Table 4 Identification of transcripts encoding putative regulatory proteins. Sequences were identified based on HMM searches suported by p-score < 1e-10 with PFAM profiles available for families of regulatory proteins. The PFAM accessions for which no homology was found in SpruceDB through HMM search were not reported.
From: Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters
Protein family | PFAM accession | Number of spruce transcripts |
|---|---|---|
Zinc finger, C3HC4 type (RING finger) | PF00097 | 66 |
WD, G-beta repeat | PF00400 | 44 |
AP2 domain-B3 DNA binding domain | PF00847 | 19 |
HMG (high mobility group) box | PF00505 | 16 |
MADS Family – SRF-type transcription factor – K-box region | PF00319 | 14 |
MYB DNA-binding | PF00249 | 13 |
AUX/IAA | PF02309 | 12 |
Histone-like transcription factor (CBF/NF-Y) and archaeal histone | PF00808 | 11 |
PHD finger – CW-type Zinc Finger | PF00628 | 10 |
No apical meristem (NAM) protein | PF02365 | 10 |
GRAS Family | PF03514 | 10 |
WRKY DNA-binding domain | PF03106 | 9 |
NAC domain | PF01849 | 9 |
Homeobox domain | PF00046 | 8 |
bZIP transcription factor – bZIP Maf transcription factor-G-box binding protein MFMR | PF00170 | 8 |
B-box zinc finger | PF00643 | 6 |
TUB Family | PF01167 | 6 |
Helix-loop-helix DNA-binding domain – Myc amino-terminal region | PF00010 | 5 |
KNOX2 domain | PF03791 | 3 |
LIM domain family – PET Domain | PF00412 | 5 |
Dof domain, zinc finger | PF02701 | 4 |
GATA zinc finger | PF00320 | 3 |
TCP family transcription factor | PF03634 | 2 |
CCAAT-HAP2 Family CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B | PF02045 | 2 |
SBP (Sqamosa-promoter binding protein) floral development | PF03110 | 1 |
HSF Family (Heat shock protein promoter binding) | PF00447 | 1 |
EIL Family ethylene insensitive 3 | PF04873 | 1 |
B3 DNA binding domain | PF02362 | 1 |
ARID/BRIGHT DNA binding domain – ELM2 domain | PF01388 | 1 |