Sphingomonas naphthae strain KACC 18716 plasmid unnamed1, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas.
Genome sequence of Sphingomonas naphthae
Submitted (02-FEB-2023) Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, 166, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP117412.1.\nBacteria and source DNA available from Korean Agricultural Culture\nCollection (KACC).\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 :: HiFiasm v. 0.16.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 542.0x\nSequencing Technology :: PacBio Sequel; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/13/2023 19:21:37\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) :: 4,196\nCDSs (total) :: 4,140\nGenes (coding) :: 4,102\nCDSs (with protein) :: 4,102\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 38\nCDSs (without protein) :: 38\nPseudo Genes (ambiguous residues) :: 0 of 38\nPseudo Genes (frameshifted) :: 14 of 38\nPseudo Genes (incomplete) :: 25 of 38\nPseudo Genes (internal stop) :: 4 of 38\nPseudo Genes (multiple problems) :: 5 of 38\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_017183571.1
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]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004212870.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007406847.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039112.1
COORDINATES: similar to AA sequence:RefSeq:WP_011608154.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_043766072.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213258.1
GDCCVxC domain-containing (seleno)protein
COORDINATES: protein motif:HMM:NF014465.2
mercuric transporter MerT family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017980798.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980797.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017980796.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188993.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Cu(I)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010219218.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017980793.1
COORDINATES: similar to AA sequence:RefSeq:WP_020486672.1
COORDINATES: similar to AA sequence:RefSeq:WP_007407020.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017980790.1
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017980789.1
GO:0006825 - copper ion transport [Evidence IEA]
copper homeostasis membrane protein CopD
COORDINATES: similar to AA sequence:RefSeq:WP_010165216.1
GO:0042597 - periplasmic space [Evidence IEA]
GO:0005507 - copper ion binding [Evidence IEA]
copper homeostasis periplasmic binding protein CopC
COORDINATES: similar to AA sequence:RefSeq:WP_019368249.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219223.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251214.1
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_017980784.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0005375 - copper ion transmembrane transporter activity [Evidence IEA]
copper resistance system multicopper oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_010219226.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980781.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980780.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980779.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212951.1
COORDINATES: similar to AA sequence:RefSeq:WP_013079633.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251209.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018251208.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980774.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980773.1
COORDINATES: similar to AA sequence:RefSeq:WP_010546049.1
COORDINATES: similar to AA sequence:RefSeq:WP_007988184.1
CDF family Co(II)/Ni(II) efflux transporter DmeF
COORDINATES: similar to AA sequence:RefSeq:WP_010543460.1
metal/formaldehyde-sensitive transcriptional repressor
COORDINATES: protein motif:HMM:NF023367.2
COORDINATES: similar to AA sequence:RefSeq:WP_018319076.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008827682.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008603797.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688877.1
COORDINATES: similar to AA sequence:RefSeq:WP_014077331.1
GO:0015109 - chromate transmembrane transporter activity [Evidence IEA]
GO:0015703 - chromate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010501318.1
COORDINATES: similar to AA sequence:RefSeq:WP_010127398.1
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: similar to AA sequence:RefSeq:WP_018250482.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212865.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212864.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009824028.1
COORDINATES: similar to AA sequence:RefSeq:WP_010220034.1
COORDINATES: protein motif:HMM:NF025126.2
COORDINATES: similar to AA sequence:RefSeq:WP_007406260.1
COORDINATES: similar to AA sequence:RefSeq:WP_011299921.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406255.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406239.1
COORDINATES: protein motif:HMM:NF014373.2
COORDINATES: similar to AA sequence:RefSeq:WP_007406227.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406272.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406242.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830651.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406258.1
COORDINATES: protein motif:HMM:NF024950.2
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF012334.2
COORDINATES: protein motif:HMM:NF012417.2
COORDINATES: similar to AA sequence:RefSeq:WP_003600985.1
L-dopachrome tautomerase-related protein
COORDINATES: similar to AA sequence:RefSeq:WP_020095762.1
COORDINATES: similar to AA sequence:RefSeq:WP_007437949.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950575.1
xanthine dehydrogenase family protein subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_015929550.1
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: protein motif:HMM:NF018446.2
COORDINATES: similar to AA sequence:RefSeq:WP_014501024.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503026.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007406876.1
zinc-dependent alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012783831.1
COORDINATES: similar to AA sequence:RefSeq:NP_308438.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0051903 - S-(hydroxymethyl)glutathione dehydrogenase activity [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]; GO:0009404 - toxin metabolic process [Evidence IEA]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_009823887.1
