Alicyclobacillus dauci strain DSM 28700 plasmid unnamed1, complete sequence.
Bacteria; Bacillota; Bacilli; Bacillales; Alicyclobacillaceae; Alicyclobacillus.
Alicyclobacillus dauci DSM2870, complete genome
Submitted (31-AUG-2022) College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang, Shaanxi 712100, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP104065.1.\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 :: Canu v. v1.5; GATK v. v1.6-13\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 452.96x\nSequencing Technology :: Illumina; PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/08/2022 11:41:33\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\nGenes (total) :: 4,892\nCDSs (total) :: 4,746\nGenes (coding) :: 4,598\nCDSs (with protein) :: 4,598\nGenes (RNA) :: 146\nrRNAs :: 11, 11, 11 (5S, 16S, 23S)\ncomplete rRNAs :: 11, 11, 11 (5S, 16S, 23S)\ntRNAs :: 109\nncRNAs :: 4\nPseudo Genes (total) :: 148\nCDSs (without protein) :: 148\nPseudo Genes (ambiguous residues) :: 0 of 148\nPseudo Genes (frameshifted) :: 79 of 148\nPseudo Genes (incomplete) :: 63 of 148\nPseudo Genes (internal stop) :: 20 of 148\nPseudo Genes (multiple problems) :: 14 of 148\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF027969.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012770.2
COORDINATES: protein motif:HMM:NF036525.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017798002.1
GO:0016853 - isomerase activity [Evidence IEA]
GO:1901135 - carbohydrate derivative metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007432969.1
GO:0043801 - hexulose-6-phosphate synthase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014971144.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016765150.1
COORDINATES: similar to AA sequence:RefSeq:WP_006448281.1
GO:0009326 - formate dehydrogenase complex [Evidence IEA]
GO:0008863 - formate dehydrogenase (NAD+) activity [Evidence IEA]
GO:0015942 - formate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF019464.2
COORDINATES: similar to AA sequence:RefSeq:WP_006445825.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010074890.1
COORDINATES: protein motif:HMM:NF016203.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_003227854.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_020617607.1
GO:0005971 - ribonucleoside-diphosphate reductase complex [Evidence IEA]
GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
GO:0009265 - 2'-deoxyribonucleotide biosynthetic process [Evidence IEA]
ribonucleoside-diphosphate reductase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_010234685.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0009263 - deoxyribonucleotide biosynthetic process [Evidence IEA]
ribonucleotide-diphosphate reductase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_010601437.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010346708.1
methylated-DNA--[protein]-cysteine S-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_019119672.1
COORDINATES: protein motif:HMM:NF017015.2
COORDINATES: protein motif:HMM:NF024676.2
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_013074275.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000815862.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0004076 - biotin synthase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0009102 - biotin biosynthetic process [Evidence IEA]
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:NF015213.2
GO:0033573 - high-affinity iron permease complex [Evidence IEA]; GO:0016020 - membrane [Evidence IEA]
GO:0005381 - iron ion transmembrane transporter activity [Evidence IEA]
GO:0034755 - iron ion transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014095511.1
bile acid:sodium symporter family protein
COORDINATES: protein motif:HMM:NF016159.2
COORDINATES: similar to AA sequence:RefSeq:WP_015845212.1
COORDINATES: similar to AA sequence:RefSeq:WP_011565907.1
GO:0050570 - 4-hydroxythreonine-4-phosphate dehydrogenase activity [Evidence IEA]
GO:0008615 - pyridoxine biosynthetic process [Evidence IEA]
4-hydroxythreonine-4-phosphate dehydrogenase PdxA
COORDINATES: protein motif:HMM:NF018682.2
four-carbon acid sugar kinase family protein
COORDINATES: protein motif:HMM:NF012669.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017811671.1
GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF033547.1
COORDINATES: protein motif:HMM:NF024854.2
COORDINATES: similar to AA sequence:RefSeq:WP_013487547.1
COORDINATES: similar to AA sequence:RefSeq:WP_014642997.1
COORDINATES: similar to AA sequence:RefSeq:WP_013489921.1
GO:0004124 - cysteine synthase activity [Evidence IEA]
GO:0006535 - cysteine biosynthetic process from serine [Evidence IEA]
