Table 1

Numbers of domains detected by SMART in the yeast genome, and in the yeast and human fractions of the Swiss Prot database

DomainFull name or functionNumber of domains annotated
Yeast genome SwissProt: S. cerevisiaeSwissProt: Homo sapiens
SMARTSMARTSPaPfambSMARTSPaPfamb
14-3-314-3-3 proteins2222666
ADFActin depolymerization factor4323422
ARFArf subfamily of small GTPases5443121212
ArfGapGAP for Arf-like GTPases65020
ARMArmadillo repeat1414141402113
B41Band 4.1 homology0000999
BTKBTK-like zinc finger00040
C1PKC conserved region 12222383230
C2PKC conserved region 218141110211917
CARDCaspase recruitment domain000090
CBSCystathionine β-synthase-like domain17170230
CHCalponin homology6442352618
CNHCitron homology32000
cNMPCyclic nucleotide monophosphate-binding domain4423121214
CYCcAdenylyl/guanylyl cyclase1110151515
DAGKaDAG kinase (accessory)00060
DAGKcDAG kinase (catalytic)20066
DAXIn Dsh and axin00010
DEATHRegulator of cell death0001410
DEPIn Dsh. egl-10 and pleckstrin55020
DYNcDynamin3333444
EFhEF-hand242417712412462
FCHFes/CIP4 homology domain44030
FHAForkhead associated domain14989111
FYVEIn Fab1, YOTB, Vac1, and EEA165210
GAFIn cGMP-PDEs, adenylyl cyclases, and E. coli fh1A00040
HECTcHomologous to E6-AP carboxyl terminus; ubiquitin ligases54344
HR1PRK kinase homology region 122000
IPPcInositol polyphosphate phosphatase4222222
IQCalmodulin-binding motif663102
KIScKinesin, catalytic domain6666666
LIMZinc finger in Lin-11, Is1-1, Mec-39753505030
MYScMyosin, catalytic domain5555666
OPROcticosapeptide repeat11040
PACMotif, C-terminal to PAS00030
PASDomain in Per, ARNT, Sim11066
PBDp21 Rho-binding domain33032
PDZIn PSD-95, D1g, ZO-10003115
PHPleckstrin homology domain27191213363027
PI3K_PI3KbPI3K: p85-binding domain000020
PI3K_rbdP13K: Ras-binding domain000030
P13KaP13K accessory domain22040
P13KcPhosphoinositide kinase8887555
PLAcPhospholipase A2, catalytic domain44411
PLCXcPhospholipase C, domain X1111555
PLCYcPhospholipase C, domain Y1111555
PLDcPhospholipase D, conserved motif22022
PP2AcProtein phosphatases 2A12121212101010
PP2CcProtein phosphatases 2C7652222
Protein kinasesTyrKc: Tyr-specific0007069
 S_TKc: Ser/Thr-specific6158586262
 STYKc: Ser/Thr/Tyr-specific564946104(all)5149184(all)
Protein phosphatasesPTPc: Tyr-specific3333353435
 DSPc: Dual-specific55577
 PTPc_DSPc: Tyr-,/Ser-/Thr-33221
PTBPhosphotyrosine-binding domain000044
PXPhox proteins’ domain1410130
RAIn RalGDS, AF-6 (Ras-associating)11040
RAS-like small RAB9991919
 GTPases RAN22211
 RAS3331111
 RHO6661313
 SAR11100
 Others1110724(all)5348(all)
RanBDRan-binding domain33155
RasGAPGAP for Ras-like GTPases43333
RasGEFGEF for Ras-like GTPases55400
RasGEFNIn some RasGEFs44000
RGSRegulator of G-protein signaling311116
RhoGAPGAP for Rho-like GTPases96384
RhoGEFGEF for Rho-like GTPases44376
SAMSterile alpha motif630111
SH2Src homology 21111515151
SH3Src homology 328252525656357
SPRYIn sp1A and Ryanodine receptors33070
TBCIn Tre-2, BUB2p, and Cdc16p107010
TPRTetratricopeptide repeat726939164007
UBAUbiquitin-associated domain1080120
UBCcUbiquitin-conjugating enzyme13131313121212
UBXUbiquitin-related domain84010
VHSIn VPS-27, Hrs and STAM43000
VPS9In VPS-9-like proteins21110
WH1WASp homology domain 111020
WWConserved WW motif9877999
ZU5In ZO-1 and UNC-500040
ZZDystrophin-like zinc finger22041
Totals866225443832901,137886704
  • Numbers of domains detected by SMART in the yeast genome, and in the yeast and human fractions of the SwissProt database are compared with the numbers of domains derived from HMMer analysis and Pfam HMMs scanned against these database fractions, and the numbers of annotations in SwissProt. Many of these domains are reviewed elsewhere (5, 6), and additional references may be found via the SMART Web site (http://www.bork.embl-heidelberg.de/Modules/sinput.shtml). 

  • a Annotations in SwissProt. 

  • b Annotations using the hmmfs program of the HMMer package with Pfam-derived HMMs (“–” indicates where no Pfam HMM was available).