Lactobacillus amylolyticus strain L5 plasmid p1, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus.
Comparative genomics of Lactobacillus amylolyticus L5 and L6 focusing on their probiotic characteristics
Submitted (21-AUG-2018) School of Food Science and Engineering, South China University of Tecnology, Wushan, Guangzhou, Guangdong 510642, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP031836.1.\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 :: SOAPdenovo v. 2; SMRT Analysis 2.3.0\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina; PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/30/2022 11:48:15\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) :: 1,669\nCDSs (total) :: 1,590\nGenes (coding) :: 1,475\nCDSs (with protein) :: 1,475\nGenes (RNA) :: 79\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 61\nncRNAs :: 3\nPseudo Genes (total) :: 115\nCDSs (without protein) :: 115\nPseudo Genes (ambiguous residues) :: 0 of 115\nPseudo Genes (frameshifted) :: 66 of 115\nPseudo Genes (incomplete) :: 55 of 115\nPseudo Genes (internal stop) :: 32 of 115\nPseudo Genes (multiple problems) :: 34 of 115\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_008472737.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
peptide ABC transporter substrate-binding 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_006351257.1
GO:0008837 - diaminopimelate epimerase activity [Evidence IEA]
GO:0009089 - lysine biosynthetic process via diaminopimelate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006351258.1
GO:0004072 - aspartate kinase activity [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF00168
Lysine riboswitch is most abundant in Firmicutes and Gammaproteobacteria where they are found upstream of a number of genes involved in lysine biosynthesis, transport and catabolism; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_012211730.1
GO:0008836 - diaminopimelate decarboxylase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003668295.1
GO:0047200 - tetrahydrodipicolinate N-acetyltransferase activity [Evidence IEA]
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_019252632.1
COORDINATES: similar to AA sequence:RefSeq:WP_003546883.1
GO:0008840 - 4-hydroxy-tetrahydrodipicolinate synthase activity [Evidence IEA]
4-hydroxy-tetrahydrodipicolinate synthase
COORDINATES: similar to AA sequence:RefSeq:WP_005718904.1
GO:0008839 - 4-hydroxy-tetrahydrodipicolinate reductase [Evidence IEA]
4-hydroxy-tetrahydrodipicolinate reductase
COORDINATES: similar to AA sequence:RefSeq:WP_006351265.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_005718906.1
GO:0004073 - aspartate-semialdehyde dehydrogenase activity [Evidence IEA]; GO:0051287 - NAD binding [Evidence IEA]; GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Evidence IEA]
GO:0008652 - amino acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003626950.1
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_004895528.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351269.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351270.1
COORDINATES: protein motif:HMM:NF013382.2
COORDINATES: similar to AA sequence:RefSeq:WP_004895952.1
COORDINATES: similar to AA sequence:RefSeq:WP_005722898.1
COORDINATES: similar to AA sequence:RefSeq:WP_003626619.1
COORDINATES: similar to AA sequence:RefSeq:WP_006352368.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007126549.1
COORDINATES: similar to AA sequence:RefSeq:WP_006352363.1
COORDINATES: similar to AA sequence:RefSeq:WP_006352362.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003628651.1
COORDINATES: protein motif:HMM:NF015679.2
COORDINATES: protein motif:HMM:NF015692.2
ADP-ribosylglycohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006352357.1
COORDINATES: similar to AA sequence:RefSeq:WP_006352355.1
(deoxy)nucleoside triphosphate pyrophosphohydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_013854075.1
COORDINATES: similar to AA sequence:RefSeq:WP_013436876.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016182950.1
COORDINATES: similar to AA sequence:RefSeq:WP_014939130.1
COORDINATES: similar to AA sequence:RefSeq:WP_006352302.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005719616.1
COORDINATES: similar to AA sequence:RefSeq:WP_006352300.1
COORDINATES: protein motif:HMM:NF024950.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014563352.1
COORDINATES: similar to AA sequence:RefSeq:WP_013641949.1
COORDINATES: protein motif:HMM:NF013539.2
GO:0097367 - carbohydrate derivative binding [Evidence IEA]
GO:1901135 - carbohydrate derivative metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013577.2
COORDINATES: protein motif:HMM:NF012948.2
LPXTG cell wall anchor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006732615.1
COORDINATES: protein motif:HMM:TIGR01167.1
GO:0009986 - cell surface [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003632732.1
COORDINATES: similar to AA sequence:RefSeq:WP_016497185.1
