I am trying to looking for homologous genes using the PSI-BLAST function.
1.) I created a blast database of conserved genes that I had downloaded from uniprot
makeblastdb -in mamA.AA.fasta -input_type fasta -dbtype prot -out mamA_db -parse_seqids
2.) I wanted to query my contigs - assembled from a metagenomics dataset and genes were predicted with the prodigal software - against the database that I have created.
psiblast -query contigs.prodigal.faa -db mamA_db -out mamA.psi.blast -num_iterations 3 -out_pssm mamA.checkpoint -num_threads 10 -comp_based_stats 1 -out_ascii_pssm mamA.pssm
However, it came out with these warning: Warning: [psiblast] lcl|Query_46 NODE_1_length_138104_cov_11.046462_46 # 25949 # 26596 # 1 # ID=1_46;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.407: Warning: Frequency ratios for PSSM are all zeros, frequency ratios for BLOSUM62 will be used during traceback in composition based statistics
Am I doing something wrong here? Will appreciate if someone could help.