Paucilactobacillus hokkaidonensis JCM 18461 strain LOOC260 plasmid pLOOC260-2, complete sequence.
Paucilactobacillus hokkaidonensis JCM 18461
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Paucilactobacillus.
Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260(T), a psychrotrophic lactic acid bacterium isolated from silage
DOI:10.1186/s12864-015-1435-2 Publication Status: Online-Only
Submitted (10-NOV-2014) Contact:Masanori Tohno National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Animal Feeding and Management Research Division; Senbonmatsu 768, Nasushiobara, Tochigi 329-2793, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP014682.1.\nAnnotated by GenomeRefine.\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 :: HGAP SMRTAnalysis v. 2.1\nGenome Coverage :: 300X\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/12/2023 15:05:52\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) :: 2,388\nCDSs (total) :: 2,316\nGenes (coding) :: 2,277\nCDSs (with protein) :: 2,277\nGenes (RNA) :: 72\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 56\nncRNAs :: 4\nPseudo Genes (total) :: 39\nCDSs (without protein) :: 39\nPseudo Genes (ambiguous residues) :: 0 of 39\nPseudo Genes (frameshifted) :: 12 of 39\nPseudo Genes (incomplete) :: 24 of 39\nPseudo Genes (internal stop) :: 7 of 39\nPseudo Genes (multiple problems) :: 4 of 39\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Lactobacillus hokkaidonensis
COORDINATES: similar to AA sequence:RefSeq:WP_005728424.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003691009.1
COORDINATES: similar to AA sequence:RefSeq:WP_014567980.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_003603789.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552807.1
COORDINATES: similar to AA sequence:RefSeq:WP_003603791.1
COORDINATES: similar to AA sequence:RefSeq:WP_008212308.1
COORDINATES: similar to AA sequence:RefSeq:WP_003680239.1
COORDINATES: similar to AA sequence:RefSeq:WP_016370337.1
CagC family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_014216295.1
COORDINATES: similar to AA sequence:RefSeq:WP_016381866.1
TrsD/TraD family conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_003680243.1
COORDINATES: similar to AA sequence:RefSeq:WP_016370339.1
COORDINATES: similar to AA sequence:RefSeq:WP_003680247.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552815.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552816.1
COORDINATES: similar to AA sequence:RefSeq:WP_003712734.1
COORDINATES: similar to AA sequence:RefSeq:WP_007745068.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003660147.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552820.1
COORDINATES: similar to AA sequence:RefSeq:WP_002825296.1
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_015474742.1
COORDINATES: similar to AA sequence:RefSeq:WP_002346505.1
COORDINATES: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019770252.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006293513.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006293512.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014567995.1
COORDINATES: similar to AA sequence:RefSeq:WP_002286155.1
COORDINATES: similar to AA sequence:RefSeq:WP_003680400.1
COORDINATES: similar to AA sequence:RefSeq:WP_011681376.1
COORDINATES: similar to AA sequence:RefSeq:WP_014608508.1
COORDINATES: protein motif:HMM:NF033516.0
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_013355080.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF015431.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011101506.1
COORDINATES: similar to AA sequence:RefSeq:WP_053338758.1
IS30-like element ISLpl1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_010010724.1
GlsB/YeaQ/YmgE family stress response membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_010010721.1
COORDINATES: similar to AA sequence:RefSeq:WP_016511608.1
GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF037206.2
S-4TM family putative pore-forming effector
COORDINATES: similar to AA sequence:RefSeq:WP_016527412.1
COORDINATES: similar to AA sequence:RefSeq:WP_016370331.1
COORDINATES: similar to AA sequence:RefSeq:WP_010492166.1