Supplementary Table S3- List of putative conserved domains in unknown/hypothetical proteins homologues of Rice.

Contig no / Protein Name / Domain / Pfam no / Description /
Taz11 / Os06g0231300 / CS / pfam04969 / The CS and CHORD (pfam04968) are fused into a single polypeptide chain in metazoans but are found in separate proteins in plants
Taz19 / Os03g0266300 / HSP20 / cd00298 / Family of small stress induced proteins ranging from 12 -43 kDa, whose common feature is the alpha-crystallin domain. They are generally active as large oligomers consisting of multiple subunits.
Taz62 / Os05g0125500 / Acyl-CoA_dh_N / cd01156 / Isovaleryl-CoA dehydrogenase (IVD) is an is an acyl-CoA dehydrogenase, which catalyzes the third step in leucine catabolism, the conversion of isovaleryl-CoA
Taz86 / Os03g0646100 / Tubulin domain / cd02201 / FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin.
PRK09330 / cell division protein FtsZ
Taz125 / Os01g0748900 / MACPF domain / pfam01823 / The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death.
Taz161 / Os02g0133100 / SEC14 domain / cd00170 / Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1)
Taz179 / Os08g0154600 / TOPEUc domain / cd00659 / Topo_IB_C; DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA.
COG3569 / Topoisomerase IB [DNA replication, recombination, and repair]
smart00435
/ TOPEUc; DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras
cd03489 / Topoisomer_IB_N_LdtopoI_like; Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni.
Tau03 / Osi_012607 / RING and Transmembrane Domain / E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Tau09 / Os03g0277300 / HSP70 / pfam00012 / Hsp70 assisted folding involves repeated cycles of substrate binding and release.
Tau64 / Os10g0387000 / CTP_transf_2 domain / cd02173 / catalyzes the conversion of phosphoethanolamine to CDP-ethanolamine as part of the CDP#ethanolamine biosynthesis pathway.
cd02174 / Catalyzes the condensation of CTP and phosphocholine to form CDP-choline as the rate-limiting and regulatory step in the CDP-choline pathway.
Tau80 / Os09g0133600 / PAP_fibrillin / pfam04755 / This family identifies a conserved region found in a number of plastid lipid-associated proteins (PAPs), and in a number of putative fibrillin proteins.
Tau88 / Os06g0643100 / Proteasome / cd03759 / The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus
Tau89 / Os03g0731900 / BRLZ / PRK01045 / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Tau92 / AT5G52360 / ADF / cd00013 / present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
Tau111 / Os09g0133600 / SNARE_assoc / pfam09335 / This is a family of SNARE associated Golgi proteins. The yeast member of this family localises with the t-SNARE Tlg2.
Tau192 / OsI_028494 / Aha1_N /

PF09229

/ Members of this family, which are predominantly found in the protein 'Activator of Hsp90 ATPase' adopt a secondary structure consisting of an N-terminal alpha-helix leading into a four-stranded meandering antiparallel beta-sheet, followed by a C-terminal alpha-helix. The two helices are packed together, with the beta-sheet curving around them. They bind to the molecular chaperone HSP82 and stimulate its ATPase activity
Tax22 / Os05g0498400 / SUI1 / cd00474 / This describes a heat shock chaperonin-binding motif found in the stress-inducible phosphoprotein STI1. Both N- and C-termini of STI1 are capable of binding heat shock proteins and the domain is found .
Tax56 / OsI_010824 / DnaJ / The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues.
Tax90 / OsJ_005462 / AAA / AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Tax104 / OsI_010106 / Inos-1-P_synth /

PF01658

/ Inositol-1-phosphate catalyses the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated to inositol
Tax105 / Os10g0462900 / Cpn60_TCP1 / cd03344 / GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits.
PRK12850 / chaperonin GroEL
Tax111 / Os07g0222300 / PINT / pfam01399
/ This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
pfam09440 / eIF3 subunit 6 N terminal domain. This is the N terminal domain of subunit 6 translation initiation factor eIF3.
Tax112 / Os01g0328700 / DAO / PRK06115 / dihydrolipoamide dehydrogenase
pfam00070 / Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
pfam02852 / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases.
Tax113 / Os12g0116000 / PA andEGF_like / cd02125 / Domain-containing plant vacuolar sorting receptor (VSR). This group includes various PA domain-containing VSRs such as garden pea BP-80, pumpkin PV72, and various Arabidopsis VSRs including AtVSR1.
Tax121 / Os03g0804300 / zf-DHHC / COG5273 / Uncharacterized protein containing DHHC-type Zn finger
pfam01529 / DHHC zinc finger domain. This domain is also known as NEW1. This domain is predicted to be a zinc binding domain.
Tax122 / Os08g0562700 / Peptidase_M1 / pfam01433 / Peptidase family M1. Members of this family are aminopeptidases. The members differ widely in specificity, hydrolysing acidic, basic or neutral N-terminal residues.
Tax133 / OsI_000858 / Lipase_GDSL /

