Novosphingobium aromaticivorans DSM 12444 plasmid pNL1, complete sequence.
Novosphingobium aromaticivorans DSM 12444
Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Novosphingobium.
Complete sequence of plasmid pNL1 of Novosphingobium aromaticivorans DSM 12444
Submitted (12-APR-2007) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000676.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 2351474\nSource DNA and bacteria available from Margie\nRomine(margie.romine@pnl.gov)\nContact: Margie Romine (margie.romine@pnl.gov)\n Paul Richardson (microbes@cuba.jgi-psf.org)\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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 :: 12/07/2022 16:55:16\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) :: 4,086\nCDSs (total) :: 4,018\nGenes (coding) :: 3,992\nCDSs (with protein) :: 3,992\nGenes (RNA) :: 68\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 56\nncRNAs :: 3\nPseudo Genes (total) :: 26\nCDSs (without protein) :: 26\nPseudo Genes (ambiguous residues) :: 0 of 26\nPseudo Genes (frameshifted) :: 6 of 26\nPseudo Genes (incomplete) :: 20 of 26\nPseudo Genes (internal stop) :: 2 of 26\nPseudo Genes (multiple problems) :: 2 of 26\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Sphingomonas aromaticivorans
COORDINATES: similar to AA sequence:RefSeq:WP_007015997.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008829816.1
aromatic-ring-hydroxylating dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_007015995.1
aromatic ring-hydroxylating dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_008829814.1
GO:0016829 - lyase activity [Evidence IEA]
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015993.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_008829811.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832829.1
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_008831827.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834094.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828560.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828561.1
3-phenylpropionate/cinnamic acid dioxygenase subunit beta
COORDINATES: protein motif:HMM:NF019335.2
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: similar to AA sequence:RefSeq:WP_008828148.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891009.1
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_014752880.1
3-(cis-5,6-dihydroxycyclohexa-1, 3-dien-1-yl)propanoate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_013832820.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054254.1
2Fe-2S iron-sulfur cluster binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015986.1
4-oxalocrotonate tautomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013832818.1
GO:0003824 - catalytic activity [Evidence IEA]
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008828141.1
GO:0008701 - 4-hydroxy-2-oxovalerate aldolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010891016.1
GO:0008774 - acetaldehyde dehydrogenase (acetylating) activity [Evidence IEA]
acetaldehyde dehydrogenase (acetylating)
COORDINATES: similar to AA sequence:RefSeq:WP_010891017.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828138.1
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_007015980.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015979.1
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_008828135.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828134.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010891023.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828132.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010891025.1
4-hydroxythreonine-4-phosphate dehydrogenase PdxA
COORDINATES: similar to AA sequence:RefSeq:WP_013832806.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828129.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828128.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828127.1
non-heme iron oxygenase ferredoxin subunit
COORDINATES: similar to AA sequence:RefSeq:WP_008828126.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828125.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828124.1
2-hydroxychromene-2-carboxylate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_008828123.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828122.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828121.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_008828120.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828119.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832794.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008828117.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828116.1
GO:0016831 - carboxy-lyase activity [Evidence IEA]
non-oxidative hydroxyarylic acid decarboxylases subunit C
COORDINATES: similar to AA sequence:RefSeq:WP_010891041.1
non-oxidative hydroxyarylic acid decarboxylases subunit D
COORDINATES: similar to AA sequence:RefSeq:WP_008828114.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828113.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828105.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
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_014496864.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011906638.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828102.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828101.1
GO:0018817 - 2-oxo-hept-3-ene-1,7-dioate hydratase activity [Evidence IEA]
2-oxo-hepta-3-ene-1,7-dioic acid hydratase
COORDINATES: similar to AA sequence:RefSeq:WP_010891051.1
HpcH/HpaI aldolase/citrate lyase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013832785.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890869.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828097.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828096.1
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010890872.1
This protein belongs to a clade of FMN-dependent monooxygenases, within a broader family of flavin-dependent oxidoreductases, the luciferase-like monooxygenase (LMM) family, some of whose members use coenzyme F420 rather than FMN; Derived by automated computational analysis using gene prediction method: Protein Homology.
NtaA/DmoA family FMN-dependent monooxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_008828094.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828093.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828092.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828091.1
GO:0009027 - tartrate dehydrogenase activity [Evidence IEA]
GO:0046395 - carboxylic acid catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013834072.1
GO:0008677 - 2-dehydropantoate 2-reductase activity [Evidence IEA]
GO:0015940 - pantothenate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832849.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890877.1
GO:0050242 - pyruvate, phosphate dikinase activity [Evidence IEA]
GO:0015976 - carbon utilization [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008827667.1
COORDINATES: similar to AA sequence:RefSeq:WP_008827666.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906634.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834066.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823401.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_004208106.1
EmrA/EmrK family multidrug efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_004208107.1
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_006834195.1
COORDINATES: similar to AA sequence:RefSeq:WP_019966484.1
COORDINATES: similar to AA sequence:RefSeq:WP_007163782.1
COORDINATES: similar to AA sequence:RefSeq:WP_020820330.1
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:NF016430.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_006953681.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949334.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054504.1
COORDINATES: similar to AA sequence:RefSeq:WP_007014145.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_006949340.1
COORDINATES: similar to AA sequence:RefSeq:WP_007014149.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950533.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949344.1
COORDINATES: similar to AA sequence:RefSeq:WP_014332393.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015932.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015931.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006949349.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054763.1
COORDINATES: protein motif:HMM:NF019997.2
COORDINATES: similar to AA sequence:RefSeq:WP_011906624.1
reverse transcriptase domain-containing protein
COORDINATES: protein motif:HMM:NF037521.2
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020818725.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039033.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039034.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039035.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054830.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949361.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015913.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015912.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015910.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015909.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015908.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015907.1
COORDINATES: protein motif:HMM:NF037255.2
COORDINATES: similar to AA sequence:RefSeq:WP_016558253.1
COORDINATES: similar to AA sequence:RefSeq:WP_016558256.1
COORDINATES: similar to AA sequence:RefSeq:WP_005854566.1
COORDINATES: protein motif:HMM:NF024977.2
COORDINATES: protein motif:HMM:TIGR03187.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054215.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949380.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054217.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054460.1
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_006949384.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054219.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015884.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949390.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906613.1
COORDINATES: similar to AA sequence:RefSeq:WP_006468203.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015881.1
COORDINATES: similar to AA sequence:RefSeq:WP_012278615.1
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_004636337.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949400.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054225.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054469.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949408.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054806.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054805.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019054804.1
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_006949416.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011540772.1
COORDINATES: protein motif:HMM:NF014691.2
COORDINATES: similar to AA sequence:RefSeq:WP_010890951.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890953.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949427.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949435.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952605.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054377.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006949444.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949446.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054374.1
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_006949450.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054372.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054371.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949453.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611376.1
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_019054085.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950641.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890971.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053924.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015858.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949467.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_015460511.1
COORDINATES: similar to AA sequence:RefSeq:WP_007016053.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953576.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_007016051.1
COORDINATES: similar to AA sequence:RefSeq:WP_007016050.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_019054096.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949478.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054098.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949485.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949487.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949488.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_006949489.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054103.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_010890987.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053908.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053907.1
COORDINATES: similar to AA sequence:RefSeq:WP_007016038.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007016000.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834082.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834083.1