Lactococcus garvieae strain FDAARGOS_929 plasmid unnamed, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Streptococcaceae; Lactococcus.
FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS): Supporting development and validation of Infectious Disease Dx tests
Submitted (02-DEC-2020) Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993-0002, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP065636.1.\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 Method :: SMRT v. 2.3.0, HGAP v. 3\nGenome Coverage :: 1739x\nSequencing Technology :: Pacbio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 01/01/2023 09:55:04\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) :: 2,110\nCDSs (total) :: 2,031\nGenes (coding) :: 1,993\nCDSs (with protein) :: 1,993\nGenes (RNA) :: 79\nrRNAs :: 6, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 5, 5 (5S, 16S, 23S)\ntRNAs :: 60\nncRNAs :: 3\nPseudo Genes (total) :: 38\nCDSs (without protein) :: 38\nPseudo Genes (ambiguous residues) :: 0 of 38\nPseudo Genes (frameshifted) :: 23 of 38\nPseudo Genes (incomplete) :: 18 of 38\nPseudo Genes (internal stop) :: 18 of 38\nPseudo Genes (multiple problems) :: 15 of 38\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_019292342.1
GO:0016154 - pyrimidine-nucleoside phosphorylase activity [Evidence IEA]
GO:0006213 - pyrimidine nucleoside metabolic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002830585.1
nucleoside transporter C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017371238.1
COORDINATES: similar to AA sequence:RefSeq:WP_017371033.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012898729.1
COORDINATES: similar to AA sequence:RefSeq:WP_017371035.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_003136603.1
COORDINATES: similar to AA sequence:RefSeq:WP_017371037.1
COORDINATES: similar to AA sequence:RefSeq:WP_017370612.1
COORDINATES: similar to AA sequence:RefSeq:WP_015063485.1
GO:0004803 - transposase activity [Evidence IEA]
IS6-like element ISS1S family transposase
COORDINATES: protein motif:HMM:NF012920.2
COORDINATES: similar to AA sequence:RefSeq:WP_015082503.1
COORDINATES: similar to AA sequence:RefSeq:WP_003331415.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611914.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014571979.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
polysaccharide deacetylase family protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF015893.2
COORDINATES: similar to AA sequence:RefSeq:WP_019293556.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010905402.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_003136637.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010868911.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017370780.1
COORDINATES: similar to AA sequence:RefSeq:WP_003136454.1
COORDINATES: similar to AA sequence:RefSeq:WP_000120771.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013851196.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_001825357.1
COORDINATES: protein motif:HMM:NF040132.1
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011675413.1
internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012294795.1
COORDINATES: similar to AA sequence:RefSeq:WP_010620873.1
COORDINATES: protein motif:HMM:NF015347.2
BspA family leucine-rich repeat surface protein
COORDINATES: protein motif:HMM:NF028245.2
COORDINATES: similar to AA sequence:RefSeq:WP_017370770.1
COORDINATES: similar to AA sequence:RefSeq:WP_002321606.1