Pacificitalea manganoxidans strain DY25 plasmid pDY25-C, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Pacificitalea.
Comparative genomic and metabolic analysis of manganese-oxidizing mechanisms in Celeribater manganoxidans DY25T: its adaption to the environment of polymetallic nodule
Submitted (22-MAY-2017) College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, Shandong 266003, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP021407.1.\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 Method :: Canu v. 1.3\nAssembly Name :: CelManDY25\nLong Assembly Name :: Celeribacter manganoxidans DY25\nGenome Coverage :: 100x\nSequencing Technology :: Complete Genomics\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/31/2022 01:54:42\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) :: 3,656\nCDSs (total) :: 3,599\nGenes (coding) :: 3,554\nCDSs (with protein) :: 3,554\nGenes (RNA) :: 57\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 4\nPseudo Genes (total) :: 45\nCDSs (without protein) :: 45\nPseudo Genes (ambiguous residues) :: 0 of 45\nPseudo Genes (frameshifted) :: 19 of 45\nPseudo Genes (incomplete) :: 30 of 45\nPseudo Genes (internal stop) :: 5 of 45\nPseudo Genes (multiple problems) :: 8 of 45\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Celeribacter manganoxidans
COORDINATES: similar to AA sequence:RefSeq:WP_007803901.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007803899.1
FAD-binding and (Fe-S)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017268460.1
COORDINATES: similar to AA sequence:RefSeq:WP_008884335.1
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017265561.1
COORDINATES: similar to AA sequence:RefSeq:WP_015930309.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008885571.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014531224.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_017264925.1
branched-chain amino acid ABC transporter ATP-binding protein/permease
COORDINATES: similar to AA sequence:RefSeq:WP_002966212.1
COORDINATES: similar to AA sequence:RefSeq:WP_012317356.1
GO:0004316 - 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity [Evidence IEA]; GO:0051287 - NAD binding [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803606.1
COORDINATES: similar to AA sequence:RefSeq:WP_009449347.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GMC family oxidoreductase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007596647.1
COORDINATES: similar to AA sequence:RefSeq:WP_018301228.1
sulfite exporter TauE/SafE family protein
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_009603958.1
COORDINATES: similar to AA sequence:RefSeq:WP_005851802.1
COORDINATES: similar to AA sequence:RefSeq:WP_008229498.1
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_008194520.1
COORDINATES: similar to AA sequence:RefSeq:WP_005851792.1
COORDINATES: similar to AA sequence:RefSeq:WP_008888103.1
FAD-dependent tricarballylate dehydrogenase TcuA
COORDINATES: similar to AA sequence:RefSeq:WP_009450407.1
tricarballylate utilization 4Fe-4S protein TcuB
COORDINATES: similar to AA sequence:RefSeq:WP_013169092.1
isocitrate/isopropylmalate dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007772288.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007256370.1
GO:0005515 - protein binding [Evidence IEA]
hybrid sensor histidine kinase/response regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005852007.1
COORDINATES: protein motif:HMM:NF013757.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF014608.2
COORDINATES: protein motif:HMM:NF015445.2
C4-dicarboxylate TRAP transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: similar to AA sequence:RefSeq:WP_010437378.1
COORDINATES: protein motif:HMM:NF024809.2
glutathione S-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020043032.1
COORDINATES: similar to AA sequence:RefSeq:WP_010140519.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
putative selenate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009503690.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007794716.1
COORDINATES: similar to AA sequence:RefSeq:WP_008185797.1
COORDINATES: similar to AA sequence:RefSeq:WP_020058600.1
GO:0018576 - catechol 1,2-dioxygenase activity [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
GO:0009712 - catechol-containing compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008194914.1
COORDINATES: similar to AA sequence:RefSeq:WP_010437374.1
COORDINATES: similar to AA sequence:RefSeq:WP_007678480.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012177641.1
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010437367.1
COORDINATES: similar to AA sequence:RefSeq:WP_008281646.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802775.1
COORDINATES: protein motif:HMM:NF013862.2
GO:0006629 - lipid metabolic process [Evidence IEA]
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017407222.1
COORDINATES: similar to AA sequence:RefSeq:WP_012971760.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_007206657.1
COORDINATES: similar to AA sequence:RefSeq:WP_011569788.1
GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0009045 - xylose isomerase activity [Evidence IEA]
GO:0042732 - D-xylose metabolic process [Evidence IEA]; GO:0006098 - pentose-phosphate shunt [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018633999.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018698844.1
histidine kinase dimerization/phosphoacceptor domain -containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007812583.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]
GO:0006276 - plasmid maintenance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007812581.1
type II toxin-antitoxin system CcdA family antitoxin
COORDINATES: protein motif:HMM:NF012575.2
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008942826.1
GO:0019213 - deacetylase activity [Evidence IEA]; GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
amidohydrolase/deacetylase family metallohydrolase
COORDINATES: protein motif:HMM:NF018275.2
COORDINATES: similar to AA sequence:RefSeq:WP_018263874.1
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018389520.1
COORDINATES: similar to AA sequence:RefSeq:WP_012335366.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007577311.1
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008942822.1
COORDINATES: similar to AA sequence:RefSeq:WP_018389532.1
COORDINATES: similar to AA sequence:RefSeq:WP_018389533.1
COORDINATES: similar to AA sequence:RefSeq:WP_008942814.1
COORDINATES: similar to AA sequence:RefSeq:WP_006019507.1
COORDINATES: similar to AA sequence:RefSeq:WP_008942817.1
amino acid ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018916926.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018916923.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574234.1
COORDINATES: similar to AA sequence:RefSeq:WP_020043035.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005861667.1
COORDINATES: similar to AA sequence:RefSeq:WP_013368559.1
COORDINATES: similar to AA sequence:RefSeq:WP_007426070.1
COORDINATES: similar to AA sequence:RefSeq:WP_018303025.1
COORDINATES: similar to AA sequence:RefSeq:WP_007426072.1
COORDINATES: similar to AA sequence:RefSeq:WP_008838566.1
COORDINATES: similar to AA sequence:RefSeq:WP_017929957.1
COORDINATES: similar to AA sequence:RefSeq:WP_009030984.1
COORDINATES: similar to AA sequence:RefSeq:WP_015666057.1
COORDINATES: similar to AA sequence:RefSeq:WP_006938828.1
COORDINATES: similar to AA sequence:RefSeq:WP_011575122.1
COORDINATES: similar to AA sequence:RefSeq:WP_012316331.1
GO:0070403 - NAD+ binding [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006938831.1
COORDINATES: similar to AA sequence:RefSeq:WP_006938832.1
COORDINATES: similar to AA sequence:RefSeq:WP_006938833.1
COORDINATES: similar to AA sequence:RefSeq:WP_018701091.1
COORDINATES: similar to AA sequence:RefSeq:WP_016493048.1
COORDINATES: similar to AA sequence:RefSeq:WP_010394359.1
3-keto-5-aminohexanoate cleavage protein
COORDINATES: protein motif:HMM:NF018513.2
COORDINATES: protein motif:HMM:NF012607.2
COORDINATES: protein motif:HMM:NF012766.2
COORDINATES: similar to AA sequence:RefSeq:WP_012114078.1