Companilactobacillus alimentarius DSM 20249 plasmid pLDW-11, complete sequence.
Companilactobacillus alimentarius DSM 20249
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Companilactobacillus.
The whole genome sequencing and assembly of Lactobacillus alimentarius DSM 20249T strain
Submitted (20-DEC-2016) Kyungpook National University, School of Applied Biosciences, 80 Daehak-Ro, Bukgu, Daegu 41566, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP018868.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: SMRT analysis 2.3 v. HGAP protocol 2\nGenome Coverage :: 261.51\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 07:20:35\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) :: 2,344\nCDSs (total) :: 2,274\nGenes (coding) :: 2,249\nCDSs (with protein) :: 2,249\nGenes (RNA) :: 70\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 3\nPseudo Genes (total) :: 25\nCDSs (without protein) :: 25\nPseudo Genes (ambiguous residues) :: 0 of 25\nPseudo Genes (frameshifted) :: 20 of 25\nPseudo Genes (incomplete) :: 7 of 25\nPseudo Genes (internal stop) :: 2 of 25\nPseudo Genes (multiple problems) :: 4 of 25\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Lactobacillus alimentarius
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
CagC family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_003680239.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016526684.1
COORDINATES: similar to AA sequence:RefSeq:WP_003660197.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013729135.1
frameshifted; 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_007124583.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
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]
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010014830.1
COORDINATES: similar to AA sequence:RefSeq:WP_003712273.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002825830.1
COORDINATES: similar to AA sequence:RefSeq:WP_013729126.1
COORDINATES: similar to AA sequence:RefSeq:WP_002825823.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010499758.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002328814.1
COORDINATES: similar to AA sequence:RefSeq:WP_015639662.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
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_013727908.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF033550.5
COORDINATES: similar to AA sequence:RefSeq:WP_010499751.1
COORDINATES: similar to AA sequence:RefSeq:WP_010499750.1
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_003554089.1
GlsB/YeaQ/YmgE family stress response membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_053338758.1
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_012477736.1
COORDINATES: similar to AA sequence:RefSeq:WP_011101558.1
GO:0019812 - type I site-specific deoxyribonuclease complex [Evidence IEA]
GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
HsdR family type I site-specific deoxyribonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_003603853.1
GO:0015666 - restriction endodeoxyribonuclease activity [Evidence IEA]; GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]; GO:0009307 - DNA restriction-modification system [Evidence IEA]
type I restriction-modification system subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_005693055.1
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: protein motif:HMM:NF028245.2
COORDINATES: similar to AA sequence:RefSeq:WP_002346505.1
COORDINATES: similar to AA sequence:RefSeq:WP_015474742.1
COORDINATES: similar to AA sequence:RefSeq:WP_002825295.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002825296.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552820.1
COORDINATES: similar to AA sequence:RefSeq:WP_003660147.1
COORDINATES: similar to AA sequence:RefSeq:WP_003712736.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003660141.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552816.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552815.1
COORDINATES: similar to AA sequence:RefSeq:WP_003680247.1
COORDINATES: similar to AA sequence:RefSeq:WP_016370339.1
COORDINATES: similar to AA sequence:RefSeq:WP_003680243.1
COORDINATES: similar to AA sequence:RefSeq:WP_016381866.1
TrsD/TraD family conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_014216295.1
COORDINATES: similar to AA sequence:RefSeq:WP_016370337.1
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_014386872.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF037926.2