COORDINATES: similar to AA sequence:RefSeq:WP_014132971.1
type 1 glutamine amidotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014132970.1
glutathione-independent formaldehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_017504343.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503034.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503035.1
COORDINATES: similar to AA sequence:RefSeq:WP_007684618.1
COORDINATES: similar to AA sequence:RefSeq:WP_013169102.1
COORDINATES: similar to AA sequence:RefSeq:WP_003613735.1
COORDINATES: similar to AA sequence:RefSeq:WP_003044989.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
zinc-binding alcohol dehydrogenase family protein
COORDINATES: protein motif:HMM:NF006615.0
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013849042.1
COORDINATES: similar to AA sequence:RefSeq:WP_011241460.1
GO:0022627 - cytosolic small ribosomal subunit [Evidence IEA]; GO:0000314 - organellar small ribosomal subunit [Evidence IEA]
GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017980894.1
COORDINATES: similar to AA sequence:RefSeq:WP_017977383.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954973.1
COORDINATES: similar to AA sequence:RefSeq:WP_016509344.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219940.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010164983.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010165429.1
COORDINATES: similar to AA sequence:RefSeq:WP_010184885.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611976.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010336802.1
GO:0006313 - transposition, DNA-mediated [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:TIGR00229.1
COORDINATES: similar to AA sequence:RefSeq:WP_004208626.1
COORDINATES: protein motif:HMM:NF017081.2
GO:0009975 - cyclase activity [Evidence IEA]
GO:0009966 - regulation of signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019368236.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251177.1
GO:0045300 - acyl-[acyl-carrier-protein] desaturase activity [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018251178.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251179.1
GO:0009055 - electron transfer activity [Evidence IEA]
cytochrome b/b6 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011993056.1
COORDINATES: similar to AA sequence:RefSeq:WP_008994751.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_018251182.1
COORDINATES: similar to AA sequence:RefSeq:WP_019370852.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212896.1
COORDINATES: similar to AA sequence:RefSeq:WP_010403603.1
COORDINATES: similar to AA sequence:RefSeq:WP_007404734.1
COORDINATES: similar to AA sequence:RefSeq:WP_007404834.1
COORDINATES: similar to AA sequence:RefSeq:WP_017979330.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF013862.2
GO:0006629 - lipid metabolic process [Evidence IEA]
patatin-like phospholipase family protein
COORDINATES: protein motif:HMM:NF024675.2
GO:0016790 - thiolester hydrolase activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017503243.1
COORDINATES: similar to AA sequence:RefSeq:WP_005664110.1
COORDINATES: similar to AA sequence:RefSeq:WP_002855261.1
COORDINATES: protein motif:HMM:NF012655.2
COORDINATES: similar to AA sequence:RefSeq:WP_007715221.1
COORDINATES: similar to AA sequence:RefSeq:WP_007598236.1
COORDINATES: similar to AA sequence:RefSeq:WP_006766388.1
COORDINATES: similar to AA sequence:RefSeq:WP_013168502.1
COORDINATES: similar to AA sequence:RefSeq:WP_006766386.1
COORDINATES: protein motif:HMM:NF015531.2
COORDINATES: similar to AA sequence:RefSeq:WP_010409162.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008030522.1
COORDINATES: protein motif:HMM:NF016724.2
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_008071219.1
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:NF033580.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008603927.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054123.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010544511.1
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF041492.1
COORDINATES: similar to AA sequence:RefSeq:WP_016746114.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406600.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251268.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409227.1
COORDINATES: similar to AA sequence:RefSeq:WP_006022055.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980827.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018251258.1
arsenic resistance N-acetyltransferase ArsN2
COORDINATES: similar to AA sequence:RefSeq:WP_017980825.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011157810.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
This arsenate reductase requires both glutathione and glutaredoxin to convert arsenate to arsenite, after which the efflux transporter formed by ArsA and ArsB can extrude the arsenite from the cell, providing resistance; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010542917.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_007406231.1
COORDINATES: similar to AA sequence:RefSeq:WP_017182407.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368261.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980819.1
COORDINATES: protein motif:HMM:NF014691.2
COORDINATES: similar to AA sequence:RefSeq:WP_010218574.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406854.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368200.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251228.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212886.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212885.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212882.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251224.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406841.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368193.1
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0001539 - cilium or flagellum-dependent cell motility [Evidence IEA]
flagellar hook-basal body complex protein FliE
COORDINATES: similar to AA sequence:RefSeq:WP_007406844.1
COORDINATES: similar to AA sequence:RefSeq:WP_020820506.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251219.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_004212877.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039111.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980802.1