COORDINATES: protein motif:HMM:NF033542.1
COORDINATES: protein motif:HMM:NF013698.2
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_003182679.1
COORDINATES: similar to AA sequence:RefSeq:WP_018781828.1
COORDINATES: similar to AA sequence:RefSeq:WP_011248378.1
MerR family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013369649.1
COORDINATES: similar to AA sequence:RefSeq:WP_020614832.1
CGNR zinc finger domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011881127.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006636201.1
COORDINATES: similar to AA sequence:RefSeq:WP_019943407.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_020617899.1
COORDINATES: similar to AA sequence:RefSeq:WP_007916163.1
helix-turn-helix domain containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014650215.1
COORDINATES: similar to AA sequence:RefSeq:WP_009894511.1
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_014684053.1
COORDINATES: protein motif:HMM:NF012655.2
COORDINATES: similar to AA sequence:RefSeq:WP_019466759.1
COORDINATES: similar to AA sequence:RefSeq:WP_019119409.1
COORDINATES: protein motif:HMM:NF018431.2
COORDINATES: similar to AA sequence:RefSeq:WP_006717416.1
COORDINATES: similar to AA sequence:RefSeq:WP_017208797.1
COORDINATES: protein motif:HMM:NF019490.2
COORDINATES: similar to AA sequence:RefSeq:WP_009794449.1
glutathione-dependent formaldehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_006676595.1
COORDINATES: similar to AA sequence:RefSeq:WP_017247082.1
COORDINATES: similar to AA sequence:RefSeq:WP_000807597.1
COORDINATES: protein motif:HMM:NF016668.2
COORDINATES: similar to AA sequence:RefSeq:WP_005549376.1
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF013775.2
COORDINATES: similar to AA sequence:RefSeq:WP_018758965.1
COORDINATES: protein motif:HMM:NF012706.2
COORDINATES: similar to AA sequence:RefSeq:WP_019909369.1
COORDINATES: protein motif:HMM:NF015783.2
GO:0009847 - spore germination [Evidence IEA]
COORDINATES: protein motif:HMM:NF012673.2
COORDINATES: similar to AA sequence:RefSeq:WP_019119359.1
COORDINATES: similar to AA sequence:RefSeq:WP_019007707.1
COORDINATES: similar to AA sequence:RefSeq:WP_019913773.1
COORDINATES: similar to AA sequence:RefSeq:WP_004891988.1
fumarylacetoacetate hydrolase family protein
COORDINATES: protein motif:HMM:NF019349.2
FadR/GntR family transcriptional regulator
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF014081.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF018944.2
COORDINATES: similar to AA sequence:RefSeq:WP_012832538.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_011744160.1
COORDINATES: protein motif:HMM:NF036304.2
COORDINATES: similar to AA sequence:RefSeq:WP_019007860.1
COORDINATES: similar to AA sequence:RefSeq:WP_003545062.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF040103.1
COORDINATES: protein motif:HMM:NF025080.2
COORDINATES: similar to AA sequence:RefSeq:WP_014464595.1
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:NF014684.2
COORDINATES: protein motif:HMM:NF012235.2
sugar ABC transporter ATP-binding protein
COORDINATES: protein motif:HMM:NF024799.2
COORDINATES: similar to AA sequence:RefSeq:WP_009593218.1
COORDINATES: protein motif:HMM:NF014670.2
COORDINATES: protein motif:HMM:NF018739.2
COORDINATES: protein motif:HMM:NF019322.2
COORDINATES: protein motif:HMM:TIGR01312.1
GO:0005515 - protein binding [Evidence IEA]; GO:0004856 - xylulokinase activity [Evidence IEA]
GO:0042732 - D-xylose metabolic process [Evidence IEA]; GO:0005997 - xylulose metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF019826.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012160382.1
COORDINATES: similar to AA sequence:RefSeq:WP_013240442.1
COORDINATES: similar to AA sequence:RefSeq:WP_008410472.1
COORDINATES: protein motif:HMM:TIGR02678.1
COORDINATES: protein motif:HMM:TIGR02680.1
COORDINATES: protein motif:HMM:NF023224.2
COORDINATES: protein motif:HMM:NF014505.2
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_021296342.1
COORDINATES: protein motif:HMM:NF013984.2
GO:0004520 - endodeoxyribonuclease activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005836160.1
GO:0004521 - endoribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018759340.1
COORDINATES: protein motif:HMM:NF015735.2
COORDINATES: protein motif:HMM:NF013757.2
COORDINATES: similar to AA sequence:RefSeq:WP_003330866.1
COORDINATES: similar to AA sequence:RefSeq:WP_014464606.1
COORDINATES: protein motif:HMM:NF013706.2
COORDINATES: protein motif:HMM:NF019241.2
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019395284.1
COORDINATES: similar to AA sequence:RefSeq:WP_017729310.1
COORDINATES: protein motif:HMM:NF014625.2