
[A] RNA processing and modification (NONE)
[K] Transcription (5)
B34 6 ACG28870.1 Zea mays Transcription factor BTF3 3.00E-40 KOG2240
E14 2 BAD08114.1 Oryza sativa Putative SET domain protein SDG117 1.00E-34 KOG1082
A62 8 NP_001054968.1 Oryza sativa RNA polymerase I-associated factor PAF67 1.00E-39 KOG3677
C11 1 NP_001060344.1 Oryza sativa Myb-related protein B (B-Myb) 7.00E-86 KOG0048
B30 1 EEE62186.1 Oryza sativa Hypothetical protein OsJ_16973 7.00E-50 KOG1878
A47 2 EEE62186.1 Oryza sativa Hypothetical protein OsJ_16973 1.00E-59 KOG1878
[L] Replication, recombination and repair (1)
C54 5 EEE66658.1 Oryza sativa Hypothetical protein OsJ_23285 3.00E-50 KOG4585
[B] Chromatin structure and dynamics (3)
C41 3 NP_569031.1 Arabidopsis thaliana Transducin family protein / WD-40 repeat family protein 1.00E-59 KOG1446
B86 2 NP_001047885.1 Oryza sativa Nuclear protein SET domain containing protein 7.00E-121 KOG1082
A76 1 CAL54140.1 Ostreococcus tauri Histones H3 and H4 (ISS) 3.00E-15 KOG1745
CELLULAR PROCESSES AND SIGNALING (21)
[D] Cell cycle control, cell division, chromosome partitioning (2)
D22 1 ABG65960.1 Oryza sativa PAP/25A associated domain containing protein, expressed (Nucleotidyltransferase domain) 7.00E-17 KOG2277
D27 1 AAY23369.1 Oryza sativa Retinoblastoma-related protein 2 4.00E-35 KOG1010
[Y] Nuclear structure (NONE)
[V] Defense mechanisms (NONE)
[T] Signal transduction mechanisms (3)
B00 2 NP_194324.2 Arabidopsis thaliana Epsin N-terminal homology (ENTH) domain-containing protein 1.00E-08 KOG0251
D66 1 NP_001056986.1 Oryza sativa Hypothetical protein(Two-component response regulator ARR14) 5.00E-35 COG0745
E43 31 NP_001148041.1 Zea mays CBL-interacting serine/threonine-protein kinase 15 1.00E-82 KOG0583
[M] Cell wall/membrane/envelope biogenesis (3)
F70 1 AAO72599.1 Oryza sativa Putative 2-dehydro-3-deoxyphosphooctonate aldolase 9.00E-66 COG2877
E73 1 AAT80327.1 Hordeum vulgare UDP-D-glucuronate decarboxylase 2.00E-36 KOG1429
A21 5 AAT80327.1 Hordeum vulgare UDP-D-glucuronate decarboxylase 3.00E-17 KOG1429
[N] Cell motility (NONE)
[Z] Cytoskeleton (2)
B38 6 NP_563908.1 Arabidopsis thaliana ARK3(ARMADILLO REPEAT KINESIN 3); ATP binding/ binding/microtubule motor 1.00E-18 KOG0240
C80 11 NP_171697.3 Arabidopsis thaliana Armadillo/ß-catenin repeat family protein/kinesin motor family protein 3.00E-86 KOG0240
[W] Extracellular structures (NONE)
[U] Intracellular trafficking, secretion, and vesicular transport (4)
F48 1 ABA95598.1 Oryza sativa Clathrin heavy chain, putative, expressed 5.00E-08 KOG0985
D80 1 ABF95668.1 Oryza sativa Serologically defined breastcancer antigen NY-BR-84, putative, expressed 2.00E-69 KOG2667
F23 1 ACG31280.1 Zea mays ADP-ribosylation factor 1 9.00E-18 KOG0070
E39 1 NP_001150650.1 Zea mays Serologically defined breast cancer antigen NY-BR-84 6.00E-32 KOG2667
[O] Posttranslational modification, protein turnover, chaperones (7)
