Rhizorhabdus wittichii strain MPO218 plasmid pIBU218, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Rhizorhabdus.
Isolation and genomic analysis of the ibuprofen-degrading bacterium Sphingomonas strain MPO218
Submitted (02-JUL-2020) Microbiology, Centro Andaluz de Biologia del Desarrollo (UPO-CSIC-JA), Ctra/ Utrera, Km1, Sevilla, Sevilla 41013, Spain
REFSEQ INFORMATION: The reference sequence is identical to\nCP059320.1.\nBacteria and source DNA available from CABD.\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 Date :: 30-NOV-2018\nAssembly Method :: SPAdes v. 3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 30.0x\nSequencing Technology :: Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/31/2022 04:21:17\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;\n repeat_region\nGenes (total) :: 5,859\nCDSs (total) :: 5,800\nGenes (coding) :: 5,725\nCDSs (with protein) :: 5,725\nGenes (RNA) :: 59\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 5\nPseudo Genes (total) :: 75\nCDSs (without protein) :: 75\nPseudo Genes (ambiguous residues) :: 0 of 75\nPseudo Genes (frameshifted) :: 34 of 75\nPseudo Genes (incomplete) :: 48 of 75\nPseudo Genes (internal stop) :: 9 of 75\nPseudo Genes (multiple problems) :: 14 of 75\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Wastewater treatment of pharmaceutical company
COORDINATES: similar to AA sequence:RefSeq:WP_002932128.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF017872.2
COORDINATES: similar to AA sequence:RefSeq:WP_004333999.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-54-dependent Fis family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013039628.1
COORDINATES: similar to AA sequence:RefSeq:WP_008069198.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818450.1
GO:0008701 - 4-hydroxy-2-oxovalerate aldolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018992142.1
GO:0008774 - acetaldehyde dehydrogenase (acetylating) activity [Evidence IEA]
acetaldehyde dehydrogenase (acetylating)
COORDINATES: similar to AA sequence:RefSeq:WP_007684774.1
GO:0016853 - isomerase activity [Evidence IEA]
GO:0006725 - cellular aromatic compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020818448.1
GO:0047437 - 4-oxalocrotonate decarboxylase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007684772.1
GO:0003824 - catalytic activity [Evidence IEA]
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010567291.1
GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Evidence IEA]
2-hydroxymuconic semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_007684768.1
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008827964.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013846859.1
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:NF024503.2
COORDINATES: similar to AA sequence:RefSeq:WP_012049931.1
COORDINATES: similar to AA sequence:RefSeq:WP_012049930.1
COORDINATES: similar to AA sequence:RefSeq:WP_007405941.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012049928.1
COORDINATES: similar to AA sequence:RefSeq:WP_012049927.1
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_012049926.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006662 - glycerol ether metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012049925.1
COORDINATES: similar to AA sequence:RefSeq:WP_012049924.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_016747693.1
COORDINATES: similar to AA sequence:RefSeq:WP_012334279.1
putative sulfate exporter family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_011951796.1
COORDINATES: similar to AA sequence:RefSeq:WP_007405943.1
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:TIGR02857.1
GO:0055051 - ATP-binding cassette (ABC) transporter complex, integrated substrate binding [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0033230 - ABC-type cysteine transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
GO:0033228 - cysteine export across plasma membrane [Evidence IEA]
thiol reductant ABC exporter subunit CydD
COORDINATES: similar to AA sequence:RefSeq:WP_007405998.1
GO:0070069 - cytochrome complex [Evidence IEA]
GO:0009055 - electron transfer activity [Evidence IEA]
GO:0019646 - aerobic electron transport chain [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010338006.1
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_015460560.1
COORDINATES: similar to AA sequence:RefSeq:WP_012049917.1
COORDINATES: similar to AA sequence:RefSeq:WP_012049916.1
DNA starvation/stationary phase protection protein
COORDINATES: similar to AA sequence:RefSeq:WP_012049915.1
COORDINATES: similar to AA sequence:RefSeq:WP_007405981.1
COORDINATES: similar to AA sequence:RefSeq:WP_003609949.1
COORDINATES: similar to AA sequence:RefSeq:WP_007405935.1
COORDINATES: similar to AA sequence:RefSeq:WP_012049911.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406003.1
COORDINATES: similar to AA sequence:RefSeq:WP_012049909.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406015.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_015460568.1
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007405978.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460570.1
COORDINATES: similar to AA sequence:RefSeq:WP_007405958.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015460572.1
carboxymuconolactone decarboxylase family protein
COORDINATES: protein motif:HMM:NF012264.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004210278.1
GO:0004096 - catalase activity [Evidence IEA]; GO:0004601 - peroxidase activity [Evidence IEA]
GO:0006979 - response to oxidative stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013038873.1
COORDINATES: similar to AA sequence:RefSeq:WP_016744742.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
GO:0004803 - transposase activity [Evidence IEA]
IS6-like element IS6100 family transposase
COORDINATES: protein motif:HMM:NF019335.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
TonB-dependent receptor plug domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019931607.1
COORDINATES: protein motif:HMM:NF013920.2
COORDINATES: protein motif:HMM:NF012596.2
COORDINATES: protein motif:HMM:NF014564.2
CaiB/BaiF CoA-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010891021.1
COORDINATES: similar to AA sequence:RefSeq:WP_011475381.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008827651.1
non-heme iron oxygenase ferredoxin subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013832802.1
COORDINATES: protein motif:HMM:NF025019.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611773.1
COORDINATES: protein motif:HMM:NF024850.2
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014160700.1
COORDINATES: similar to AA sequence:RefSeq:WP_009080229.1
COORDINATES: similar to AA sequence:RefSeq:WP_014161605.1
aromatic-ring-hydroxylating dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_015006995.1