frameshifted; internal stop; 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:NF020523.2
COORDINATES: similar to AA sequence:RefSeq:WP_006352240.1
COORDINATES: similar to AA sequence:RefSeq:WP_006352241.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004040404.1
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011162040.1
COORDINATES: similar to AA sequence:RefSeq:WP_005719479.1
COORDINATES: similar to AA sequence:RefSeq:WP_005719477.1
COORDINATES: similar to AA sequence:RefSeq:WP_003612591.1
COORDINATES: similar to AA sequence:RefSeq:WP_014565888.1
COORDINATES: similar to AA sequence:RefSeq:WP_003547496.1
COORDINATES: similar to AA sequence:RefSeq:WP_006352252.1
Rgg/GadR/MutR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014566252.1
COORDINATES: similar to AA sequence:RefSeq:WP_005720196.1
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_006352257.1
COORDINATES: similar to AA sequence:RefSeq:WP_003547349.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211857.1
COORDINATES: protein motif:HMM:NF014035.2
COORDINATES: similar to AA sequence:RefSeq:WP_006352262.1
GO:0015658 - branched-chain amino acid transmembrane transporter activity [Evidence IEA]
GO:0015803 - branched-chain amino acid transport [Evidence IEA]
branched-chain amino acid transport system II carrier protein
COORDINATES: similar to AA sequence:RefSeq:WP_002877735.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007126429.1
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: similar to AA sequence:RefSeq:WP_013437948.1
COORDINATES: similar to AA sequence:RefSeq:WP_013437949.1
GO:0009358 - polyphosphate kinase complex [Evidence IEA]
GO:0008976 - polyphosphate kinase activity [Evidence IEA]
GO:0006799 - polyphosphate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006352269.1
COORDINATES: similar to AA sequence:RefSeq:WP_006352270.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011254509.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016120.2
COORDINATES: similar to AA sequence:RefSeq:WP_006352273.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003699301.1
COORDINATES: similar to AA sequence:RefSeq:WP_005725358.1
COORDINATES: similar to AA sequence:RefSeq:WP_008473829.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013854028.1
COORDINATES: similar to AA sequence:RefSeq:WP_008421629.1
carbon-nitrogen hydrolase family protein
CPBP family intramembrane metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_014563640.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351389.1
COORDINATES: similar to AA sequence:RefSeq:WP_005725692.1
frameshifted; internal stop; 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_006351386.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351385.1
COORDINATES: protein motif:HMM:NF037692.2
COORDINATES: similar to AA sequence:RefSeq:WP_006351381.1
COORDINATES: similar to AA sequence:RefSeq:WP_003647665.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351379.1
GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006351378.1
GO:0004077 - biotin-[acetyl-CoA-carboxylase] ligase activity [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006351377.1
COORDINATES: similar to AA sequence:RefSeq:WP_002877455.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351375.1
acetyl-CoA carboxylase carboxyltransferase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_013642350.1
GO:0009317 - acetyl-CoA carboxylase complex [Evidence IEA]
GO:0003989 - acetyl-CoA carboxylase activity [Evidence IEA]; GO:0004075 - biotin carboxylase activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
acetyl-CoA carboxylase biotin carboxylase subunit
COORDINATES: similar to AA sequence:RefSeq:WP_016183031.1
COORDINATES: similar to AA sequence:RefSeq:WP_005727254.1
GO:0003989 - acetyl-CoA carboxylase activity [Evidence IEA]
acetyl-CoA carboxylase biotin carboxyl carrier protein
COORDINATES: similar to AA sequence:RefSeq:WP_014562166.1
GO:0004315 - 3-oxoacyl-[acyl-carrier-protein] synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019251300.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351369.1
COORDINATES: similar to AA sequence:RefSeq:WP_005727260.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351367.1
COORDINATES: similar to AA sequence:RefSeq:WP_005727264.1
COORDINATES: protein motif:HMM:NF019589.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005719435.1
COORDINATES: similar to AA sequence:RefSeq:WP_013642219.1
COORDINATES: similar to AA sequence:RefSeq:WP_011161674.1
iron export ABC transporter permease subunit FetB
COORDINATES: similar to AA sequence:RefSeq:WP_007126823.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006351356.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351353.1
GO:0008661 - 1-deoxy-D-xylulose-5-phosphate synthase activity [Evidence IEA]
GO:0016114 - terpenoid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005686835.1
COORDINATES: protein motif:HMM:NF013777.2
winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007125593.1
GO:0008788 - alpha,alpha-phosphotrehalase activity [Evidence IEA]
GO:0005991 - trehalose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005729597.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003547194.1
GO:0009401 - phosphoenolpyruvate-dependent sugar phosphotransferase system [Evidence IEA]
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003650378.1
COORDINATES: protein motif:HMM:NF014841.2
COORDINATES: similar to AA sequence:RefSeq:WP_003684880.1
GO:0004084 - branched-chain-amino-acid transaminase activity [Evidence IEA]
GO:0009081 - branched-chain amino acid metabolic process [Evidence IEA]
branched-chain amino acid aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_003676214.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013702.2
lysophospholipid acyltransferase family protein
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013086240.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00380
The M-box (ykoK) riboswitch appears to function as a genetic 'off' switch that is important for maintaining magnesium homeostasis in bacteria; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_006734023.1
GO:0015444 - P-type magnesium transporter activity [Evidence IEA]
GO:0015693 - magnesium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014918760.1
COORDINATES: similar to AA sequence:RefSeq:WP_007125750.1
COORDINATES: protein motif:HMM:NF024502.2
phage integrase SAM-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009558923.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: protein motif:HMM:NF024945.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012392.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003655830.1
COORDINATES: similar to AA sequence:RefSeq:WP_006585261.1
COORDINATES: similar to AA sequence:RefSeq:WP_012845668.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: similar to AA sequence:RefSeq:WP_013642252.1
GO:0004645 - 1,4-alpha-oligoglucan phosphorylase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011161449.1
COORDINATES: similar to AA sequence:RefSeq:WP_000711263.1
COORDINATES: similar to AA sequence:RefSeq:WP_005719537.1
COORDINATES: similar to AA sequence:RefSeq:WP_013086588.1
COORDINATES: similar to AA sequence:RefSeq:WP_005719539.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013436997.1
COORDINATES: similar to AA sequence:RefSeq:WP_004897354.1
COORDINATES: similar to AA sequence:RefSeq:WP_014919164.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00050
FMN riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_005721297.1
GO:0008703 - 5-amino-6-(5-phosphoribosylamino)uracil reductase activity [Evidence IEA]; GO:0008835 - diaminohydroxyphosphoribosylaminopyrimidine deaminase activity [Evidence IEA]
bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD
COORDINATES: similar to AA sequence:RefSeq:WP_006351216.1
COORDINATES: similar to AA sequence:RefSeq:WP_005729483.1
GO:0003935 - GTP cyclohydrolase II activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006351218.1
GO:0009349 - riboflavin synthase complex [Evidence IEA]
GO:0000906 - 6,7-dimethyl-8-ribityllumazine synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006351336.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016396158.1
COORDINATES: similar to AA sequence:RefSeq:WP_005726202.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF027395.2
COORDINATES: protein motif:HMM:NF020044.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0140658 - ATP-dependent chromatin remodeler activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006351228.1
ECF-type riboflavin transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005722926.1
COORDINATES: similar to AA sequence:RefSeq:WP_003652815.1
energy-coupling factor transporter transmembrane component T
COORDINATES: similar to AA sequence:RefSeq:WP_005722311.1
COORDINATES: protein motif:HMM:NF037610.2
sterol carrier protein domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006351235.1
COORDINATES: similar to AA sequence:RefSeq:WP_008472392.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351237.1
COORDINATES: similar to AA sequence:RefSeq:WP_003647245.1
COORDINATES: protein motif:HMM:NF023805.2
COORDINATES: similar to AA sequence:RefSeq:WP_006351240.1
COORDINATES: similar to AA sequence:RefSeq:WP_007122048.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351242.1
COORDINATES: protein motif:HMM:NF024242.2
COORDINATES: similar to AA sequence:RefSeq:WP_011162277.1
COORDINATES: protein motif:HMM:NF013098.2
COORDINATES: similar to AA sequence:RefSeq:WP_006351247.1
COORDINATES: similar to AA sequence:RefSeq:WP_013854938.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013854263.1
iron-sulfur cluster biosynthesis family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006351250.1
COORDINATES: similar to AA sequence:RefSeq:WP_020807612.1
COORDINATES: similar to AA sequence:RefSeq:WP_006351252.1