Table 1.
Numbers of domains detected by SMART in the yeast genome, and in the yeast and human fractions of the Swiss Prot database
| Domain | Full name or function | Number of
domains annotated
|
||||||
|---|---|---|---|---|---|---|---|---|
| Yeast genome
|
SwissProt:
S. cerevisiae
|
SwissProt: Homo sapiens
|
||||||
| SMART | SMART | SPa | Pfamb | SMART | SPa | Pfamb | ||
| 14-3-3 | 14-3-3 proteins | 2 | 2 | 2 | 2 | 6 | 6 | 6 |
| ADF | Actin depolymerization factor | 4 | 3 | 2 | 3 | 4 | 2 | 2 |
| ARF | Arf subfamily of small GTPases | 5 | 4 | 4 | 3 | 12 | 12 | 12 |
| ArfGap | GAP for Arf-like GTPases | 6 | 5 | 0 | – | 2 | 0 | – |
| ARM | Armadillo repeat | 14 | 14 | 14 | 1 | 40 | 21 | 13 |
| B41 | Band 4.1 homology | 0 | 0 | 0 | 0 | 9 | 9 | 9 |
| BTK | BTK-like zinc finger | 0 | 0 | 0 | – | 4 | 0 | – |
| C1 | PKC conserved region 1 | 2 | 2 | 2 | 2 | 38 | 32 | 30 |
| C2 | PKC conserved region 2 | 18 | 14 | 11 | 10 | 21 | 19 | 17 |
| CARD | Caspase recruitment domain | 0 | 0 | 0 | 0 | 9 | 0 | – |
| CBS | Cystathionine β-synthase-like domain | 17 | 17 | 0 | – | 23 | 0 | – |
| CH | Calponin homology | 6 | 4 | 4 | 2 | 35 | 26 | 18 |
| CNH | Citron homology | 3 | 2 | 0 | – | 0 | 0 | – |
| cNMP | Cyclic nucleotide monophosphate-binding domain | 4 | 4 | 2 | 3 | 12 | 12 | 14 |
| CYCc | Adenylyl/guanylyl cyclase | 1 | 1 | 1 | 0 | 15 | 15 | 15 |
| DAGKa | DAG kinase (accessory) | 0 | 0 | 0 | – | 6 | 0 | – |
| DAGKc | DAG kinase (catalytic) | 2 | 0 | 0 | – | 6 | 6 | – |
| DAX | In Dsh and axin | 0 | 0 | 0 | – | 1 | 0 | – |
| DEATH | Regulator of cell death | 0 | 0 | 0 | – | 14 | 10 | – |
| DEP | In Dsh. egl-10 and pleckstrin | 5 | 5 | 0 | – | 2 | 0 | – |
| DYNc | Dynamin | 3 | 3 | 3 | 3 | 4 | 4 | 4 |
| EFh | EF-hand | 24 | 24 | 17 | 7 | 124 | 124 | 62 |
| FCH | Fes/CIP4 homology domain | 4 | 4 | 0 | – | 3 | 0 | – |
| FHA | Forkhead associated domain | 14 | 9 | 8 | 9 | 1 | 1 | 1 |
| FYVE | In Fab1, YOTB, Vac1, and EEA1 | 6 | 5 | 2 | – | 1 | 0 | – |
| GAF | In cGMP-PDEs, adenylyl cyclases, and E. coli fh1A | 0 | 0 | 0 | – | 4 | 0 | – |
| HECTc | Homologous to E6-AP carboxyl terminus; ubiquitin ligases | 5 | 4 | 3 | – | 4 | 4 | – |
| HR1 | PRK kinase homology region 1 | 2 | 2 | 0 | – | 0 | 0 | – |
| IPPc | Inositol polyphosphate phosphatase | 4 | 2 | 2 | 2 | 2 | 2 | 2 |
| IQ | Calmodulin-binding motif | 6 | 6 | 3 | – | 10 | 2 | – |
| KISc | Kinesin, catalytic domain | 6 | 6 | 6 | 6 | 6 | 6 | 6 |
| LIM | Zinc finger in Lin-11, Is1-1, Mec-3 | 9 | 7 | 5 | 3 | 50 | 50 | 30 |
| MYSc | Myosin, catalytic domain | 5 | 5 | 5 | 5 | 6 | 6 | 6 |
| OPR | Octicosapeptide repeat | 1 | 1 | 0 | – | 4 | 0 | – |
| PAC | Motif, C-terminal to PAS | 0 | 0 | 0 | – | 3 | 0 | – |
| PAS | Domain in Per, ARNT, Sim | 1 | 1 | 0 | – | 6 | 6 | – |
| PBD | p21 Rho-binding domain | 3 | 3 | 0 | – | 3 | 2 | – |
| PDZ | In PSD-95, D1g, ZO-1 | 0 | 0 | 0 | – | 31 | 15 | – |
| PH | Pleckstrin homology domain | 27 | 19 | 12 | 13 | 36 | 30 | 27 |
| PI3K_PI3Kb | PI3K: p85-binding domain | 0 | 0 | 0 | 0 | 2 | 0 | – |
