Table 3

Predominant Pfam domains within the chromosome 12 predicted rice proteome. All non-TE related proteins were searched using the Hmmpfam program and Pfam domains above the trusted cutoff were parsed out. Only the top 20 Pfam domains are listed.

Pfam accession

Numbers of matched proteins

Pfam common name

PF00069

74

Protein kinase domain

PF00560

60

Leucine Rich Repeat

PF00646

51

F-box domain

PF00931

49

NB-ARC domain

PF00098

28

Zinc knuckle

PF01535

28

PPR repeat

PF03578

27

HGWP repeat

PF00097

25

Zinc finger, C3HC4 type (RING finger)

PF05699

22

hAT family dimerisation domain

PF00036

18

EF hand

PF00249

16

Myb-like DNA-binding domain

PF00067

14

Cytochrome P450

PF00076

13

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

PF00004

11

ATPase, AAA family

PF00010

11

Helix-loop-helix DNA-binding domain

PF00400

11

WD domain, G-beta repeat

PF02892

11

BED zinc finger

PF06654

11

Protein of unknown function (DUF1165)

PF07197

11

Protein of unknown function (DUF1409)

PF00023

10

Ankyrin repeat

The Rice Chromosomes 11 and 12 Sequencing Consortia* BMC Biology 2005 3:20   doi:10.1186/1741-7007-3-20