Sphingomonas naphthae strain KACC 18716 plasmid unnamed2, 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\nCP117413.1.\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_004212842.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010188938.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004212840.1
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004212839.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212838.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212837.1
antitoxin of toxin-antitoxin stability system
COORDINATES: similar to AA sequence:RefSeq:WP_004212836.1
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_004883039.1
COORDINATES: similar to AA sequence:RefSeq:WP_010567760.1
COORDINATES: similar to AA sequence:RefSeq:WP_012286061.1
COORDINATES: protein motif:HMM:NF023204.2
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_018083701.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF012266.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_017507270.1
COORDINATES: protein motif:HMM:TIGR01844.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010218094.1
COORDINATES: protein motif:HMM:NF025724.2
COORDINATES: similar to AA sequence:RefSeq:WP_012112820.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018250437.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212834.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212830.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212828.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849894.1
COORDINATES: similar to AA sequence:RefSeq:WP_006967369.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_013849768.1
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.; 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_016744714.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018251258.1
arsenic resistance N-acetyltransferase ArsN2
COORDINATES: similar to AA sequence:RefSeq:WP_007688070.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007682945.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019051906.1
COORDINATES: similar to AA sequence:RefSeq:WP_016744708.1
COORDINATES: protein motif:HMM:NF013736.2
COORDINATES: similar to AA sequence:RefSeq:WP_013849896.1
COORDINATES: similar to AA sequence:RefSeq:WP_003041647.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950805.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011950806.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251311.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849899.1
COORDINATES: similar to AA sequence:RefSeq:WP_017500339.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688055.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039043.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950776.1
COORDINATES: similar to AA sequence:RefSeq:WP_020820479.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950814.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF024242.2
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_017182751.1
COORDINATES: similar to AA sequence:RefSeq:WP_007684604.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010339498.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010188963.1
COORDINATES: similar to AA sequence:RefSeq:WP_010218643.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_013039065.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683405.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683402.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072616.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_006949650.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_013039070.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831137.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008831136.1
COORDINATES: similar to AA sequence:RefSeq:WP_011542799.1
phytanoyl-CoA dioxygenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611555.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017182766.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015449333.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849920.1
COORDINATES: similar to AA sequence:RefSeq:WP_008837483.1
COORDINATES: similar to AA sequence:RefSeq:WP_008994751.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_014725841.1
COORDINATES: similar to AA sequence:RefSeq:WP_012286454.1
GO:0009055 - electron transfer activity [Evidence IEA]
cytochrome b/b6 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017772981.1
COORDINATES: similar to AA sequence:RefSeq:WP_008994753.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008994754.1
COORDINATES: similar to AA sequence:RefSeq:WP_016747685.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_008994756.1
COORDINATES: similar to AA sequence:RefSeq:WP_003039487.1
COORDINATES: protein motif:HMM:NF016060.2
COORDINATES: similar to AA sequence:RefSeq:WP_012226942.1
COORDINATES: similar to AA sequence:RefSeq:WP_003039481.1
COORDINATES: similar to AA sequence:RefSeq:WP_007011514.1
COORDINATES: protein motif:HMM:NF022142.2
COORDINATES: similar to AA sequence:RefSeq:WP_011907978.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_006965685.1
COORDINATES: similar to AA sequence:RefSeq:WP_010685770.1
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor [Evidence IEA]
cytochrome d ubiquinol oxidase subunit II
COORDINATES: similar to AA sequence:RefSeq:WP_006948747.1
COORDINATES: similar to AA sequence:RefSeq:WP_013268145.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013268146.1
bifunctional protein tyrosine phosphatase family protein/NAD(P)/FAD-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013268147.1
COORDINATES: similar to AA sequence:RefSeq:WP_013268149.1
COORDINATES: similar to AA sequence:RefSeq:WP_017181621.1
YeeE/YedE thiosulfate transporter family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012049928.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501480.1
GO:0051920 - peroxiredoxin activity [Evidence IEA]; GO:0008379 - thioredoxin peroxidase activity [Evidence IEA]
GO:0098869 - cellular oxidant detoxification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008830445.1
COORDINATES: similar to AA sequence:RefSeq:WP_008108799.1
COORDINATES: similar to AA sequence:RefSeq:WP_010185695.1
COORDINATES: similar to AA sequence:RefSeq:WP_014993631.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188090.1
COORDINATES: protein motif:HMM:NF024420.2
COORDINATES: similar to AA sequence:RefSeq:WP_018390183.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830650.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830651.1
COORDINATES: similar to AA sequence:RefSeq:WP_017182151.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830653.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339501.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830655.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830656.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339503.1
COORDINATES: similar to AA sequence:RefSeq:WP_009210487.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
phospholipase D-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019831362.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830660.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339505.1
voltage-gated chloride channel family protein
COORDINATES: nucleotide motif:Rfam:14.4:RF01734
Fluoride riboswitches increase expression of downstream genes that help mitigate the toxic effects of very high levels of fluoride; They are found in a wide variety of bacteria and archaea; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_008827836.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406383.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183652.1
COORDINATES: similar to AA sequence:RefSeq:WP_007688084.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183650.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212853.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188931.1
COORDINATES: similar to AA sequence:RefSeq:WP_010188936.1