Identification of Bai Proteins in Clostridium scindens genomes

[breister2]

To identify Bai proteins in each of the Clostridium scindens genomes, hmmsearch was used against the concatenated amino acid fasta files of with the query being the previously generated HMM profiles with the flag --cut_tc.

for f in *.hmm; do hmmsearch --cut_tc --noali --tblout All_C_scindens_Protein_Seqs_vs_${f%.*}.tblout $f ../../Clostridium_scindens_genomes_and_metadata/Clostridium_scindens_genomes_final_header_renamed_amino_acid_sequences/All_C_scindens_protein_seqs.faa; done &

[breister2]

For 12beta-HSDH, 3beta-HSDH, and 3alpha-HSDH, there were no hits identified for any of the genomes, so these HMM profiles were used with hmmsearch --noali without using trusted cutoffs.

• For 3alpha-HSDH, the resulting hmmsearch output was trimmed at a score of 212.433, because the largest drops in score for the output were 221.1 - 212.8 - 203.4
• For 12beta-HSDH, the resulting hmmsearch output was trimmed at a a score of 159.1, because the largest drop in score was 178.2 - 140

For 3beta-HSDH, the HMM profile was incorrect, which likely resulted in the failure to identify hits, so the HMM profile was remade to get accurate results.