Identification of East Asian cagA and vacA motifs in strain 98-10 is consistent with the results of the MLST analysis, which classified strain 98-10 as a member of the East Asian population cluster of H. pylori strains.
The zinc finger motifs, which are classified based on the arrangement of the zinc-binding amino acids, are present in many transcription factors and play critical roles in interactions with other molecules [ 1, 2].
In addition, we found that OsSMF1 bound to a new motif termed the ATGA motif, which can be considered a novel OsSMF1 binding motif.
The CGCCACGT motif, which contains the OsIRO2-binding sequence (CACGTGG) and was named OsIRO2-binding sequence-containing motif (OsIRO2BS), attained the sixth highest MAMA score.
Unless you're shooting for the Pay By The Hour Motel motif, which I do not recommend.
The CaM Target Database classifies CaM binding targets into 5 groups, each characterized by certain motifs: 3 predominantly calcium-dependent motifs (1 10, 1 14 and 1 16, named according to the position of large hydrophobic residues), the IQ motif which is typically not dependent on calcium concentration, and others.
Among 40 motifs, motif 1 is the most common motif, which was found in 25 AtMYBs and 23 SmMYBs.
Since we do not have negative data (escape variants), all discontinuous motifs extracted from these strains were classified as neutralized motifs, which were recognized as functional in neutralizing assays.
Methods for finding transcription factors (as motifs which are statistically over-represented in sequences) can be broadly classified as those based on phylogenetic footprinting, and those which are not.
A motif search of the SiLEA14 protein in InterProScan revealed that it contains a "LEA_2" motif (PF03186, 3.4e-20), wasclassifiedssintod into subgroup 5C (D-95) according to Battaglia's classification of LEA proteins [ 12].
