Pseudooceanicola algae strain Lw-13e plasmid p111, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Pseudooceanicola.
Genome sequence of Rhodobacteraceae bacterium Lw-13e
Submitted (19-AUG-2020) Genomic and Applied Microbiology & Goettingen Genomics Laboratory, Georg-August-University Goettingen, Grisebachstr. 8, Goettingen, Lower Saxony 37077, Germany
Submitted (11-APR-2018) Genomic and Applied Microbiology & Goettingen Genomics Laboratory, Georg-August-University Goettingen, Grisebachstr. 8, Goettingen, Lower Saxony 37077, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP060438.1.\nBacteria and source DNA available from Thorsten Brinkhoff,\nOldenburg.\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 :: Unicycler v. v0.4.7\nCoverage :: 120\nSequencing Technology :: Illumina; Nanopore\n##Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/21/2022 01:45:54\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) :: 3,848\nCDSs (total) :: 3,788\nGenes (coding) :: 3,741\nCDSs (with protein) :: 3,741\nGenes (RNA) :: 60\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 3\nPseudo Genes (total) :: 47\nCDSs (without protein) :: 47\nPseudo Genes (ambiguous residues) :: 0 of 47\nPseudo Genes (frameshifted) :: 14 of 47\nPseudo Genes (incomplete) :: 36 of 47\nPseudo Genes (internal stop) :: 9 of 47\nPseudo Genes (multiple problems) :: 11 of 47\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_018237608.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016486297.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573166.1
GO:0004370 - glycerol kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009573167.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009573168.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861103.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573170.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573171.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802789.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573173.1
GO:0009331 - glycerol-3-phosphate dehydrogenase complex [Evidence IEA]
GO:0004368 - glycerol-3-phosphate dehydrogenase (quinone) activity [Evidence IEA]
GO:0006072 - glycerol-3-phosphate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012177309.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011242084.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335840.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749186.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011910852.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_010140106.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010140105.1
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: protein motif:HMM:NF018979.2
tripartite tricarboxylate transporter TctB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010140103.1
tripartite tricarboxylate transporter permease
COORDINATES: protein motif:HMM:NF014585.2
hydantoinase B/oxoprolinase family protein
COORDINATES: protein motif:HMM:NF017215.2
hydantoinase/oxoprolinase family protein
COORDINATES: protein motif:HMM:NF016040.2
GO:0050385 - ureidoglycolate lyase activity [Evidence IEA]
GO:0000256 - allantoin catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010140118.1
COORDINATES: similar to AA sequence:RefSeq:WP_018698509.1
COORDINATES: protein motif:HMM:NF012575.2
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010140115.1
aromatic ring-hydroxylating dioxygenase subunit alpha
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019955685.1
COORDINATES: protein motif:HMM:NF014958.2
5-carboxymethyl-2-hydroxymuconate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_010140112.1
COORDINATES: similar to AA sequence:RefSeq:WP_010140111.1
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: protein motif:HMM:NF015445.2
TRAP transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF013757.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002724223.1
COORDINATES: similar to AA sequence:RefSeq:WP_008229743.1
glutathionylspermidine synthase family protein
COORDINATES: protein motif:HMM:TIGR02937.1
COORDINATES: similar to AA sequence:RefSeq:WP_008885889.1
endonuclease/exonuclease/phosphatase family protein
COORDINATES: protein motif:HMM:TIGR03169.1
COORDINATES: similar to AA sequence:RefSeq:WP_008032221.1
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF012738.2
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008945944.1
COORDINATES: similar to AA sequence:RefSeq:WP_006724892.1
CDP-alcohol phosphatidyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010321954.1
bifunctional TVP38/TMEM64 family protein/FAD-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018304829.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018304828.1
