Pediococcus claussenii strain TMW 2.53 plasmid pL253-2, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Pediococcus.
Pediococcus and Lactobacillus from brewery environment - whole genome sequencing and assembly
Submitted (18-MAR-2016) Technische Mikrobiologie, Technische Universitaet Muenchen, Gregor-Mendel-Strasse 4, Freising, Bavaria 85354, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP014935.1.\nSource DNA or bacteria available from the culture collection of the\nTechnische Mikrobiologie Weihenstephan upon request and only if\npermitted by a potential cooperation partner. Individual decisions.\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 :: Pclaussenii253-1\nLong Assembly Name :: Pediococcus claussenii TMW 2.53 1\nGenome Coverage :: 192\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/24/2022 04:03:52\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) :: 1,947\nCDSs (total) :: 1,874\nGenes (coding) :: 1,847\nCDSs (with protein) :: 1,847\nGenes (RNA) :: 73\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 57\nncRNAs :: 4\nPseudo Genes (total) :: 27\nCDSs (without protein) :: 27\nPseudo Genes (ambiguous residues) :: 0 of 27\nPseudo Genes (frameshifted) :: 7 of 27\nPseudo Genes (incomplete) :: 15 of 27\nPseudo Genes (internal stop) :: 10 of 27\nPseudo Genes (multiple problems) :: 5 of 27\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011668134.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013355080.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002833166.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011674067.1
COORDINATES: similar to AA sequence:RefSeq:WP_005717330.1
COORDINATES: similar to AA sequence:RefSeq:WP_005717323.1
COORDINATES: similar to AA sequence:RefSeq:WP_002823702.1
COORDINATES: similar to AA sequence:RefSeq:WP_005693113.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612162.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS5-like element ISLpl3 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_002823700.1
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_003603789.1
COORDINATES: similar to AA sequence:RefSeq:WP_013729135.1
COORDINATES: similar to AA sequence:RefSeq:WP_003603791.1
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_016373353.1
COORDINATES: similar to AA sequence:RefSeq:WP_003593321.1
COORDINATES: similar to AA sequence:RefSeq:WP_016373351.1
COORDINATES: protein motif:HMM:NF013718.2
COORDINATES: similar to AA sequence:RefSeq:WP_002820251.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_032488692.1
COORDINATES: protein motif:HMM:NF024110.2
COORDINATES: protein motif:HMM:NF012655.2
COORDINATES: similar to AA sequence:RefSeq:WP_003680034.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013727908.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_003594411.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005215 - transporter activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008841923.1
GO:0004634 - phosphopyruvate hydratase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF01734
Fluoride riboswitches increase expression of downstream genes that help mitigate the toxic effects of very high levels of fluoride; They are found in a wide variety of bacteria and archaea; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_013726950.1
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_011668133.1