Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 plasmid pAACI02, complete sequence.
Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
Bacteria; Bacillota; Bacilli; Bacillales; Alicyclobacillaceae; Alicyclobacillus.
Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA)
The complete plasmid2 of Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
Submitted (03-SEP-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001729.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4083332\nSource DNA and organism available from Hans-Peter Klenk at the\nGerman Collection of Microorganisms and Cell Cultures (DSMZ)\n(hans-peter.klenk@dsmz.de)\nContacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-LANL\nAnnotation by JGI-ORNL and JGI-PGF\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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##Metadata-START##\nOrganism Display Name :: Alicyclobacillus acidocaldarius\n acidocaldarius 104-IA, DSM 446\nCulture Collection ID :: DSM 446, ATCC 27009\nGOLD Stamp ID :: Gi02324\nFunding Program :: DOE-GEBA 2007\nGene Calling Method :: GeneMark\nIsolation Site :: \"Yellowstone National Park, acid hot\n spring\"\nIsolation Country :: USA\nLatitude :: 44.376262\nLongitude :: -110.690383\nOxygen Requirement :: Aerobe\nCell Shape :: Rod-shaped\nSporulation :: Sporulating\nTemperature Range :: Thermophile\nTemperature Optimum :: 60C\npH :: 3 - 4\nGram Staining :: gram+\nBiotic Relationship :: Free living\nDiseases :: None\nPhenotypes :: Thermoacidophile\nEnergy Source :: Chemoorganotroph\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/02/2023 01:38:04\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) :: 3,188\nCDSs (total) :: 3,104\nGenes (coding) :: 3,066\nCDSs (with protein) :: 3,066\nGenes (RNA) :: 84\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 62\nncRNAs :: 4\nPseudo Genes (total) :: 38\nCDSs (without protein) :: 38\nPseudo Genes (ambiguous residues) :: 0 of 38\nPseudo Genes (frameshifted) :: 11 of 38\nPseudo Genes (incomplete) :: 28 of 38\nPseudo Genes (internal stop) :: 7 of 38\nPseudo Genes (multiple problems) :: 8 of 38\nCRISPR Arrays :: 4\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Alicyclobacillus acidocaldarius
COORDINATES: similar to AA sequence:RefSeq:WP_012810838.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
sigma factor-like helix-turn-helix DNA-binding protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF025574.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012812175.1
COORDINATES: protein motif:HMM:NF017528.2
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_012810609.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014463046.1
COORDINATES: protein motif:HMM:NF014717.2
COORDINATES: similar to AA sequence:RefSeq:WP_020619816.1
GO:0005515 - protein binding [Evidence IEA]
ankyrin repeat domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012809937.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016428646.1
COORDINATES: protein motif:HMM:NF024835.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF017273.2
COORDINATES: similar to AA sequence:RefSeq:WP_008340285.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012812186.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008340296.1
GO:0009847 - spore germination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012812190.1
Ger(x)C family spore germination C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008340299.1
COORDINATES: similar to AA sequence:RefSeq:WP_012812191.1
COORDINATES: protein motif:HMM:NF024816.2
COORDINATES: nucleotide motif:Rfam:14.4:RF01051
cyclic di-GMP riboswitch class I; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF015894.2
COORDINATES: similar to AA sequence:RefSeq:WP_008340306.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012812195.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008340309.1
COORDINATES: similar to AA sequence:RefSeq:WP_006285559.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013985376.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013985377.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008341598.1
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_012810502.1
gamma-glutamylcyclotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008341603.1
COORDINATES: similar to AA sequence:RefSeq:WP_008341590.1
COORDINATES: similar to AA sequence:RefSeq:WP_008341588.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809972.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809973.1
COORDINATES: protein motif:HMM:NF015947.2
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008340688.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008340687.1
COORDINATES: similar to AA sequence:RefSeq:WP_008341320.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014465167.1
COORDINATES: similar to AA sequence:RefSeq:WP_012810538.1
COORDINATES: similar to AA sequence:RefSeq:WP_012812214.1
COORDINATES: similar to AA sequence:RefSeq:WP_008340681.1
COORDINATES: similar to AA sequence:RefSeq:WP_012812217.1
COORDINATES: similar to AA sequence:RefSeq:WP_012812218.1
COORDINATES: similar to AA sequence:RefSeq:WP_008340677.1
COORDINATES: similar to AA sequence:RefSeq:WP_008340676.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809985.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809986.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809987.1
COORDINATES: similar to AA sequence:RefSeq:WP_008340672.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809989.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809990.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809991.1
COORDINATES: similar to AA sequence:RefSeq:WP_008340667.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809993.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809995.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809996.1
COORDINATES: similar to AA sequence:RefSeq:WP_012809997.1
COORDINATES: similar to AA sequence:RefSeq:WP_012812234.1
COORDINATES: similar to AA sequence:RefSeq:WP_008340658.1
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: similar to AA sequence:RefSeq:WP_012809566.1
COORDINATES: similar to AA sequence:RefSeq:WP_008340656.1
COORDINATES: similar to AA sequence:RefSeq:WP_012812238.1
COORDINATES: similar to AA sequence:RefSeq:WP_012810003.1
COORDINATES: similar to AA sequence:RefSeq:WP_012812241.1
COORDINATES: similar to AA sequence:RefSeq:WP_008340645.1
COORDINATES: similar to AA sequence:RefSeq:WP_008340644.1
COORDINATES: similar to AA sequence:RefSeq:WP_008340643.1
COORDINATES: similar to AA sequence:RefSeq:WP_008340641.1
COORDINATES: similar to AA sequence:RefSeq:WP_012810009.1
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012810010.1
COORDINATES: similar to AA sequence:RefSeq:WP_012812248.1
COORDINATES: similar to AA sequence:RefSeq:WP_008341335.1
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012810015.1