PF00657

/ A variety of lipolytic enzymes with serine as part of the active site have been identified
Tax145 / Os07g0655400 / DUF1751 / pfam08551 / Eukaryotic integral membrane protein (DUF1751). This domain is found in eukaryotic integral membrane proteins. An uncharacterized Saccharomyces cerervisiae protein, YOL107W, has been shown to localise COP II vesicles.
Tax146 / OsJ_030021 / ZnF_C2HC / Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule.
RVT_1 and /

PF00078

/ A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses
Tax148 / Os02g0773200 / Usp / cd00293
/ Small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents.
Tax207 / Os03g0262300 / AT_hook / PRK04195 / eplication factor C large subunit
Tax211 / Os03g0345200 / Ribosomal_S21e / pfam01249
/ Ribosomal protein S21e.
Tax230 / Os05g0498700 / DCD / DCD is a plant specific domain in proteins involved in development and programmed cell death
Tax263 / Os02g0644100 / STI1and TBR / cd00189 / found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, pl
smart00727 / Heat shock chaperonin-binding motif
Tax264 / Os01g0502400 / P4Hc / smart00702
/ Mammalian enzymes catalyse hydroxylation of collagen, for example. Prokaryotic enzymes might catalyse hydroxylation of antibiotic peptides.
Taw37 / Os01g0600000 / ATP-synt_G / pfam04718 / Mitochondrial ATP synthase g subunit. The Fo sector of the ATP synthase is a membrane bound complex which mediates proton transport.
Taw66 / Os03g0131300 / UBQ,STI1and UBA / cd00194 / Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases.
cd01809 / Scythe_N; Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus.
Taw74 / OsI_008543 / Mito_carr /

PF00153

/ uch proteins include: ADP,ATP carrier protein (ADP/ATP translocase); 2-oxoglutarate/malate carrier protein; phosphate carrier protein; tricarboxylate transport protein (or citrate transport protein); Graves disease carrier protein; yeast mitochondrial proteins MRS3 and MRS4; yeast mitochondrial FAD carrier protein; and many others.
Taw128 / Os03g0822200 / 3Beta_HSD / pfam01073
/ 3-beta hydroxysteroid dehydrogenase/isomerase family.
pfam01370
/ NAD dependent epimerase/dehydratase family. This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions.
Taw146 / Os12g0405700 / Wound_ind / pfam08186
/ Wound-inducible basic protein family. This family consists of the wound-inducible basic proteins from plants. The metabolic activities of plants are dramatically altered upon mechanical injury or pathogen attack.
Taw182 / Os03g0712400 / STYKc / cd00180 / Serine/Threonine protein kinases, catalytic domain.Phosphotransferases of the serine or threonine-specific kinase subfamily.
Taw191 / Os01g0679700 / Ribosomal_L37ae / pfam01780
/ Ribosomal L37ae protein family. This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc.
Taw 204 / Os07g0180900 / Ribosomal_L4 / PRK04042 / 50S ribosomal protein L4P
Taw207 / Os11g0629200 / Vps26 domain / pfam03643 / Vacuolar protein sorting-associated protein 26. Vacuolar protein sorting-associated protein (Vps) 26 is one of around 50 proteins involved in protein trafficking.
Taw214 / Os02g0491400 / FKBP_C and TPR / cd00189
/ Tetratricopeptide repeat domain; typically contains 34 amino
pfam00254 / FKBP_C; FKBP-type peptidyl-prolyl cis-trans isomerase.
Taw215 / Os06g0247500 / PFK domain / cd00765
/ Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate.
Taw216 / Os05g0149600 / CULLIN / COG5647 / Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
pfam00888
/ Cullin family
Taw222 / OsJ_030609 / DUF608 /

PF04685

/ This family represents a conserved region with a pankaryotic distribution in a number of uncharacterised proteins
Taw226 / OsJ_031062 / STI1and UBA / This describes a heat shock chaperonin-binding motif found in the stress-inducible phosphoprotein STI1. Both N- and C-termini of STI1 are capable of binding heat shock proteins and the domain is found both singly and duplicated in other proteins.
UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair
Taw248 / Os07g0631900 / RRM / smart00360
/ RNA recognition motif