Pseudonocardia autotrophica strain NBRC 12743 plasmid pPA12743CP, al1l pseudoknot.
Bacteria; Actinomycetota; Actinomycetes; Pseudonocardiales; Pseudonocardiaceae; Pseudonocardia.
Complete Genome Sequence of an Efficient Vitamin D3-Hydroxylating Bacterium, Pseudonocardia autotrophica NBRC 12743
Microbiol Resour Announc 7, e01105-18 (2018)
DOI:10.1128/MRA.01105-18 Publication Status: Online-Only
Submitted (22-AUG-2018) Contact:Tomohiro Tamura Advanced Industrial Science and Technology, Bioproduction Research Institute; 2-17-2-1, Tsukisamu-Higashi, Sapporo, Hokkaido 062-8517, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP018921.1.\nAnnotated at DFAST https://dfast.nig.ac.jp/\n\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 :: Unicycler v. 0.4.6\nGenome Coverage :: 67x\nSequencing Technology :: PacBio RS II; HiSeq PE\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/25/2022 05:01:48\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) :: 7,101\nCDSs (total) :: 7,032\nGenes (coding) :: 6,915\nCDSs (with protein) :: 6,915\nGenes (RNA) :: 69\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 53\nncRNAs :: 4\nPseudo Genes (total) :: 117\nCDSs (without protein) :: 117\nPseudo Genes (ambiguous residues) :: 0 of 117\nPseudo Genes (frameshifted) :: 22 of 117\nPseudo Genes (incomplete) :: 104 of 117\nPseudo Genes (internal stop) :: 2 of 117\nPseudo Genes (multiple problems) :: 10 of 117\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Pseudonocardia autotrophica
COORDINATES: similar to AA sequence:RefSeq:WP_014375714.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013470199.1
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012919198.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015656208.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010242855.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_018560760.1
COORDINATES: similar to AA sequence:RefSeq:WP_010142804.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558047.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020629625.1
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_005477046.1
COORDINATES: similar to AA sequence:RefSeq:WP_005449335.1
COORDINATES: similar to AA sequence:RefSeq:WP_016699795.1
cytochrome c biogenesis CcdA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010225654.1
COORDINATES: similar to AA sequence:RefSeq:WP_005443044.1
GO:0020037 - heme binding [Evidence IEA]
GO:0017004 - cytochrome complex assembly [Evidence IEA]
c-type cytochrome biogenesis protein CcsB
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013678815.1
COORDINATES: similar to AA sequence:RefSeq:WP_020502092.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009883809.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612328.1
ISL3-like element ISPfr2 family transposase
COORDINATES: protein motif:HMM:NF013672.2
polysaccharide deacetylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018334301.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558364.1
COORDINATES: similar to AA sequence:RefSeq:WP_015309541.1
COORDINATES: similar to AA sequence:RefSeq:WP_016691652.1
COORDINATES: protein motif:HMM:NF012382.2
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_013132172.1
COORDINATES: similar to AA sequence:RefSeq:WP_007268351.1
COORDINATES: protein motif:HMM:NF013915.2
GO:0005886 - plasma membrane [Evidence IEA]
GO:0008961 - phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]
prolipoprotein diacylglyceryl transferase
COORDINATES: similar to AA sequence:RefSeq:WP_013415883.1
COORDINATES: similar to AA sequence:RefSeq:WP_010225306.1
COORDINATES: protein motif:HMM:NF015763.2
COORDINATES: similar to AA sequence:RefSeq:WP_009322187.1
COORDINATES: similar to AA sequence:RefSeq:WP_007028474.1
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.
