Lactococcus raffinolactis strain WiKim0068 plasmid pWiKim0068-1, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Streptococcaceae; Lactococcus.
Complete genome sequence of Lactococcus raffinolactis WiKim0068
Submitted (11-SEP-2017) Microbiology and Functionality Research Group, World Institute of Kimchi, 86 Kimchi-Ro, Nam-Gu, Gwangju 61755, Republic of Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP023393.1.\nBacteria and source DNA available from World Institute of Kimchi.\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##Assembly-Data-START##\nAssembly Method :: HGAP v. 3.0\nSequencing Technology :: PacBio\n##Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/23/2023 02:34:29\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,283\nCDSs (total) :: 2,212\nGenes (coding) :: 2,161\nCDSs (with protein) :: 2,161\nGenes (RNA) :: 71\nrRNAs :: 5, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 4, 4 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 3\nPseudo Genes (total) :: 51\nCDSs (without protein) :: 51\nPseudo Genes (ambiguous residues) :: 0 of 51\nPseudo Genes (frameshifted) :: 15 of 51\nPseudo Genes (incomplete) :: 33 of 51\nPseudo Genes (internal stop) :: 13 of 51\nPseudo Genes (multiple problems) :: 10 of 51\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_010868911.1
GO:0004803 - transposase activity [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000126416.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012477736.1
IS6-like element ISS1N family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_064305258.1
COORDINATES: similar to AA sequence:RefSeq:WP_015426478.1
COORDINATES: similar to AA sequence:RefSeq:WP_017370594.1
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_014011543.1
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_011835140.1
GlsB/YeaQ/YmgE family stress response membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_003131013.1
alkaline shock response membrane anchor protein AmaP
COORDINATES: similar to AA sequence:RefSeq:WP_011835142.1
COORDINATES: similar to AA sequence:RefSeq:WP_004256348.1
Asp23/Gls24 family envelope stress response 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_017865271.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017865329.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011669095.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_017865327.1
GO:0008961 - phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activity [Evidence IEA]
GO:0009249 - protein lipoylation [Evidence IEA]
prolipoprotein diacylglyceryl transferase
COORDINATES: similar to AA sequence:RefSeq:WP_011669097.1
COORDINATES: similar to AA sequence:RefSeq:WP_011669041.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558257.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010905590.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0015662 - P-type ion transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003590746.1
COORDINATES: similar to AA sequence:RefSeq:WP_009490494.1
COORDINATES: similar to AA sequence:RefSeq:WP_003139719.1
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_003139721.1
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002389461.1
COORDINATES: protein motif:HMM:NF013431.2
GO:0030246 - carbohydrate binding [Evidence IEA]; GO:0016857 - racemase and epimerase activity, acting on carbohydrates and derivatives [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012870.2
GO:0015074 - DNA integration [Evidence IEA]
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004903833.1
COORDINATES: similar to AA sequence:RefSeq:WP_003137758.1
COORDINATES: similar to AA sequence:RefSeq:WP_019292892.1
GO:0008801 - beta-phosphoglucomutase activity [Evidence IEA]
GO:0046352 - disaccharide catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002363316.1
GO:0015144 - carbohydrate transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002342391.1
endonuclease/exonuclease/phosphatase family protein
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
type I toxin-antitoxin system toxin PepG1
IS6-like element IS1216 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_000931877.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014294099.1
GO:0005971 - ribonucleoside-diphosphate reductase complex [Evidence IEA]
GO:0030145 - manganese ion binding [Evidence IEA]; GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
GO:0009265 - 2'-deoxyribonucleotide biosynthetic process [Evidence IEA]
class 1b ribonucleoside-diphosphate reductase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_004182514.1
GO:0016684 - oxidoreductase activity, acting on peroxide as acceptor [Evidence IEA]; GO:0008379 - thioredoxin peroxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011915235.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
GO:0009263 - deoxyribonucleotide biosynthetic process [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]
ribonucleotide-diphosphate reductase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_017865351.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
class 1b ribonucleoside-diphosphate reductase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_014294095.1
class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI
COORDINATES: similar to AA sequence:RefSeq:WP_004234906.1
GO:0030552 - cAMP binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Crp/Fnr family transcriptional regulator
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007123752.1
GO:0016787 - hydrolase activity [Evidence IEA]