Pediococcus damnosus strain TMW 2.1536 plasmid pL21536-2, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Pediococcus.
The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr
Submitted (04-AUG-2015) Technische Mikrobiologie, Technische Universitaet Muenchen, Gregor-Mendel-Stra##e 4, Freising, Bavaria 85354, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP012296.1.\nBacteria available from Technische Mikrobiologie Weihenstephan\n(Technische Universitaet Muenchen).\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 :: Celera Assembler v. 1\nAssembly Name :: Pda21536-1\nLong Assembly Name :: Pediococus damnosus TMW2.1536 1\nGenome Coverage :: 137\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/12/2023 23:41:38\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) :: 2,081\nCDSs (total) :: 2,004\nGenes (coding) :: 1,968\nCDSs (with protein) :: 1,968\nGenes (RNA) :: 77\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 62\nncRNAs :: 3\nPseudo Genes (total) :: 36\nCDSs (without protein) :: 36\nPseudo Genes (ambiguous residues) :: 0 of 36\nPseudo Genes (frameshifted) :: 17 of 36\nPseudo Genes (incomplete) :: 12 of 36\nPseudo Genes (internal stop) :: 8 of 36\nPseudo Genes (multiple problems) :: 1 of 36\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_002287843.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF019604.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004039692.1
COORDINATES: similar to AA sequence:RefSeq:WP_014563300.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_002326559.1
COORDINATES: similar to AA sequence:RefSeq:WP_002295193.1
GO:0003934 - GTP cyclohydrolase I activity [Evidence IEA]
GO:0042559 - pteridine-containing compound biosynthetic process [Evidence IEA]; GO:0046654 - tetrahydrofolate biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003625288.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010625626.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015638851.1
COORDINATES: similar to AA sequence:RefSeq:WP_050892470.1
ISL3-like element IS1165 family transposase
COORDINATES: protein motif:HMM:NF019474.2
COORDINATES: similar to AA sequence:RefSeq:WP_004270763.1
GO:0004459 - L-lactate dehydrogenase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005714139.1
COORDINATES: protein motif:HMM:NF024109.2
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_003586220.1
COORDINATES: similar to AA sequence:RefSeq:WP_003596745.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014296.2
GO:0004489 - methylenetetrahydrofolate reductase (NAD(P)H) activity [Evidence IEA]
GO:0006555 - methionine metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003577771.1
COORDINATES: protein motif:HMM:NF019540.2
GO:0003729 - mRNA binding [Evidence IEA]
type II toxin-antitoxin system HicA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008461894.1
COORDINATES: similar to AA sequence:RefSeq:WP_003637411.1
GO:0047324 - phosphoenolpyruvate-glycerone phosphotransferase activity [Evidence IEA]
dihydroxyacetone kinase phosphoryl donor subunit DhaM
COORDINATES: similar to AA sequence:RefSeq:WP_003581768.1
GO:0004371 - glycerone kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013437296.1
COORDINATES: similar to AA sequence:RefSeq:WP_003581774.1
COORDINATES: protein motif:HMM:NF012655.2
COORDINATES: similar to AA sequence:RefSeq:WP_016511122.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552807.1
COORDINATES: similar to AA sequence:RefSeq:WP_003603789.1
COORDINATES: similar to AA sequence:RefSeq:WP_003691010.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015474624.1
COORDINATES: similar to AA sequence:RefSeq:WP_010620892.1
COORDINATES: similar to AA sequence:RefSeq:WP_005693113.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014386872.1
COORDINATES: similar to AA sequence:RefSeq:WP_016511818.1
COORDINATES: similar to AA sequence:RefSeq:WP_003645725.1
COORDINATES: similar to AA sequence:RefSeq:WP_015639693.1
COORDINATES: similar to AA sequence:RefSeq:WP_004562667.1
COORDINATES: similar to AA sequence:RefSeq:WP_020090523.1
COORDINATES: similar to AA sequence:RefSeq:WP_010009086.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012870.2
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_014569090.1
COORDINATES: similar to AA sequence:RefSeq:WP_003591692.1
GO:0015486 - glycoside-pentoside-hexuronide:cation symporter activity [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0006812 - monoatomic cation transport [Evidence IEA]
glycoside-pentoside-hexuronide (GPH):cation symporter
COORDINATES: similar to AA sequence:RefSeq:WP_003680034.1