B28 1 AAK51086.1 Avicennia marina Mitochondrial processing peptidase 2.00E-50 KOG0960
A32 1 BAB78487.1 Oryza sativa 26S proteasome regulatory particle non-ATPase subunit8 1.00E-21 KOG1556
C67 2 BAF00213.1 Arabidopsis thaliana Polyubiquitin 4 UBQ4 5.00E-31 KOG0001
B58 1 NP_001054802.1 Oryza sativa Zn-finger, RING domain containing protein 5.00E-57 KOG0800
04C04 1 ACG31834.1 Zea mays Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 7.00E-38 KOG3258
D56 3 NP_001147507.1 Zea mays ATP-dependent Clp protease ATP-binding subunit clpX 8.00E-08 KOG0745
D60 1 NP_001149461.1 Zea mays Pyrrolidone carboxyl peptidase 9.00E-44 KOG4755
METABOLISM (23)
[C] Energy production and conversion (5)
D01 10 AF162665_1 Oryza sativa Aldehyde dehydrogenase 5.00E-61 KOG2450
E05 3 BAB44155.1 Bruguiera, gymnorhiza Hydroxypyruvate reductase 8.00E-29 KOG0069
C01 1 NP_176968.1 Arabidopsis, thaliana HPR; glycerate dehydrogenase/poly(U) binding 2.00E-29 KOG0069
D14 25 ABB47885.1 Oryza sativa Electron transfer flavoprotein- ubiquinone oxidoreductase, mitochondrial precursor, putative, expressed 7.00E-95 KOG2415
D33 2 NP_001149476.1 Zea mays Vacuolar ATP synthase subunit F 2.00E-25 KOG3432
[G] Carbohydrate transport and metabolism (8)
F66 1 AAA82047.1 Oryza sativa Glyceraldehyde-3-phosphate dehydrogenase 2.00E-48 KOG0657
A15 1 AAO27794.1 Gossypium hirsutum Glycosyl hydrolase (sugar binding domain) 6.00E-30 KOG2230
E47 22 ABG22500.1 Oryza sativa Glycosyl hydrolases family 38 protein, expressed 5.00E-48 KOG1959
A64 1 ACG45298.1 Zea mays Nucleotide-sugar transporter/ sugar porter 2.00E-52 KOG2234
A74 1 ACJ86329.1 Oryza sativa ADP-glucose pyrophosphorylase small subunit 0.00E+00 COG0448
E73 1 AAT80327.1 Hordeum vulgare UDP-D-glucuronate decarboxylase 2.00E-36 KOG1429
A21 5 AAT80327.1 Hordeum vulgare UDP-D-glucuronate decarboxylase 3.00E-17 KOG1429
2B03 1 BAC75533.1 Oryza sativa Isoamylase 7.00E-66 GKOG0470
[E] Amino acid transport and metabolism (3)
E28 1 P37833.1 Oryza sativa Aspartate aminotransferase, cytoplasmic 4.00E-23 KOG1411
E42 5 ACG39804.1 Zea mays Histidinol-phosphate aminotransferase 2.00E-76 KOG0633
F16 1 NP_001147070.1 Zea mays Nicalin 4.00E-16 KOG2526
[F] Nucleotide transport and metabolism (NONE)
[H] Coenzyme transport and metabolism (1)
F89 1 ACG34051.1 Zea mays Farnesyl pyrophosphate synthetase 5.00E-07 KOG0711
[I] Lipid transport and metabolism (NONE)
[P] Inorganic ion transport and metabolism (2)
F76 1 AAP31024.1 Oryza sativa Zinc transporter 7.00E-31 KOG1482
04F04 1 NP_001149686.1 Zea mays Carbonic anhydrase 3.00E-13 KOG1578
[Q] Secondary metabolites biosynthesis, transport and catabolism (4)
D58 56 AAB19117.1 Oryza sativa Class III ADH enzyme 2.00E-98 KOG0022
A41 1 NP_176471.1 Arabidopsis thaliana LDL1 (LSD1-LIKE1); amine oxidase/ electron carrier/ oxidoreductase 1.00E-38 KOG0029
E72 9 ACM17649.1 Oryza rufipogon Alcohol dehydrogenase family-2 3.00E-25 KOG0022
