in the National Center for Biotechnology Information (NCBI), we searched the sequences based on the query (UniprotKB ID: Q9H3M7) with which we generated the five templates for Thioredoxin which are shown in (Figure 1).
Iterated profile searches with PSI-BLAST -a tool for discovery in protein databases.
Contig-5199 Proteina regulatoria de la adhesion PSI-BLAST celular ARM_1, EB30-H4.
Likewise, PSI-BLAST searches failed to identify MBP homologs.
Extending the analyses to the Ciona intestinalis EST database and with PSI-BLAST both failed to identify [P.
An additional candidate (ci0100150877--DM-3) was obtained from the PSI-BLAST search (Table 2).
A gene model (ci0100130899, 1138 amino acids) related to CNP, though not to gRICH sequences, was identified from searches of the Ciona EST database and through a PSI-BLAST search.
The original PSI-BLAST results were used for the sequences where no rules could be induced.
Applying PSI-BLAST to the data produced three proteins in the twilight zone: (1) allophycocyanin alpha-b chain (Anabena), (2) erythroid transcription factor (gata-1 Mus musculus), and (3) oryzain gamma chain precursor (Oryza sativa).
MAG HMMs have been shown to be more sensitive than either PSI-BLAST
or Pfam on both full sequences and sequence fragments.