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A search for conserved domain architecture (using Conserved Domain Architecture Retrieval Tool [ 51]) resulted in three major types, as outlined in Fig. 4.
Protein active sites were determined using (Conserved Domain Architecture Retrieval Tool (CDART) [ 37] and the conserved domain database (CDD) [ 38].
LATS conserved domain 1.
LATS conserved domain 2. N-terminal regulatory domain.
LATS1/2 proteins share LATS conserved domain 1 (LCD1) and LATS conserved domain 2 (LCD2), which are conserved in all vertebrate LATS1/2 homologues.
The gene sequence alignment of flavin nucleotide binding domain indicates that this is a highly conserved domain across many azoreductases.
PstP has conserved domain architecture of PP2C-phosphatases (PPM family).
HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications.
Among the weak, conserved domain hits was an RRM_1 domain we found in Ssp2.
We find ∼4500 cross-species validated, remotely conserved domain predictions in the human proteome alone.
We could confirm this remotely conserved domain by PSI-BLAST [7] searches (data not shown).
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