Lactococcus raffinolactis strain WiKim0068 plasmid pWiKim0068-2, 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\nCP023394.1.\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_010052224.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016174521.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010018019.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558031.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [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_011834662.1
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_015426184.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]; GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
type I restriction endonuclease subunit R
COORDINATES: similar to AA sequence:RefSeq:WP_015082072.1
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_002323630.1
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0004518 - nuclease activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_014125701.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012920.2
COORDINATES: similar to AA sequence:RefSeq:WP_011669134.1
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_011669088.1
COORDINATES: similar to AA sequence:RefSeq:WP_001284805.1
COORDINATES: similar to AA sequence:RefSeq:WP_012477736.1
GO:0004803 - transposase activity [Evidence IEA]
IS6-like element ISS1N family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_014093787.1
COORDINATES: similar to AA sequence:RefSeq:WP_014093788.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: protein motif:HMM:NF024908.2
COORDINATES: similar to AA sequence:RefSeq:WP_002962809.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002265614.1
COORDINATES: similar to AA sequence:RefSeq:WP_002295591.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [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:NF024754.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010052215.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005605877.1
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018165022.1
ABC transporter substrate-binding protein