metal ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018304827.1
COORDINATES: similar to AA sequence:RefSeq:WP_008755981.1
GO:0046872 - metal ion binding [Evidence IEA]
zinc ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_019956229.1
COORDINATES: similar to AA sequence:RefSeq:WP_009571056.1
COORDINATES: similar to AA sequence:RefSeq:WP_011455374.1
COORDINATES: similar to AA sequence:RefSeq:WP_009571055.1
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_009571054.1
COORDINATES: similar to AA sequence:RefSeq:WP_009571053.1
COORDINATES: similar to AA sequence:RefSeq:WP_009571052.1
COORDINATES: similar to AA sequence:RefSeq:WP_009828579.1
COORDINATES: similar to AA sequence:RefSeq:WP_009804145.1
COORDINATES: similar to AA sequence:RefSeq:WP_009506395.1
COORDINATES: similar to AA sequence:RefSeq:WP_009506396.1
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_009504786.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_013152406.1
COORDINATES: similar to AA sequence:RefSeq:WP_005001139.1
YihY/virulence factor BrkB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120125.1
COORDINATES: similar to AA sequence:RefSeq:WP_009504792.1
COORDINATES: protein motif:HMM:NF023697.2
COORDINATES: similar to AA sequence:RefSeq:WP_011454653.1
COORDINATES: similar to AA sequence:RefSeq:WP_005614889.1
COORDINATES: similar to AA sequence:RefSeq:WP_009818129.1
COORDINATES: similar to AA sequence:RefSeq:WP_009175686.1
COORDINATES: similar to AA sequence:RefSeq:WP_009818131.1
COORDINATES: similar to AA sequence:RefSeq:WP_009818132.1
COORDINATES: similar to AA sequence:RefSeq:WP_006700298.1
COORDINATES: similar to AA sequence:RefSeq:WP_017271789.1
amino acid ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003528591.1
COORDINATES: similar to AA sequence:RefSeq:WP_007528825.1
COORDINATES: similar to AA sequence:RefSeq:WP_020009842.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019951399.1
COORDINATES: similar to AA sequence:RefSeq:WP_019951398.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011771069.1
functions to transport ribose at high affinity; forms a complex with RbsA2C2B; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009492582.1
COORDINATES: similar to AA sequence:RefSeq:WP_014369231.1
COORDINATES: similar to AA sequence:RefSeq:WP_014267920.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008741 - ribulokinase activity [Evidence IEA]
GO:0019569 - L-arabinose catabolic process to xylulose 5-phosphate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012071554.1
COORDINATES: similar to AA sequence:RefSeq:WP_019966344.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138136.1
COORDINATES: similar to AA sequence:RefSeq:WP_005849097.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: protein motif:HMM:NF025605.2
COORDINATES: similar to AA sequence:RefSeq:WP_007798580.1
COORDINATES: similar to AA sequence:RefSeq:WP_007798793.1
COORDINATES: similar to AA sequence:RefSeq:WP_008886182.1
COORDINATES: similar to AA sequence:RefSeq:WP_007798959.1
COORDINATES: similar to AA sequence:RefSeq:WP_008884894.1
COORDINATES: similar to AA sequence:RefSeq:WP_007798962.1
COORDINATES: similar to AA sequence:RefSeq:WP_006940451.1
COORDINATES: similar to AA sequence:RefSeq:WP_007798966.1
COORDINATES: similar to AA sequence:RefSeq:WP_009179448.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574263.1
COORDINATES: similar to AA sequence:RefSeq:WP_020812567.1
GO:0008697 - 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity [Evidence IEA]
GO:0045490 - pectin catabolic process [Evidence IEA]
5-dehydro-4-deoxy-D-glucuronate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_003517922.1
GO:0008678 - 2-deoxy-D-gluconate 3-dehydrogenase activity [Evidence IEA]; GO:0051287 - NAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0000272 - polysaccharide catabolic process [Evidence IEA]
2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD
COORDINATES: similar to AA sequence:RefSeq:WP_020043627.1
GO:0005451 - monovalent cation:proton antiporter activity [Evidence IEA]
GO:0098662 - inorganic cation transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002721312.1
GO:0015075 - ion transmembrane transporter activity [Evidence IEA]
GO:0034220 - ion transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008330174.1
GO:0008324 - cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005853258.1
monovalent cation/H+ antiporter subunit D
COORDINATES: similar to AA sequence:RefSeq:WP_011048594.1
COORDINATES: similar to AA sequence:RefSeq:WP_009502662.1
monovalent cation/H+ antiporter subunit A