Secundilactobacillus malefermentans strain CBA3618 plasmid unnamed1, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Secundilactobacillus.
Genome analyses of bacteria isolated from kimchi
Submitted (14-JUN-2019) Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, Gwangju, Gwangju 61755, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP042372.1.\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/\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP v. v 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 459.16x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/24/2022 01:10:25\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 2,075\nCDSs (total) :: 1,992\nGenes (coding) :: 1,947\nCDSs (with protein) :: 1,947\nGenes (RNA) :: 83\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 64\nncRNAs :: 4\nPseudo Genes (total) :: 45\nCDSs (without protein) :: 45\nPseudo Genes (ambiguous residues) :: 0 of 45\nPseudo Genes (frameshifted) :: 14 of 45\nPseudo Genes (incomplete) :: 23 of 45\nPseudo Genes (internal stop) :: 12 of 45\nPseudo Genes (multiple problems) :: 4 of 45\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_003678450.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_002328814.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016526921.1
COORDINATES: similar to AA sequence:RefSeq:WP_053338758.1
IS30-like element ISLpl1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_004271064.1
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017866940.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004271068.1
COORDINATES: similar to AA sequence:RefSeq:WP_016612022.1
metal-sensitive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005693113.1
internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system antitoxin, RelB/DinJ family
COORDINATES: similar to AA sequence:RefSeq:WP_002823700.1
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_010620812.1
COORDINATES: similar to AA sequence:RefSeq:WP_010620813.1
COORDINATES: similar to AA sequence:RefSeq:WP_010620814.1
COORDINATES: protein motif:HMM:NF016133.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_002287843.1
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: similar to AA sequence:RefSeq:WP_004039692.1
COORDINATES: similar to AA sequence:RefSeq:WP_014563300.1
COORDINATES: similar to AA sequence:RefSeq:WP_002326559.1
COORDINATES: similar to AA sequence:RefSeq:WP_010492191.1
GO:0003934 - GTP cyclohydrolase I activity [Evidence IEA]
GO:0042559 - pteridine-containing compound biosynthetic process [Evidence IEA]; GO:0046654 - tetrahydrofolate biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013677.2
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_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
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_015639662.1
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_076611112.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003671674.1
COORDINATES: similar to AA sequence:RefSeq:WP_003631123.1
COORDINATES: similar to AA sequence:RefSeq:WP_013439000.1
GlsB/YeaQ/YmgE family stress response membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_016371047.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
Asp23/Gls24 family envelope stress response protein
COORDINATES: similar to AA sequence:RefSeq:WP_003672587.1
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_003584267.1
COORDINATES: similar to AA sequence:RefSeq:WP_019898422.1
COORDINATES: similar to AA sequence:RefSeq:WP_012491505.1
COORDINATES: similar to AA sequence:RefSeq:WP_019864080.1
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
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015474644.1
COORDINATES: similar to AA sequence:RefSeq:WP_011222016.1
COORDINATES: similar to AA sequence:RefSeq:WP_015639692.1
COORDINATES: similar to AA sequence:RefSeq:WP_016511930.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552803.1
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:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015474742.1
COORDINATES: similar to AA sequence:RefSeq:WP_002346505.1
COORDINATES: protein motif:HMM:NF028245.2
COORDINATES: similar to AA sequence:RefSeq:WP_003678449.1
CadD family cadmium resistance transporter