Computational protocol: Draft genome sequence of Micrococcus luteus strain O'Kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates

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Protocol publication

[…] Gene models were created using the prokaryotic gene calling software package Prodigal . A total of 2318 gene models of average gene size 1004 bp were predicted. To functionally annotate the predicted protein sequences, we used a combination of NCBI Blast C ++ homology search and HMMER 3.0 hmmscan against the PFAM 26.0 database . Additional gene analysis and functional annotation were carried out through the Integrated Microbial Genomes Expert Review (IMG-ER) platform. […]

Pipeline specifications

Software tools Prodigal, BLASTN, HMMER, HMMER hmmscan
Databases Pfam
Application Amino acid sequence alignment
Organisms Micrococcus luteus, Erythranthe lutea
Chemicals Alanine, Aspartic Acid, Cysteine, Fatty Acids, Fructose, Galactose, Glucose, Glycine, Mannose, Methionine, Glutamic Acid