Table 4.
Protein families in gene models and alternatively spliced genes in tomato plants∗.
| Pfam ID | Total | AS genes | % | Pfam abbreviation | Pfam description |
|---|---|---|---|---|---|
| pfam00069 | 631 | 503 | 79.7 | Pkinase | Protein kinase domain |
| pfam07714 | 467 | 388 | 83.1 | Pkinase_Tyr | Protein tyrosine kinase |
| pfam00067 | 337 | 216 | 64.1 | p450 | Cytochrome P450 |
| pfam13041 | 316 | 247 | 78.2 | PPR_2 | PPR repeat family |
| pfam13639 | 223 | 140 | 62.8 | zf-RING_2 | Ring finger domain |
| pfam00931 | 217 | 151 | 69.6 | NB-ARC | NB-ARC domain |
| pfam00076 | 179 | 162 | 90.5 | RRM_1 | RNA recognition motif |
| pfam00249 | 178 | 111 | 62.4 | Myb_DNA-binding | Myb-like DNA-binding domain |
| pfam00201 | 169 | 86 | 50.9 | UDPGT | UDP-glucoronosyl and UDP-glucosyl transferase |
| pfam10536 | 167 | 101 | 60.5 | PMD | Plant mobile domain |
| pfam03171 | 147 | 87 | 59.2 | 2OG-FeII_Oxy | 2OG-Fe(II) oxygenase superfamily |
| pfam00847 | 137 | 62 | 45.3 | AP2 | AP2 domain |
| pfam02519 | 130 | 35 | 26.9 | Auxin_inducible | Auxin responsive protein |
| pfam00141 | 123 | 81 | 65.9 | peroxidase | Peroxidase |
| pfam05699 | 118 | 28 | 23.7 | Dimer_Tnp_hAT | hAT family C-terminal dimerisation |
| pfam00319 | 109 | 34 | 31.2 | SRF-TF | SRF-type transcription factor |
| pfam02458 | 99 | 51 | 51.5 | Transferase | Transferase family |
| pfam14432 | 95 | 68 | 71.6 | DYW_deaminase | DYW family of nucleic acid deaminases |
| pfam00481 | 91 | 79 | 86.8 | PP2C | Protein phosphatase 2C |
| pfam00854 | 86 | 75 | 87.2 | PTR2 | POT family |
| pfam01095 | 85 | 42 | 49.4 | Pectinesterase | Pectinesterase |
| pfam00561 | 84 | 70 | 83.3 | Abhydrolase_1 | alpha/beta hydrolase fold |
| pfam00657 | 83 | 65 | 78.3 | Lipase_GDSL | GDSL-like Lipase/Acylhydrolase |
| pfam00010 | 82 | 70 | 85.4 | HLH | Helix-loop-helix DNA-binding domain |
| pfam03106 | 82 | 54 | 65.9 | WRKY | WRKY DNA -binding domain |
| pfam01554 | 77 | 66 | 85.7 | MatE | MatE |
| pfam13839 | 75 | 63 | 84.0 | PC-Esterase | GDSL/SGNH-like Acyl-Esterase family found |
| pfam00004 | 74 | 64 | 86.5 | AAA | ATPase family associated with various cellular |
| pfam02362 | 74 | 49 | 66.2 | B3 | B3 DNA binding domain |
| pfam00071 | 73 | 58 | 79.5 | Ras | Ras family |
| pfam00083 | 73 | 53 | 72.6 | Sugar_tr | Sugar (and other) transporter |
| pfam05695 | 72 | 13 | 18.1 | DUF825 | Plant protein of unknown function (DUF825) |
| pfam00082 | 71 | 41 | 57.7 | Peptidase_S8 | Subtilase family |
| pfam13499 | 71 | 40 | 56.3 | EF-hand_7 | EF-hand domain pair |
| Others | 17227 | 13078 | 75.9 | ||
| Total | 22322 | 16531 | 74.1 |