Pediococcus claussenii strain TMW 2.53 plasmid pL253-1, 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\nCP014934.1.\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_050892470.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
ISL3-like element IS1165 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_003561820.1
IS982-like element ISLpl4 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_005918105.1
COORDINATES: similar to AA sequence:RefSeq:WP_003649837.1
COORDINATES: similar to AA sequence:RefSeq:WP_003649838.1
COORDINATES: similar to AA sequence:RefSeq:WP_007124949.1
COORDINATES: similar to AA sequence:RefSeq:WP_003553350.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002369988.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_001748276.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013727908.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003581702.1
COORDINATES: similar to AA sequence:RefSeq:WP_003581705.1
COORDINATES: similar to AA sequence:RefSeq:WP_010621836.1
COORDINATES: similar to AA sequence:RefSeq:WP_010078380.1
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_016381866.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_003593321.1
COORDINATES: similar to AA sequence:RefSeq:WP_016373351.1
COORDINATES: similar to AA sequence:RefSeq:WP_002826711.1
COORDINATES: similar to AA sequence:RefSeq:WP_016373349.1
COORDINATES: similar to AA sequence:RefSeq:WP_016511774.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_002820251.1
COORDINATES: similar to AA sequence:RefSeq:WP_013355080.1
COORDINATES: similar to AA sequence:RefSeq:WP_003577309.1
COORDINATES: similar to AA sequence:RefSeq:WP_005917937.1
COORDINATES: similar to AA sequence:RefSeq:WP_053338758.1
IS30-like element ISLpl1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_003596745.1
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_019901252.1
COORDINATES: similar to AA sequence:RefSeq:WP_003716822.1
COORDINATES: protein motif:HMM:NF028245.2
COORDINATES: similar to AA sequence:RefSeq:WP_014567995.1
COORDINATES: similar to AA sequence:RefSeq:WP_002825823.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012870.2
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF024908.2
COORDINATES: protein motif:HMM:NF033516.0
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 - cation transport [Evidence IEA]
glycoside-pentoside-hexuronide (GPH):cation symporter
COORDINATES: similar to AA sequence:RefSeq:WP_003660036.1
COORDINATES: protein motif:HMM:NF013235.2
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_012211205.1
COORDINATES: similar to AA sequence:RefSeq:WP_020807835.1