HoxN/HupN/NixA family nickel/cobalt transporter
COORDINATES: protein motif:HMM:NF013594.2
COORDINATES: similar to AA sequence:RefSeq:WP_013476078.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
BlaI/MecI/CopY family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017590119.1
COORDINATES: similar to AA sequence:RefSeq:WP_012919624.1
COORDINATES: similar to AA sequence:RefSeq:WP_018639042.1
COORDINATES: similar to AA sequence:RefSeq:WP_017982166.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010242837.1
metal-sensitive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012378072.1
COORDINATES: similar to AA sequence:RefSeq:WP_017974994.1
COORDINATES: similar to AA sequence:RefSeq:WP_010640181.1
COORDINATES: similar to AA sequence:RefSeq:WP_003964675.1
GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
GO:0042773 - ATP synthesis coupled electron transport [Evidence IEA]
NADH-quinone oxidoreductase subunit NuoK
COORDINATES: similar to AA sequence:RefSeq:WP_012378069.1
proton-conducting transporter membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003964673.1
GO:0008137 - NADH dehydrogenase (ubiquinone) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012378067.1
COORDINATES: protein motif:HMM:NF040012.1
COORDINATES: similar to AA sequence:RefSeq:WP_010242843.1
COORDINATES: similar to AA sequence:RefSeq:WP_009948226.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF013465.2
GO:0046872 - metal ion binding [Evidence IEA]
zinc ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018331503.1
COORDINATES: similar to AA sequence:RefSeq:WP_014379987.1
COORDINATES: similar to AA sequence:RefSeq:WP_012399384.1
GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: protein motif:HMM:NF015658.2
COORDINATES: protein motif:HMM:NF019009.2
type II toxin-antitoxin system CcdA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_005453798.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012921525.1
COORDINATES: protein motif:HMM:NF016432.2
COORDINATES: protein motif:HMM:NF013382.2
GO:0008168 - methyltransferase activity [Evidence IEA]
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010240311.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611184.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019930178.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; 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_015745776.1
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_014374942.1
COORDINATES: similar to AA sequence:RefSeq:WP_019814752.1
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_013676314.1
COORDINATES: similar to AA sequence:RefSeq:WP_015623809.1
COORDINATES: protein motif:HMM:NF014081.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018566151.1
COORDINATES: similar to AA sequence:RefSeq:WP_010243464.1
COORDINATES: protein motif:HMM:NF012925.2
COORDINATES: protein motif:HMM:NF018447.2
COORDINATES: similar to AA sequence:RefSeq:WP_010243472.1
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010243479.1
COORDINATES: similar to AA sequence:RefSeq:WP_010243481.1
COORDINATES: similar to AA sequence:RefSeq:WP_010243483.1
COORDINATES: similar to AA sequence:RefSeq:WP_011482123.1
COORDINATES: similar to AA sequence:RefSeq:WP_014059847.1
COORDINATES: protein motif:HMM:NF014581.2
TraM recognition domain-containing protein
COORDINATES: protein motif:HMM:NF024602.2
COORDINATES: protein motif:HMM:NF013884.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009072144.1
methyltransferase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010072853.1
COORDINATES: similar to AA sequence:RefSeq:WP_014359110.1
dTDP-4-dehydrorhamnose 3,5-epimerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018825567.1
COORDINATES: protein motif:HMM:NF015692.2
ADP-ribosylglycohydrolase family protein
COORDINATES: protein motif:HMM:NF040041.1
COORDINATES: similar to AA sequence:RefSeq:WP_003963935.1
COORDINATES: similar to AA sequence:RefSeq:WP_009324518.1
COORDINATES: similar to AA sequence:RefSeq:WP_010243407.1
COORDINATES: similar to AA sequence:RefSeq:WP_011599367.1
COORDINATES: protein motif:HMM:NF040183.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF022388.2
COORDINATES: similar to AA sequence:RefSeq:WP_013678774.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013678773.1
COORDINATES: protein motif:HMM:NF013252.2
COORDINATES: similar to AA sequence:RefSeq:WP_012687133.1
COORDINATES: protein motif:HMM:NF020332.2
COORDINATES: similar to AA sequence:RefSeq:WP_013678812.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678811.1
COORDINATES: protein motif:HMM:NF014533.2
GO:0009294 - DNA-mediated transformation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007273086.1
COORDINATES: similar to AA sequence:RefSeq:WP_007445440.1
COORDINATES: similar to AA sequence:RefSeq:WP_015620709.1
COORDINATES: similar to AA sequence:RefSeq:WP_013476016.1
COORDINATES: similar to AA sequence:RefSeq:WP_010155374.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678758.1
COORDINATES: similar to AA sequence:RefSeq:WP_007622383.1
COORDINATES: similar to AA sequence:RefSeq:WP_013021468.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678804.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678803.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678799.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678798.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678796.1
COORDINATES: nucleotide motif:Rfam:14.4:RF02276
Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF024776.2
