Paucilactobacillus hokkaidonensis JCM 18461 strain LOOC260 plasmid pLOOC260-1, 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\nAP014681.1.\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_014386895.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
primase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010625604.1
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_010620841.1
COORDINATES: similar to AA sequence:RefSeq:WP_005917937.1
COORDINATES: similar to AA sequence:RefSeq:WP_003625288.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010625626.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_002287733.1
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_013102104.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
polysaccharide deacetylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_053338758.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS30-like element ISLpl1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_005470367.1
ATP-dependent Clp protease ATP-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_014081502.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF021048.2
COORDINATES: similar to AA sequence:RefSeq:WP_010078380.1
COORDINATES: similar to AA sequence:RefSeq:WP_016526818.1
COORDINATES: similar to AA sequence:RefSeq:WP_011222049.1
COORDINATES: similar to AA sequence:RefSeq:WP_003582117.1
COORDINATES: similar to AA sequence:RefSeq:WP_003582114.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_016368213.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0015446 - ATPase-coupled arsenite transmembrane transporter activity [Evidence IEA]
GO:0071722 - detoxification of arsenic-containing substance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003682896.1
COORDINATES: similar to AA sequence:RefSeq:WP_013721068.1
arsenite efflux transporter metallochaperone ArsD
COORDINATES: similar to AA sequence:RefSeq:WP_004563097.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016148.2
GO:0044423 - virion component [Evidence IEA]
GO:0016032 - viral process [Evidence IEA]; GO:0019068 - virion assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003568375.1
GlsB/YeaQ/YmgE family stress response membrane protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_016511901.1
COORDINATES: similar to AA sequence:RefSeq:WP_016511900.1
COORDINATES: similar to AA sequence:RefSeq:WP_013727908.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_050892470.1
COORDINATES: similar to AA sequence:RefSeq:WP_002831190.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014569952.1
COORDINATES: similar to AA sequence:RefSeq:WP_010011975.1
COORDINATES: similar to AA sequence:RefSeq:WP_010011974.1
COORDINATES: similar to AA sequence:RefSeq:WP_010012445.1
GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013355080.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF033550.5
COORDINATES: similar to AA sequence:RefSeq:WP_006499503.1
COORDINATES: similar to AA sequence:RefSeq:WP_010623286.1
COORDINATES: similar to AA sequence:RefSeq:WP_010623287.1
COORDINATES: similar to AA sequence:RefSeq:WP_002989480.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552803.1
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_005693113.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002823700.1
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_016511122.1
COORDINATES: similar to AA sequence:RefSeq:WP_002825295.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
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:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_011373852.1
COORDINATES: similar to AA sequence:RefSeq:WP_010491919.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0015225 - biotin transmembrane transporter activity [Evidence IEA]
GO:0015878 - biotin transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014214630.1
COORDINATES: similar to AA sequence:RefSeq:WP_003559611.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010022514.1
COORDINATES: protein motif:HMM:NF012759.2
COORDINATES: similar to AA sequence:RefSeq:WP_014082430.1
COORDINATES: similar to AA sequence:RefSeq:WP_012212322.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003625246.1
GO:0004315 - 3-oxoacyl-[acyl-carrier-protein] synthase activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010738136.1
acetyl-CoA carboxylase biotin carboxyl carrier protein subunit
COORDINATES: protein motif:HMM:NF019589.2
3-hydroxyacyl-ACP dehydratase FabZ family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011475767.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
acetyl-CoA carboxylase biotin carboxylase subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011667652.1
acetyl-CoA carboxylase carboxyltransferase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_003640418.1
GO:0009317 - acetyl-CoA carboxylase complex [Evidence IEA]
GO:0016743 - carboxyl- or carbamoyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008842116.1
COORDINATES: protein motif:HMM:TIGR00121.1
GO:0004077 - biotin-[acetyl-CoA-carboxylase] ligase activity [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: protein motif:HMM:NF016174.2
COORDINATES: similar to AA sequence:RefSeq:WP_013727994.1
COORDINATES: similar to AA sequence:RefSeq:WP_003631123.1
COORDINATES: similar to AA sequence:RefSeq:WP_013439000.1
COORDINATES: similar to AA sequence:RefSeq:WP_016371047.1
Asp23/Gls24 family envelope stress response protein
COORDINATES: similar to AA sequence:RefSeq:WP_003681705.1
COORDINATES: similar to AA sequence:RefSeq:WP_010493334.1
alkaline shock response membrane anchor protein AmaP
COORDINATES: similar to AA sequence:RefSeq:WP_014567995.1
COORDINATES: similar to AA sequence:RefSeq:WP_002825823.1
COORDINATES: similar to AA sequence:RefSeq:WP_011668997.1
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_003561734.1
COORDINATES: similar to AA sequence:RefSeq:WP_003554903.1
GO:0004751 - ribose-5-phosphate isomerase activity [Evidence IEA]
GO:0009052 - pentose-phosphate shunt, non-oxidative branch [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020090467.1
COORDINATES: similar to AA sequence:RefSeq:WP_017260795.1
COORDINATES: similar to AA sequence:RefSeq:WP_005919347.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010013316.1
COORDINATES: similar to AA sequence:RefSeq:WP_015474649.1
COORDINATES: similar to AA sequence:RefSeq:WP_003687813.1
COORDINATES: similar to AA sequence:RefSeq:WP_002823637.1
COORDINATES: similar to AA sequence:RefSeq:WP_011668824.1
COORDINATES: similar to AA sequence:RefSeq:WP_020090441.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_020090442.1
COORDINATES: similar to AA sequence:RefSeq:WP_003639769.1
DNA starvation/stationary phase protection protein
COORDINATES: protein motif:HMM:NF019322.2
COORDINATES: similar to AA sequence:RefSeq:WP_012491695.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014216285.1
COORDINATES: similar to AA sequence:RefSeq:WP_000769533.1