Sphingopyxis fribergensis strain Kp5.2 plasmid pSfKp5.2, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingopyxis.
Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid
Submitted (03-JUN-2014) CeBiTec, Bielefeld University, Universitaetsstr. 27, Bielefeld, NRW 33615, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP009123.1.\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##Assembly-Data-START##\nAssembly Method :: Newbler v. 2.8\nCoverage :: 210.0x\nSequencing Technology :: Illumina\n##Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/27/2022 02:22:11\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,960\nCDSs (total) :: 4,909\nGenes (coding) :: 4,850\nCDSs (with protein) :: 4,850\nGenes (RNA) :: 51\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 3\nPseudo Genes (total) :: 59\nCDSs (without protein) :: 59\nPseudo Genes (ambiguous residues) :: 0 of 59\nPseudo Genes (frameshifted) :: 22 of 59\nPseudo Genes (incomplete) :: 44 of 59\nPseudo Genes (internal stop) :: 7 of 59\nPseudo Genes (multiple problems) :: 13 of 59\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Sphingopyxis fribergensis
COORDINATES: similar to AA sequence:RefSeq:WP_010124856.1
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_018251372.1
COORDINATES: similar to AA sequence:RefSeq:WP_017184237.1
GO:0015109 - chromate transmembrane transporter activity [Evidence IEA]
GO:0015703 - chromate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017184236.1
COORDINATES: protein motif:HMM:NF033816.1
COORDINATES: similar to AA sequence:RefSeq:WP_017184234.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449233.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024584.2
COORDINATES: protein motif:HMM:NF016612.2
neutral/alkaline non-lysosomal ceramidase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004398858.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013832780.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406330.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_020818507.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_010405683.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_007015613.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406579.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818502.1
COORDINATES: protein motif:HMM:NF021213.2
COORDINATES: similar to AA sequence:RefSeq:WP_008828788.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818498.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_010405703.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405704.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_006952535.1
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_019054087.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406607.1
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950418.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950417.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015740143.1
COORDINATES: similar to AA sequence:RefSeq:WP_007681921.1
COORDINATES: protein motif:HMM:NF023701.2
GSU2403 family nucleotidyltransferase fold protein
COORDINATES: similar to AA sequence:RefSeq:WP_019052336.1
COORDINATES: protein motif:HMM:NF020332.2
GO:0004386 - helicase activity [Evidence IEA]
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF021897.2
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010188850.1
COORDINATES: similar to AA sequence:RefSeq:WP_010408952.1
COORDINATES: protein motif:HMM:NF014505.2
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008830218.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_017500339.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405785.1
COORDINATES: protein motif:HMM:NF017128.2
sigma factor-like helix-turn-helix DNA-binding protein
COORDINATES: protein motif:HMM:NF013561.2
COORDINATES: similar to AA sequence:RefSeq:WP_011906613.1
COORDINATES: similar to AA sequence:RefSeq:WP_007677733.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823566.1
COORDINATES: protein motif:HMM:NF025053.2
protein phosphatase 2C domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012522387.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008080 - N-acetyltransferase activity [Evidence IEA]
GO:0006040 - amino sugar metabolic process [Evidence IEA]; GO:0009254 - peptidoglycan turnover [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019831963.1
GO:0008967 - phosphoglycolate phosphatase activity [Evidence IEA]
GO:0043094 - cellular metabolic compound salvage [Evidence IEA]; GO:0008152 - metabolic process [Evidence IEA]; GO:0009853 - photorespiration [Evidence IEA]
PGP is an essential enzyme in the glycolate salvage pathway in higher organisms (photorespiration in plants). Phosphoglycolate results from the oxidase activity of RubisCO in the Calvin cycle when concentrations of carbon dioxide are low relative to oxygen. This enzyme is a member of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolase enzymes (PF00702); Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611857.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014564.2
COORDINATES: similar to AA sequence:RefSeq:WP_011581115.1
COORDINATES: similar to AA sequence:RefSeq:YP_002515827.1
GO:0008448 - N-acetylglucosamine-6-phosphate deacetylase activity [Evidence IEA]
GO:0006040 - amino sugar metabolic process [Evidence IEA]
N-acetylglucosamine-6-phosphate deacetylase
COORDINATES: similar to AA sequence:RefSeq:WP_015049160.1
COORDINATES: similar to AA sequence:RefSeq:WP_020592615.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019403.2
heparan-alpha-glucosaminide N-acetyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017979008.1
