Staphylococcus saccharolyticus strain 13T0028 plasmid p13T0028, complete sequence.
Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus.
Staphylococcus saccharolyticus Isolated From Blood Cultures and Prosthetic Joint Infections Exhibits Excessive Genome Decay
Complete genome sequences of two Staphylococcus saccharolyticus strains isolated from prosthetic joint infections
Submitted (12-JAN-2021) Department of Biomedicine, Aarhus University, Hoegh-Guldbergs Gade 10, Aarhus C 8000, Denmark
REFSEQ INFORMATION: The reference sequence is identical to\nCP068030.1.\nBacteria and source DNA available from Bo Soderquist, Oerebro\nUniversity, Sweden.\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Assembly-Data-START##\nAssembly Date :: 2020\nAssembly Method :: Unicycler v. v0.4.6\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 205.0x\nSequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/08/2023 20:14:48\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,361\nCDSs (total) :: 2,281\nGenes (coding) :: 1,864\nCDSs (with protein) :: 1,864\nGenes (RNA) :: 80\nrRNAs :: 6, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 5, 5 (5S, 16S, 23S)\ntRNAs :: 60\nncRNAs :: 4\nPseudo Genes (total) :: 417\nCDSs (without protein) :: 417\nPseudo Genes (ambiguous residues) :: 0 of 417\nPseudo Genes (frameshifted) :: 346 of 417\nPseudo Genes (incomplete) :: 52 of 417\nPseudo Genes (internal stop) :: 178 of 417\nPseudo Genes (multiple problems) :: 149 of 417\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_002494720.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001568503.1
GO:0006260 - DNA replication [Evidence IEA]
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF033608.1
type I toxin-antitoxin system Fst family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_002449607.1
COORDINATES: protein motif:HMM:TIGR03494.1
GO:0043904 - isochorismate pyruvate lyase activity [Evidence IEA]; GO:0008909 - isochorismate synthase activity [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF017538.2
COORDINATES: protein motif:HMM:NF015331.2
COORDINATES: protein motif:HMM:NF016115.2
GO:0004061 - arylformamidase activity [Evidence IEA]
GO:0019441 - tryptophan catabolic process to kynurenine [Evidence IEA]
COORDINATES: protein motif:HMM:NF014664.2
carboxymuconolactone decarboxylase family protein
COORDINATES: protein motif:HMM:NF019498.2
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: protein motif:HMM:NF013786.2
4'-phosphopantetheinyl transferase superfamily protein
COORDINATES: similar to AA sequence:RefSeq:WP_000042567.1
COORDINATES: protein motif:HMM:NF012759.2
COORDINATES: protein motif:HMM:NF012337.2
beta-ketoacyl synthase N-terminal-like domain-containing protein
beta-ketoacyl-[acyl-carrier-protein] synthase family protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF015998.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015065.2
COORDINATES: protein motif:HMM:NF012797.2
GO:0003723 - RNA binding [Evidence IEA]; GO:0008173 - RNA methyltransferase activity [Evidence IEA]
GO:0006396 - RNA processing [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001106057.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002440810.1
COORDINATES: similar to AA sequence:RefSeq:WP_002440813.1