Novosphingobium pentaromativorans US6-1 plasmid pLA1, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Novosphingobium.
Complete genome sequence of Novosphingobium pentaromativorans US6-1(T)
Submitted (28-AUG-2014) Marine Biotechnology, KIOST, 787, Haeanro, Ansan, Gyeonggi-do 426-744, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP009294.1.\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##Genome-Assembly-Data-START##\nAssembly Date :: 26-MAY-2014\nAssembly Method :: Roche gs Assembler v. 2.6; PAC Bio SMRT\n Analysis v. 2.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 128.0x\nSequencing Technology :: Illumina MiSeq; PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/08/2023 00:17:37\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) :: 5,173\nCDSs (total) :: 5,106\nGenes (coding) :: 5,011\nCDSs (with protein) :: 5,011\nGenes (RNA) :: 67\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 3\nPseudo Genes (total) :: 95\nCDSs (without protein) :: 95\nPseudo Genes (ambiguous residues) :: 0 of 95\nPseudo Genes (frameshifted) :: 38 of 95\nPseudo Genes (incomplete) :: 69 of 95\nPseudo Genes (internal stop) :: 15 of 95\nPseudo Genes (multiple problems) :: 22 of 95\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Novosphingobium pentaromativorans
COORDINATES: similar to AA sequence:RefSeq:WP_017183650.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007688084.1
COORDINATES: similar to AA sequence:RefSeq:WP_008997212.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054309.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054307.1
Mu transposase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017437.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007015769.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003046513.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015151.1
efflux RND transporter periplasmic adaptor subunit
COORDINATES: protein motif:HMM:TIGR00914.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: protein motif:HMM:NF014898.2
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008831440.1
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832783.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834120.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611527.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010891035.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_013832798.1
COORDINATES: similar to AA sequence:RefSeq:WP_015007020.1
2-hydroxychromene-2-carboxylate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_013832801.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832802.1
aromatic-ring-hydroxylating dioxygenase subunit beta
COORDINATES: protein motif:HMM:NF025178.2
non-heme iron oxygenase ferredoxin subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013832804.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832805.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
GO:0044237 - cellular metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832806.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832807.1
4-hydroxythreonine-4-phosphate dehydrogenase PdxA
COORDINATES: similar to AA sequence:RefSeq:WP_013832808.1
aromatic ring-hydroxylating dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_010891023.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832810.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832811.1
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_013832813.1
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_013832815.1
GO:0003824 - catalytic activity [Evidence IEA]
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013832816.1
GO:0008774 - acetaldehyde dehydrogenase (acetylating) activity [Evidence IEA]
acetaldehyde dehydrogenase (acetylating)
COORDINATES: similar to AA sequence:RefSeq:WP_013832817.1
GO:0008701 - 4-hydroxy-2-oxovalerate aldolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832818.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832819.1
GO:0016862 - intramolecular oxidoreductase activity, interconverting keto- and enol-groups [Evidence IEA]
GO:0006725 - cellular aromatic compound metabolic process [Evidence IEA]
2-hydroxymuconate tautomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010891012.1
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_013832820.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013834112.1
3-(cis-5,6-dihydroxycyclohexa-1, 3-dien-1-yl)propanoate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_007015990.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834092.1
GO:0043565 - sequence-specific DNA binding [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: similar to AA sequence:RefSeq:WP_008829811.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832831.1
1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_013832832.1
GO:0016829 - lyase activity [Evidence IEA]
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015995.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832834.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015997.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834083.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834082.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834081.1
COORDINATES: similar to AA sequence:RefSeq:WP_011082855.1
COORDINATES: similar to AA sequence:RefSeq:WP_011341074.1
COORDINATES: similar to AA sequence:RefSeq:WP_013634994.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611345.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: similar to AA sequence:RefSeq:WP_013832844.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832845.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834068.1
COORDINATES: similar to AA sequence:RefSeq:WP_008827667.1
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013832849.1
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_013834073.1
GO:0009027 - tartrate dehydrogenase activity [Evidence IEA]
GO:0046395 - carboxylic acid catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013834074.1
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013834075.1
COORDINATES: similar to AA sequence:RefSeq:WP_007016019.1
COORDINATES: similar to AA sequence:RefSeq:WP_004617931.1
COORDINATES: similar to AA sequence:RefSeq:WP_006438771.1
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_006834189.1
COORDINATES: similar to AA sequence:RefSeq:WP_006834188.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213210.1
COORDINATES: similar to AA sequence:RefSeq:WP_012975307.1
COORDINATES: similar to AA sequence:RefSeq:WP_007011060.1
COORDINATES: similar to AA sequence:RefSeq:WP_052096176.1
COORDINATES: similar to AA sequence:RefSeq:WP_007689240.1
COORDINATES: similar to AA sequence:RefSeq:WP_011616989.1
COORDINATES: similar to AA sequence:RefSeq:WP_007704915.1
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_007704917.1
COORDINATES: similar to AA sequence:RefSeq:WP_006961738.1
GO:0005215 - transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007704922.1
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054105.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890987.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054103.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_017184780.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_006949488.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_006949487.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054099.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053916.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949478.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053918.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906603.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_006952528.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406336.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_006949469.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406589.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_010967989.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_019054090.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_010890973.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460508.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949458.1
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_006949450.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949446.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054377.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949438.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054379.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006949427.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890953.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890951.1
COORDINATES: similar to AA sequence:RefSeq:WP_011443932.1
COORDINATES: similar to AA sequence:RefSeq:WP_011579857.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011579856.1
type II toxin-antitoxin system Y4mF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_019054472.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949406.1
COORDINATES: similar to AA sequence:RefSeq:WP_007163789.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006949401.1
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_006949400.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949398.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949392.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949390.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015884.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015885.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949386.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054461.1
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_006949381.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949380.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054215.1
COORDINATES: protein motif:HMM:NF012234.2
COORDINATES: similar to AA sequence:RefSeq:WP_007015893.1
COORDINATES: similar to AA sequence:RefSeq:WP_013831741.1
HNH endonuclease signature motif containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017183371.1
COORDINATES: similar to AA sequence:RefSeq:WP_018242524.1
COORDINATES: protein motif:HMM:NF017832.2
COORDINATES: similar to AA sequence:RefSeq:WP_003164514.1
COORDINATES: similar to AA sequence:RefSeq:WP_015599734.1
COORDINATES: similar to AA sequence:RefSeq:WP_012554549.1
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024098.2
COORDINATES: similar to AA sequence:RefSeq:WP_011906621.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015908.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015909.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054784.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890917.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906624.1
reverse transcriptase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010890914.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949361.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054830.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010890911.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039034.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890909.1
COORDINATES: similar to AA sequence:RefSeq:WP_012522046.1
COORDINATES: similar to AA sequence:RefSeq:WP_013039031.1
COORDINATES: similar to AA sequence:RefSeq:WP_020628761.1
COORDINATES: similar to AA sequence:RefSeq:WP_019863571.1
COORDINATES: similar to AA sequence:RefSeq:WP_019863569.1
COORDINATES: similar to AA sequence:RefSeq:WP_019863568.1
COORDINATES: similar to AA sequence:RefSeq:WP_019863567.1
COORDINATES: protein motif:HMM:NF019997.2
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054763.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949349.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015931.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823893.1
COORDINATES: similar to AA sequence:RefSeq:WP_010408893.1
strawberry notch C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016510927.1
COORDINATES: similar to AA sequence:RefSeq:WP_010408889.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015936.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510924.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449381.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212846.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015940.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212850.1
COORDINATES: protein motif:HMM:NF024755.2