N-acetylmuramic acid 6-phosphate etherase
COORDINATES: similar to AA sequence:RefSeq:WP_004410267.1
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: similar to AA sequence:RefSeq:WP_011542934.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_017183261.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053423.1
strawberry notch C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008831884.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010408889.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819179.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406726.1
COORDINATES: protein motif:HMM:NF015935.2
COORDINATES: similar to AA sequence:RefSeq:WP_011542759.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818526.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018251286.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606257.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019052716.1
GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
nucleotidyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018076144.1
COORDINATES: similar to AA sequence:RefSeq:WP_014857805.1
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019052713.1
COORDINATES: protein motif:HMM:NF016648.2
COORDINATES: protein motif:HMM:NF033523.0
COORDINATES: protein motif:HMM:NF012936.2
GO:0004066 - asparagine synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0006529 - asparagine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF033537.1
COORDINATES: protein motif:HMM:NF033522.2
COORDINATES: protein motif:HMM:NF012610.2
COORDINATES: protein motif:HMM:NF019886.2
sigma-70 region 4 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014077236.1
COORDINATES: similar to AA sequence:RefSeq:WP_018494858.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015460482.1
COORDINATES: similar to AA sequence:RefSeq:WP_011583115.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212783.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018250843.1
COORDINATES: similar to AA sequence:RefSeq:WP_010543785.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406711.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212858.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212859.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015951.1
COORDINATES: similar to AA sequence:RefSeq:WP_008827836.1
COORDINATES: similar to AA sequence:RefSeq:WP_007011773.1
COORDINATES: similar to AA sequence:RefSeq:WP_012521738.1
COORDINATES: similar to AA sequence:RefSeq:WP_009471749.1
COORDINATES: similar to AA sequence:RefSeq:WP_006834181.1
COORDINATES: similar to AA sequence:RefSeq:WP_018147838.1
COORDINATES: similar to AA sequence:RefSeq:WP_006834183.1
COORDINATES: similar to AA sequence:RefSeq:WP_011415898.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018147841.1
COORDINATES: similar to AA sequence:RefSeq:WP_006834186.1
COORDINATES: similar to AA sequence:RefSeq:WP_018147843.1
GO:0006744 - ubiquinone biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012274987.1
COORDINATES: similar to AA sequence:RefSeq:WP_018147845.1
COORDINATES: similar to AA sequence:RefSeq:WP_007016021.1
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_004617931.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_019966484.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890885.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611445.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012275108.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012275110.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009802138.1
COORDINATES: similar to AA sequence:RefSeq:WP_004921639.1
COORDINATES: similar to AA sequence:RefSeq:WP_007184810.1
COORDINATES: similar to AA sequence:RefSeq:WP_009506505.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012275116.1
COORDINATES: similar to AA sequence:RefSeq:WP_013053759.1
acyl-CoA dehydrogenase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012112643.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611884.1
internal stop; 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_020798873.1
COORDINATES: similar to AA sequence:RefSeq:WP_012275056.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:TIGR01845.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_076612398.1
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
internal stop; 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:NF015541.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_013802200.1
COORDINATES: protein motif:HMM:NF016513.2
COORDINATES: similar to AA sequence:RefSeq:WP_007838219.1
COORDINATES: similar to AA sequence:RefSeq:WP_004728218.1
COORDINATES: similar to AA sequence:RefSeq:WP_020078817.1
COORDINATES: similar to AA sequence:RefSeq:WP_015377885.1
COORDINATES: similar to AA sequence:RefSeq:WP_013635019.1
COORDINATES: protein motif:HMM:NF022072.2
COORDINATES: similar to AA sequence:RefSeq:WP_010488775.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003046475.1
COORDINATES: protein motif:HMM:NF024242.2
COORDINATES: similar to AA sequence:RefSeq:WP_007674948.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039112.1
COORDINATES: similar to AA sequence:RefSeq:WP_012752990.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405551.1
COORDINATES: similar to AA sequence:RefSeq:WP_007509012.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]
Cd(II)/Pb(II)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008434970.1
COORDINATES: similar to AA sequence:RefSeq:WP_017778766.1
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: protein motif:HMM:NF033580.1