Table 1.

bHLH Domain Consensus Motif

Position in the AlignmentRegionConsensus Motif Amino Acid
 Frequency within the bHLH
 Domaina (Atchley et al., 1999)Amino Acid Frequency within
 the Arabidopsis bHLH
 Domainsb (This Study)
Atchley et al.
 (1999)This
 study
11BasicK (27%), R (61%)K (22%), R (24%), other (53%)
22BasicK (16%), R (77%)K (7%), R (35%), other (58%)
913BasicE (93%)E (76%), A (10%), other (14%)
1014BasicR (81%), K (14%)R (74%), K (14%), other (12%)
1216BasicR (91%)R (91%), other (9%)
1620Helix 1I (35%), L (33%), V (23%)I (52%), L (27%), M (12%), V (3%), other (6%)
1721Helix 1N (74%)N (51%), S (19%), other (30%)
2024Helix 1F (72%), I (9%), L (14%)F (26%), I (14%), L (26%), M (20%), other (15%)
2327Helix 1L (98%)L (100%)
2428Helix 1K (35%), R (44%)K (4%), R (35%), Q (42%), G (4%), other (15%)
4739LoopK (58%), R (24%)K (66%), R (7%), other (27%)
5042Helix 2K (93%)K (45%), T (13%), other (42%)
5345Helix 2I (74%), T (15%), V(7%)I (27%), T (4%), V (16%), L (14%), M (33%), other (6%)
5446Helix 2L (98%)L (76%), V (14%), other (12%)
5749Helix 2A (76%)A (60%), I (16%), V (12%), T (9%), other (3%)
5850Helix 2I (31%), T (23%), V (27%)I (63%), T (2%), V (22%), other (13%)
6052Helix 2Y (77%)Y (78%), other (22%)
6153Helix 2I (69%), L (16%), V (8%)I (40%), L (13%), V (33%), other (14%)
6456Helix 2L (80%), M (7%)L (93%), M (1%), other (6%)
  • a Percentages refer to the 392 bHLH proteins analyzed by Atchley et al. (1999).

  • b Percentages refer to the 147 Arabidopsis bHLH proteins identified in this study.

  • Amino acids (one-letter code) and positions within the bHLH domain used to define the members of the AtbHLH protein family. The conserved amino acids that define the motif are those reported by Atchley et al. (1999). The original position for each conserved residue based on sequence alignments by Atchley et al. (1999) and the corresponding position for our multiple sequence alignments are indicated in the first two columns, respectively. In the last two columns, the frequencies of the residues at each position reported by Atchley et al. (1999) and those found in this study for the AtbHLH proteins are compared. Boldface letters indicate residues in the AtbHLH proteins that differ from the consensus motif but that have a representation in the group of at least 10%.