| PI3K_rbd | P13K: Ras-binding domain | 0 | 0 | 0 | 0 | 3 | 0 | – |
| P13Ka | P13K accessory domain | 2 | 2 | 0 | – | 4 | 0 | – |
| P13Kc | Phosphoinositide kinase | 8 | 8 | 8 | 7 | 5 | 5 | 5 |
| PLAc | Phospholipase A2, catalytic domain | 4 | 4 | 4 | – | 1 | 1 | – |
| PLCXc | Phospholipase C, domain X | 1 | 1 | 1 | 1 | 5 | 5 | 5 |
| PLCYc | Phospholipase C, domain Y | 1 | 1 | 1 | 1 | 5 | 5 | 5 |
| PLDc | Phospholipase D, conserved motif | 2 | 2 | 0 | – | 2 | 2 | – |
| PP2Ac | Protein phosphatases 2A | 12 | 12 | 12 | 12 | 10 | 10 | 10 |
| PP2Cc | Protein phosphatases 2C | 7 | 6 | 5 | 2 | 2 | 2 | 2 |
| Protein kinases | TyrKc: Tyr-specific | 0 | 0 | 0 | – | 70 | 69 | |
| S_TKc: Ser/Thr-specific | 61 | 58 | 58 | – | 62 | 62 | – | |
| STYKc: Ser/Thr/Tyr-specific | 56 | 49 | 46 | 104(all) | 51 | 49 | 184(all) | |
| Protein phosphatases | PTPc: Tyr-specific | 3 | 3 | 3 | 3 | 35 | 34 | 35 |
| DSPc: Dual-specific | 5 | 5 | 5 | – | 7 | 7 | – | |
| PTPc_DSPc: Tyr-,/Ser-/Thr- | 3 | 3 | 2 | – | 2 | 1 | – | |
| PTB | Phosphotyrosine-binding domain | 0 | 0 | 0 | 0 | 4 | 4 | – |
| PX | Phox proteins’ domain | 14 | 10 | 1 | – | 3 | 0 | – |
| RA | In RalGDS, AF-6 (Ras-associating) | 1 | 1 | 0 | – | 4 | 0 | – |
| RAS-like small | RAB | 9 | 9 | 9 | – | 19 | 19 | – |
| GTPases | RAN | 2 | 2 | 2 | – | 1 | 1 | – |
| RAS | 3 | 3 | 3 | – | 11 | 11 | – | |
| RHO | 6 | 6 | 6 | – | 13 | 13 | – | |
| SAR | 1 | 1 | 1 | – | 0 | 0 | – | |
| Others | 11 | 10 | 7 | 24(all) | 5 | 3 | 48(all) | |
| RanBD | Ran-binding domain | 3 | 3 | 1 | – | 5 | 5 | – |
| RasGAP | GAP for Ras-like GTPases | 4 | 3 | 3 | – | 3 | 3 | – |
| RasGEF | GEF for Ras-like GTPases | 5 | 5 | 4 | – | 0 | 0 | – |
| RasGEFN | In some RasGEFs | 4 | 4 | 0 | – | 0 | 0 | – |
| RGS | Regulator of G-protein signaling | 3 | 1 | 1 | – | 11 | 6 | – |
| RhoGAP | GAP for Rho-like GTPases | 9 | 6 | 3 | – | 8 | 4 | – |
| RhoGEF | GEF for Rho-like GTPases | 4 | 4 | 3 | – | 7 | 6 | – |
| SAM | Sterile alpha motif | 6 | 3 | 0 | – | 11 | 1 | – |
| SH2 | Src homology 2 | 1 | 1 | 1 | 1 | 51 | 51 | 51 |
| SH3 | Src homology 3 | 28 | 25 | 25 | 25 | 65 | 63 | 57 |
| SPRY | In sp1A and Ryanodine receptors | 3 | 3 | 0 | – | 7 | 0 | – |
| TBC | In Tre-2, BUB2p, and Cdc16p | 10 | 7 | 0 | – | 1 | 0 | – |
| TPR | Tetratricopeptide repeat | 72 | 69 | 39 | 16 | 40 | 0 | 7 |
| UBA | Ubiquitin-associated domain | 10 | 8 | 0 | – | 12 | 0 | – |
| UBCc | Ubiquitin-conjugating enzyme | 13 | 13 | 13 | 13 | 12 | 12 | 12 |
| UBX | Ubiquitin-related domain | 8 | 4 | 0 | – | 1 | 0 | – |
| VHS | In VPS-27, Hrs and STAM | 4 | 3 | 0 | – | 0 | 0 | – |
| VPS9 | In VPS-9-like proteins | 2 | 1 | 1 | – | 1 | 0 | – |
| WH1 | WASp homology domain 1 | 1 | 1 | 0 | – | 2 | 0 | – |
| WW | Conserved WW motif | 9 | 8 | 7 | 7 | 9 | 9 | 9 |
| ZU5 | In ZO-1 and UNC-5 | 0 | 0 | 0 | – | 4 | 0 | – |
| ZZ | Dystrophin-like zinc finger | 2 | 2 | 0 | – | 4 | 1 | – |
| Totals | 86 | 622 | 544 | 383 | 290 | 1,137 | 886 | 704 |
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).