COORDINATES: similar to AA sequence:RefSeq:WP_012184110.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678794.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678793.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678792.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678791.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678790.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678788.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007631252.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558251.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF012334.2
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_005477570.1
COORDINATES: similar to AA sequence:RefSeq:WP_019398465.1
COORDINATES: similar to AA sequence:RefSeq:WP_020171041.1
COORDINATES: similar to AA sequence:RefSeq:WP_016663615.1
COORDINATES: similar to AA sequence:RefSeq:WP_016663614.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]
GO:0015716 - organic phosphonate transport [Evidence IEA]
phosphonate ABC transporter, permease protein PhnE
COORDINATES: similar to AA sequence:RefSeq:WP_019174193.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0043168 - anion binding [Evidence IEA]; GO:0043225 - ATPase-coupled inorganic anion transmembrane transporter activity [Evidence IEA]
phosphate/phosphite/phosphonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_019174194.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
phosphonate ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_019481141.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
GO:0019700 - organic phosphonate catabolic process [Evidence IEA]
alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase
COORDINATES: similar to AA sequence:RefSeq:WP_019157845.1
COORDINATES: similar to AA sequence:RefSeq:WP_017838565.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678786.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678785.1
COORDINATES: similar to AA sequence:RefSeq:WP_013678784.1
COORDINATES: similar to AA sequence:RefSeq:WP_005437661.1
COORDINATES: similar to AA sequence:RefSeq:WP_010223943.1
COORDINATES: similar to AA sequence:RefSeq:WP_010234775.1
COORDINATES: similar to AA sequence:RefSeq:WP_010692749.1
COORDINATES: similar to AA sequence:RefSeq:WP_013673498.1
COORDINATES: protein motif:HMM:NF012780.2
COORDINATES: protein motif:HMM:NF012790.2
COORDINATES: protein motif:HMM:NF015216.2
COORDINATES: similar to AA sequence:RefSeq:WP_019050318.1
COORDINATES: similar to AA sequence:RefSeq:WP_012890904.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558246.1
COORDINATES: similar to AA sequence:RefSeq:WP_003860195.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558310.1
COORDINATES: protein motif:HMM:NF024803.2
COORDINATES: similar to AA sequence:RefSeq:WP_014743120.1
COORDINATES: similar to AA sequence:RefSeq:WP_009199359.1
COORDINATES: similar to AA sequence:RefSeq:WP_017581277.1
ArsO family NAD(P)H-dependent flavin-containing monooxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_005086315.1
low molecular weight phosphatase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017987828.1
COORDINATES: similar to AA sequence:RefSeq:WP_015780516.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010312188.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_007297994.1
PstS family phosphate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018788040.1
GO:0015415 - ATPase-coupled phosphate ion transmembrane transporter activity [Evidence IEA]
phosphate ABC transporter permease subunit PstC
COORDINATES: similar to AA sequence:RefSeq:WP_017201969.1
COORDINATES: similar to AA sequence:RefSeq:WP_018792047.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0015415 - ATPase-coupled phosphate ion transmembrane transporter activity [Evidence IEA]
phosphate ABC transporter ATP-binding protein PstB
COORDINATES: protein motif:HMM:NF012698.2
winged helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF033788.1
COORDINATES: similar to AA sequence:RefSeq:WP_010234874.1
COORDINATES: similar to AA sequence:RefSeq:WP_011558567.1
COORDINATES: similar to AA sequence:RefSeq:WP_019069622.1
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:NF014618.2
COORDINATES: similar to AA sequence:RefSeq:WP_014911471.1
COORDINATES: similar to AA sequence:RefSeq:WP_005464996.1
COORDINATES: similar to AA sequence:RefSeq:WP_019855543.1
COORDINATES: similar to AA sequence:RefSeq:WP_010226892.1
COORDINATES: protein motif:HMM:NF016107.2
COORDINATES: similar to AA sequence:RefSeq:WP_011558878.1
COORDINATES: similar to AA sequence:RefSeq:WP_007296048.1
COORDINATES: similar to AA sequence:RefSeq:WP_010242892.1
COORDINATES: similar to AA sequence:RefSeq:WP_003880970.1
COORDINATES: protein motif:HMM:NF015581.2
COORDINATES: similar to AA sequence:RefSeq:WP_009154804.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939517.1
COORDINATES: similar to AA sequence:RefSeq:WP_018772539.1
COORDINATES: similar to AA sequence:RefSeq:WP_011293501.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017679402.1
COORDINATES: similar to AA sequence:RefSeq:WP_019873149.1
COORDINATES: similar to AA sequence:RefSeq:WP_005465523.1
COORDINATES: protein motif:HMM:NF020123.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010244109.1
COORDINATES: similar to AA sequence:RefSeq:WP_010244107.1
COORDINATES: protein motif:HMM:TIGR01695.1
GO:0034204 - lipid translocation [Evidence IEA]; GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
murein biosynthesis integral membrane protein MurJ
COORDINATES: protein motif:HMM:NF012792.2
COORDINATES: similar to AA sequence:RefSeq:WP_009945061.1
COORDINATES: similar to AA sequence:RefSeq:WP_020660280.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012686849.1
PLP-dependent cysteine synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010242849.1
COORDINATES: similar to AA sequence:RefSeq:WP_013475518.1