Nocardia farcinica IFM 10152 plasmid pNF1, complete sequence.
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae; Nocardia.
The complete genomic sequence of Nocardia farcinica IFM 10152
Submitted (26-SEP-2003) Contact:Jun Ishikawa National Institute of Infectious Diseases; Toyama 1-23-1, Shinjuku, Tokyo 162-8640, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP006619.1.\nThis work was done in collaboration with Jun Ishikawa, Yasutaka\nHoshino, Haruyo Kurita, Kunimoto Hotta (National Institute of\nInfectious Diseases) and Yuzuru Mikami (Research Center for\nPathogenic Fungi and Microbial Toxicoses, Chiba University), and\nsupported by the Research for the Future Program of the Japan\nSociety for the Promotion of Science.\nThe genomic sequence assembly and annotation was carried out by Jun\nIshikawa (jun@nih.go.jp). The complete and fully annotated genomic\nsequence is also available at http://nocardia.nih.go.jp/\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/24/2022 02:52:16\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) :: 6,050\nCDSs (total) :: 5,984\nGenes (coding) :: 5,938\nCDSs (with protein) :: 5,938\nGenes (RNA) :: 66\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 54\nncRNAs :: 3\nPseudo Genes (total) :: 46\nCDSs (without protein) :: 46\nPseudo Genes (ambiguous residues) :: 0 of 46\nPseudo Genes (frameshifted) :: 12 of 46\nPseudo Genes (incomplete) :: 35 of 46\nPseudo Genes (internal stop) :: 3 of 46\nPseudo Genes (multiple problems) :: 4 of 46\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011767788.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005566943.1
ParB N-terminal domain-containing 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_017681129.1
COORDINATES: protein motif:HMM:NF014566.2
CPBP family intramembrane metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_019548606.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005064314.1
COORDINATES: similar to AA sequence:RefSeq:WP_019031570.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_006590978.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: protein motif:HMM:NF012464.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011212284.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212285.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212286.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212287.1
PLP-dependent cysteine synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011212288.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011212289.1
COORDINATES: similar to AA sequence:RefSeq:WP_016825555.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017565823.1
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_011212292.1
COORDINATES: protein motif:HMM:NF013088.2
COORDINATES: similar to AA sequence:RefSeq:WP_020659930.1
COORDINATES: protein motif:HMM:NF020765.2
COORDINATES: similar to AA sequence:RefSeq:WP_011780846.1
COORDINATES: similar to AA sequence:RefSeq:WP_019045662.1
COORDINATES: similar to AA sequence:RefSeq:WP_005179570.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_006902503.1
COORDINATES: similar to AA sequence:RefSeq:WP_005179567.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005179563.1
COORDINATES: similar to AA sequence:RefSeq:WP_005179560.1
COORDINATES: similar to AA sequence:RefSeq:WP_011211890.1
COORDINATES: protein motif:HMM:NF013661.2
GO:0008745 - N-acetylmuramoyl-L-alanine amidase activity [Evidence IEA]
GO:0009253 - peptidoglycan catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011558843.1
COORDINATES: similar to AA sequence:RefSeq:WP_006435987.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893708.1
COORDINATES: similar to AA sequence:RefSeq:WP_019045637.1
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019045638.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_003944602.1
COORDINATES: similar to AA sequence:RefSeq:WP_003939272.1
COORDINATES: similar to AA sequence:RefSeq:WP_007296087.1
cytochrome c biogenesis CcdA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019045002.1
COORDINATES: similar to AA sequence:RefSeq:WP_012686887.1
COORDINATES: similar to AA sequence:RefSeq:WP_016693791.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893693.1
COORDINATES: protein motif:HMM:NF016149.2
COORDINATES: protein motif:HMM:NF013594.2
COORDINATES: similar to AA sequence:RefSeq:WP_006946598.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
BlaI/MecI/CopY family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011597325.1
bifunctional SulP family inorganic anion transporter/carbonic anhydrase
COORDINATES: similar to AA sequence:RefSeq:WP_007297746.1
COORDINATES: similar to AA sequence:RefSeq:WP_014145763.1
COORDINATES: similar to AA sequence:RefSeq:WP_019045639.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211178.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331645.1
GO:0005507 - copper ion binding [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019045654.1
COORDINATES: protein motif:HMM:NF012575.2
COORDINATES: similar to AA sequence:RefSeq:WP_005322232.1
COORDINATES: similar to AA sequence:RefSeq:WP_007626258.1
Mu transposase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: protein motif:HMM:NF019913.2
COORDINATES: similar to AA sequence:RefSeq:WP_014805439.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212230.1
COORDINATES: protein motif:HMM:NF040012.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212231.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212232.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212233.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211215.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212235.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011212237.1
COORDINATES: similar to AA sequence:RefSeq:WP_016881539.1
COORDINATES: similar to AA sequence:RefSeq:WP_009299289.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247679.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007168431.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004013404.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_020171073.1
COORDINATES: protein motif:HMM:NF013382.2
COORDINATES: protein motif:HMM:NF015983.2
COORDINATES: similar to AA sequence:RefSeq:WP_014137179.1
COORDINATES: protein motif:HMM:NF003616.0
COORDINATES: protein motif:HMM:NF012905.2
COORDINATES: protein motif:HMM:NF024771.2
mandelate racemase/muconate lactonizing enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014137173.1
COORDINATES: protein motif:HMM:NF019322.2
COORDINATES: similar to AA sequence:RefSeq:WP_002622401.1
GO:0004590 - orotidine-5'-phosphate decarboxylase activity [Evidence IEA]
GO:0009220 - pyrimidine ribonucleotide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013335.2
COORDINATES: protein motif:HMM:NF040183.1
COORDINATES: protein motif:HMM:NF016070.2
COORDINATES: similar to AA sequence:RefSeq:WP_014057906.1
COORDINATES: similar to AA sequence:RefSeq:WP_019526015.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF027584.2
COORDINATES: similar to AA sequence:RefSeq:WP_005253004.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005262988.1
COORDINATES: similar to AA sequence:RefSeq:WP_005253001.1
COORDINATES: similar to AA sequence:RefSeq:WP_005252998.1
COORDINATES: similar to AA sequence:RefSeq:WP_005252996.1
COORDINATES: similar to AA sequence:RefSeq:WP_005252993.1
COORDINATES: similar to AA sequence:RefSeq:WP_020171093.1
COORDINATES: protein motif:HMM:NF013265.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007728252.1
COORDINATES: similar to AA sequence:RefSeq:WP_014987812.1
COORDINATES: similar to AA sequence:RefSeq:WP_010838469.1
COORDINATES: protein motif:HMM:NF019846.2