aromatic ring-hydroxylating dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_012430576.1
COORDINATES: similar to AA sequence:RefSeq:WP_006022908.1
COORDINATES: similar to AA sequence:RefSeq:WP_011797812.1
COORDINATES: similar to AA sequence:RefSeq:WP_011608156.1
COORDINATES: similar to AA sequence:RefSeq:WP_007011060.1
IS21-like element ISSsp5 family helper ATPase IstB
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: protein motif:HMM:NF014691.2
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: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_019054263.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_041039472.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007015987.1
2Fe-2S iron-sulfur cluster binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011004190.1
GO:0016862 - intramolecular oxidoreductase activity, interconverting keto- and enol-groups [Evidence IEA]
2-hydroxymuconate tautomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010891014.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828141.1
COORDINATES: similar to AA sequence:RefSeq:WP_000044314.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832815.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015981.1
COORDINATES: similar to AA sequence:RefSeq:WP_018993074.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015979.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954005.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954007.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954009.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954011.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015909.1
COORDINATES: similar to AA sequence:RefSeq:WP_017184786.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954019.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954021.1
COORDINATES: similar to AA sequence:RefSeq:WP_013846912.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054428.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054429.1
COORDINATES: similar to AA sequence:RefSeq:WP_010338824.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954036.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954038.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_006954041.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954043.1
COORDINATES: similar to AA sequence:RefSeq:WP_006199589.1
COORDINATES: similar to AA sequence:RefSeq:WP_006950784.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405673.1
COORDINATES: similar to AA sequence:RefSeq:WP_008068549.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952651.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006952649.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952640.1
COORDINATES: protein motif:HMM:NF025642.2
COORDINATES: similar to AA sequence:RefSeq:WP_006952635.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952632.1
COORDINATES: similar to AA sequence:RefSeq:WP_019052748.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952621.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183274.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952617.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952616.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952612.1
COORDINATES: protein motif:HMM:NF022151.2
COORDINATES: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF040421.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818472.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950430.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006952603.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015457741.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952594.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183261.1
COORDINATES: similar to AA sequence:RefSeq:WP_017184756.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952588.1
COORDINATES: similar to AA sequence:RefSeq:WP_010103182.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006952587.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952559.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949416.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013849887.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501669.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: protein motif:HMM:NF014587.2
COORDINATES: similar to AA sequence:RefSeq:WP_007015734.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828015.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213331.1
COORDINATES: similar to AA sequence:RefSeq:WP_013833388.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009242061.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015600.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054653.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406581.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952535.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015604.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_006952531.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_006952530.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952529.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_006952528.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953579.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_007015611.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405687.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054292.1
COORDINATES: similar to AA sequence:RefSeq:WP_006955514.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_017502442.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_015460523.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_010339789.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054296.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054298.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649063.1
COORDINATES: protein motif:HMM:NF016115.2
GO:0004061 - arylformamidase activity [Evidence IEA]
GO:0019441 - tryptophan catabolic process to kynurenine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012553005.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019706040.1
COORDINATES: protein motif:HMM:NF033580.1
COORDINATES: similar to AA sequence:RefSeq:WP_003598838.1
COORDINATES: similar to AA sequence:RefSeq:WP_007424544.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039625.1
COORDINATES: similar to AA sequence:RefSeq:WP_011765592.1
COORDINATES: similar to AA sequence:RefSeq:WP_002940969.1
GO:0018577 - catechol 2,3-dioxygenase activity [Evidence IEA]
GO:0009712 - catechol-containing compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019054254.1
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_007684785.1
COORDINATES: similar to AA sequence:RefSeq:WP_004252892.1
phenol 2-monooxygenase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010567293.1
COORDINATES: similar to AA sequence:RefSeq:WP_003296962.1
COORDINATES: similar to AA sequence:RefSeq:WP_014900550.1