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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