Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393 plasmid pLBCZ-1, complete sequence.
Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Lacticaseibacillus.
Genomic adaptation of the Lactobacillus casei group
DOI:10.1371/journal.pone.0075073 Publication Status: Online-Only
Submitted (27-AUG-2012) Contact:Hidetoshi Morita Azabu University, School of Veterinary Medicine; 1-17-71 Fuchinobe, Sagamihara, Kanagawa 252-5201, Japan URL :http://www.azabu-u.ac.jp/
REFSEQ INFORMATION: The reference sequence is identical to\nAP012545.1.\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 :: phrap v. 0.990329\nGenome Coverage :: 5.9x\nSequencing Technology :: 3730xl\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/12/2023 15:01:00\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) :: 2,882\nCDSs (total) :: 2,805\nGenes (coding) :: 2,646\nCDSs (with protein) :: 2,646\nGenes (RNA) :: 77\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 59\nncRNAs :: 3\nPseudo Genes (total) :: 159\nCDSs (without protein) :: 159\nPseudo Genes (ambiguous residues) :: 0 of 159\nPseudo Genes (frameshifted) :: 60 of 159\nPseudo Genes (incomplete) :: 69 of 159\nPseudo Genes (internal stop) :: 36 of 159\nPseudo Genes (multiple problems) :: 6 of 159\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_016368703.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
primase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003596745.1
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_016389114.1
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015379542.1
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_003586188.1
COORDINATES: similar to AA sequence:RefSeq:WP_012807385.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
glycoside hydrolase family 2 TIM barrel-domain containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004560356.1
COORDINATES: similar to AA sequence:RefSeq:WP_011674571.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612170.1
COORDINATES: similar to AA sequence:RefSeq:WP_011834178.1
COORDINATES: protein motif:HMM:NF018645.2
COORDINATES: similar to AA sequence:RefSeq:WP_003132622.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003590051.1
COORDINATES: similar to AA sequence:RefSeq:WP_011225851.1
PLP-dependent aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012212307.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF024673.2
COORDINATES: protein motif:HMM:NF033516.0
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS3-like element ISL1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_015474151.1
COORDINATES: similar to AA sequence:RefSeq:WP_020751798.1
COORDINATES: similar to AA sequence:RefSeq:WP_003586220.1
COORDINATES: similar to AA sequence:RefSeq:WP_019889483.1
COORDINATES: similar to AA sequence:RefSeq:WP_016363782.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_016369696.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_016388657.1
COORDINATES: similar to AA sequence:RefSeq:WP_003583182.1