C77 4 BAE00046.1 Oryza sativa Alcohol dehydrogenase 4.00E-140 KOG0022
POORLY CHARACTERIZED (9)
[R] General function prediction only (6)
C74 1 BAB69445.1 Oryza sativa Hypothetical protein 4.00E-19 KOG1901
A46 2 BAD82577.1 Oryza sativa PHD finger protein-like 8.00E-13 KOG1246
D20 1 BAD11341.1 Oryza sativa BRI1-KD interacting protein 113 (RNA recognition motif) 1.00E-51 KOG0118
F31 1 ABC94598.1 Oryza sativa NBS-LRR type R protein, Nbs2-Pi2 1.00E-80 KOG0619
C50 8 NP_001043287.1 Oryza sativa Zn-finger-like, PHD finger domain containing protein 4.00E-79 KOG1246
D53 1 EEE55043.1 Oryza sativa Hypothetical protein OsJ_02730 1.00E-114 KOG0431
D42 3 EEE55043.1 Oryza sativa Hypothetical protein 8.00E-93 KOG0431
[S] Function unknown (2)
F54 1 NP_568713.1 Arabidopsis thaliana Emb1879 (embryo defective 1879) 3.00E-47 KOG4249
C18 1 NP_001147117.1 Zea mays Nucleotide binding protein (WD40 domain) 8.00E-32 KOG0772
NO RELATED COG (3 BeTs) (26)
A44 11 BAD11344.1 Oryza sativa BRI1-KD interacting protein 116 3.00E-36 NO RELATED
C21 2 ACN85167.1 Oryza nivara MYB-CC type transfactor 5.00E-66
C27 1 ABA95230.1 Oryza sativa Retrotransposon protein, putative 9.00E-17
F81 1 Q01881.2 Oryza sativa Seed allergenic protein RA5 3.00E-08
F15 1 AAP54389.2 Oryza sativa Ulp1 protease family, C-terminal catalytic domain containing protein 7.00E-14
F32 1 NP_001052330.1 Oryza sativa Hypothetical protein 7.00E-10
A07 2 NP_001054936.1 Oryza sativa Hypothetical protein 1.00E-07
F39 1 NP_001058150.1 Oryza sativa Hypothetical protein 1.00E-41
A43 1 NP_001066171.1 Oryza sativa Conserved hypothetical protein 4.00E-07
E29 21 EAZ06308.1 Oryza sativa Hypothetical protein OsI_28542 8.00E-81
C62 3 ABR25963.1 Oryza sativa DnaJ heat shock protein 1.00E-12
C35 9 ACA04850.1 Picea abies Senescence-associated protein 8.00E-37
B45 1 EEC77808.1 Oryza sativa Hypothetical protein OsI_16996 5.00E-04
C48 1 EEC81525.1 Oryza sativa Hypothetical protein OsI_24919 1.00E-09
D54 2 EEE68920.1 Oryza sativa Hypothetical protein OsJ_27784 2.00E-100
D79 1 NP_001149805.1 Zea mays CUE domain containing protein 4.00E-06
D25 1 NP_001060116.1 Oryza sativa WRKY transcription factor 34 2.00E-72
04C03 2 BAH91806.1 Oryza sativa Conserved hypothetical protein 1.00E-04
2B02 1 EAZ06308.1 Oryza sativa Hypothetical protein OsI_28542 5.00E-54
E36 2 CAA59142.1 Oryza sativa Prolamin 4.00E-31
B11 10 AAK13589.1 Oryza sativa rRNA intron-encoded homing endonuclease 4.00E-27
C25 1 CAA38212.1 Oryza sativa Glutelin 7.00E-49
A55 1 AAM92796.1 Oryza sativa Gypothetical protein 8.00E-37
B53 2 NP_001055525.1 Oryza sativa Ubiquitin-associated domain containing protein 9.00E-54
F77 1 EEE63701.1 Oryza sativa Hypothetical protein OsJ_18519 (Ubiquitin Associated domain) 4.00E-65
D23 1 BAD38184.1 Oryza sativa C2 domain-containing protein-like 3.00E-86
NO SIMILARITY FOUND (BLAST) (26)

Zhang et al.

Zhang et al. BMC Plant Biology 2012 12:230   doi:10.1186/1471-2229-12-230

Open Data