Loigolactobacillus bifermentans strain LB003 plasmid unnamed1, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Loigolactobacillus.
Genome sequencing of Lactobacillus bifermentans
Submitted (04-NOV-2019) College of Health Science, Korea University, Anam-ro 145, Seoul 02841, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP045873.1.\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 :: PacBio SMRT Analysis v. v2.3\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 284.03x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/17/2023 01:33:58\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) :: 3,233\nCDSs (total) :: 3,145\nGenes (coding) :: 3,102\nCDSs (with protein) :: 3,102\nGenes (RNA) :: 88\nrRNAs :: 5, 6, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 6, 5 (5S, 16S, 23S)\ntRNAs :: 68\nncRNAs :: 4\nPseudo Genes (total) :: 43\nCDSs (without protein) :: 43\nPseudo Genes (ambiguous residues) :: 0 of 43\nPseudo Genes (frameshifted) :: 14 of 43\nPseudo Genes (incomplete) :: 25 of 43\nPseudo Genes (internal stop) :: 9 of 43\nPseudo Genes (multiple problems) :: 5 of 43\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_005717330.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005717323.1
COORDINATES: similar to AA sequence:RefSeq:WP_002328814.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014216312.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF020248.2
COORDINATES: similar to AA sequence:RefSeq:WP_003600575.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_014216313.1
COORDINATES: similar to AA sequence:RefSeq:WP_003660060.1
COORDINATES: similar to AA sequence:RefSeq:WP_002820395.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007122293.1
COORDINATES: similar to AA sequence:RefSeq:WP_005717332.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_005717331.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011674065.1
COORDINATES: similar to AA sequence:RefSeq:WP_011674067.1
COORDINATES: similar to AA sequence:RefSeq:WP_020090532.1
COORDINATES: similar to AA sequence:RefSeq:WP_010010558.1
COORDINATES: similar to AA sequence:RefSeq:WP_015509373.1
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_013355080.1
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010623509.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008986 - pyruvate, water dikinase activity [Evidence IEA]; GO:0016772 - transferase activity, transferring phosphorus-containing groups [Evidence IEA]
GO:0016310 - phosphorylation [Evidence IEA]; GO:0006090 - pyruvate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011373852.1
IS30-like element ISLsa1 family transposase
COORDINATES: protein motif:HMM:NF024673.2
COORDINATES: similar to AA sequence:RefSeq:WP_004270929.1
COORDINATES: similar to AA sequence:RefSeq:WP_013858482.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010619271.1
COORDINATES: similar to AA sequence:RefSeq:WP_010619272.1
COORDINATES: protein motif:HMM:NF013431.2
COORDINATES: similar to AA sequence:RefSeq:WP_003670263.1
GO:0008801 - beta-phosphoglucomutase activity [Evidence IEA]
GO:0046352 - disaccharide catabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013753.2
COORDINATES: similar to AA sequence:RefSeq:WP_053338758.1
IS30-like element ISLpl1 family transposase
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015638851.1
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_012552803.1
frameshifted; 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_003680947.1
COORDINATES: similar to AA sequence:RefSeq:WP_015638790.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF036540.2
COORDINATES: similar to AA sequence:RefSeq:WP_004563097.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013721068.1
arsenite efflux transporter metallochaperone ArsD
COORDINATES: similar to AA sequence:RefSeq:WP_003682896.1
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_003582114.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_003582117.1
COORDINATES: similar to AA sequence:RefSeq:WP_011222049.1
COORDINATES: similar to AA sequence:RefSeq:WP_003603789.1
COORDINATES: similar to AA sequence:RefSeq:WP_013729135.1
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]
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: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003603852.1
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: protein motif:HMM:NF024573.2
COORDINATES: similar to AA sequence:RefSeq:WP_003679562.1
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_016374492.1
COORDINATES: similar to AA sequence:RefSeq:WP_016511608.1
GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013727994.1
COORDINATES: similar to AA sequence:RefSeq:WP_016526617.1
COORDINATES: similar to AA sequence:RefSeq:WP_003639769.1
DNA starvation/stationary phase protection protein
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
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_002286155.1
COORDINATES: similar to AA sequence:RefSeq:WP_003680400.1
COORDINATES: similar to AA sequence:RefSeq:WP_003678958.1
COORDINATES: similar to AA sequence:RefSeq:WP_017435080.1
COORDINATES: similar to AA sequence:RefSeq:WP_017261413.1
COORDINATES: similar to AA sequence:RefSeq:WP_007124940.1
TetR/AcrR family transcriptional regulator