Table 4.
PFAM group members with more than 500 genes in the 13 Trichoderma isolates
| clusters | genes per cluster | total genes | genes/ species | HV/SLa | HV/STa | ST/SLa | singletonsb | multiplesc | C/Sd (%) | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Zn2Cys6 transcriptional regulators | PF04082 | 238 | 12.3 | 2929 | 225.3 | 1.69 | 1.21 | 1.40 | 84 | 154 | 64.7 |
| MFS permeases | PF07690 | 172 | 17.3 | 2972 | 228.6 | 1.55 | 1.06 | 1.46 | 67 | 105 | 61.0 |
| short-chain dehydrogenases/reductases | PF00106 | 121 | 17.6 | 2129 | 163.8 | 1.68 | 1.18 | 1.42 | 46 | 75 | 62.0 |
| ankyrin-containing proteins | PF00023 | 106 | 14.4 | 1524 | 117.2 | 1.84 | 1.05 | 1.75 | 20 | 86 | 81.1 |
| alpha-beta-hydrolases | PF00561, 07859, 02230 | 96 | 14.4 | 1382 | 106.3 | 2.02 | 1.27 | 1.59 | 29 | 67 | 69.8 |
| protein kinases | PF00069 | 98 | 12.4 | 1218 | 93.7 | 1.15 | 1.11 | 1.03 | 60 | 38 | 38.8 |
| zinc-dependent alcohol dehydrogenases | PF00107 | 66 | 17.6 | 1159 | 89.2 | 1.89 | 1.17 | 1.61 | 15 | 51 | 77.3 |
| FAD-binding oxidases | PF01494, 01565 | 84 | 13.8 | 1158 | 89.1 | 1.56 | 1.21 | 1.29 | 25 | 59 | 70.2 |
| methyltransferases | PF00891 | 91 | 12.7 | 1157 | 89.0 | 1.24 | 1.09 | 1.14 | 46 | 45 | 49.5 |
| AAA + -ATPasesAAA+ − ATPases | PF00004 | 85 | 13.3 | 1130 | 86.9 | 1.13 | 1.06 | 1.07 | 54 | 31 | 36.5 |
| cytochrome P450 monooxygenases | PF00067 | 59 | 15.9 | 940 | 72.3 | 1.65 | 1.69 | 0.97 | 14 | 45 | 76.3 |
| sugar transporters | PF00083 | 65 | 14.2 | 923 | 71.0 | 1.53 | 1.17 | 1.31 | 33 | 32 | 49.2 |
| ABC-transporters | PF00005 | 48 | 16.3 | 780 | 60.0 | 1.22 | 1.13 | 1.07 | 21 | 27 | 56.3 |
| vegetative heteroincompatibility (HET) proteins | PF06985, 07217, 17,108 | 72 | 10.5 | 753 | 57.9 | 1.94 | 1.24 | 1.56 | 13 | 59 | 81.9 |
| aminotransferases | PF01490 | 49 | 13.8 | 675 | 51.9 | 1.47 | 1.18 | 1.25 | 21 | 28 | 57.1 |
| amino acid permeases | PF00324 | 48 | 13.1 | 630 | 48.5 | 1.17 | 1.10 | 1.06 | 30 | 18 | 37.5 |
| amidases | PF01979, 04909 | 37 | 17.0 | 629 | 48.4 | 1.93 | 1.20 | 1.62 | 12 | 25 | 67.6 |
| acetytransferase | PF00583, 00797, 13,302, 13,523 | 49 | 12.2 | 600 | 46.2 | 1.26 | 1.10 | 1.15 | 23 | 26 | 53.1 |
| DEAD-box helicases | PF00270 | 42 | 13.5 | 567 | 43.6 | 0.97 | 0.96 | 1.01 | 33 | 9 | 21.4 |
| NmrA-like proteins, NAD-binding negative regulators of GATA-binding proteins | PF05368 | 41 | 13.5 | 552 | 42.5 | 3.01 | 1.11 | 2.70 | 10 | 31 | 75.6 |
| DnaJ molecular chaperone | PF00226 | 42 | 12.8 | 537 | 41.3 | 1.02 | 0.99 | 1.04 | 19 | 23 | 54.8 |
| RRM_1 RNA binding proteins | PF00076 | 42 | 12.8 | 537 | 41.3 | 1.00 | 0.99 | 1.01 | 40 | 2 | 4.8 |
a -ratio of the number of genes in all species belonging to one of the Trichoderma sections or clades
b - genes which are present in one a single copy per cluster
c - genes that occur in more than one copy per cluster in at least one species
d - percentage of clusters containing multiple genes