Pacificitalea manganoxidans strain DY25 plasmid pDY25-B, 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\nCP021406.1.\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_012236329.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
acetyl-CoA carboxylase biotin carboxyl carrier protein subunit
COORDINATES: similar to AA sequence:RefSeq:WP_008089184.1
COORDINATES: similar to AA sequence:RefSeq:WP_008919512.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019958.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009208003.1
COORDINATES: similar to AA sequence:RefSeq:WP_003256670.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF022586.2
COORDINATES: similar to AA sequence:RefSeq:WP_014881795.1
COORDINATES: similar to AA sequence:RefSeq:WP_014236596.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017340186.1
GO:0008410 - CoA-transferase activity [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_008758200.1
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008089192.1
an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism; Derived by automated computational analysis using gene prediction method: Protein Homology.
biotin carboxylase N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF012656.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_014239504.1
COORDINATES: similar to AA sequence:RefSeq:WP_018044014.1
COORDINATES: protein motif:HMM:NF015445.2
GO:0055085 - transmembrane transport [Evidence IEA]
TRAP transporter substrate-binding protein DctP
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: protein motif:HMM:NF018513.2
COORDINATES: similar to AA sequence:RefSeq:WP_016353439.1
COORDINATES: similar to AA sequence:RefSeq:WP_011046470.1
electron transfer flavoprotein subunit beta/FixA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009825319.1
electron transfer flavoprotein subunit alpha/FixB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013504070.1
C4-dicarboxylate TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013397193.1
COORDINATES: protein motif:HMM:NF013920.2
Zn-ribbon domain-containing OB-fold protein
COORDINATES: protein motif:HMM:NF024938.2
COORDINATES: similar to AA sequence:RefSeq:WP_003045431.1
MaoC/PaaZ C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013392802.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611905.1
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_009192232.1
CaiB/BaiF CoA-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008391824.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
GO:0019619 - 3,4-dihydroxybenzoate catabolic process [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012176898.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503126.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187172.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815553.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120686.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009503806.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282965.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327370.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808058.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807508.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009815545.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327379.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820232.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808064.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187157.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327387.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820228.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187154.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120671.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808070.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611960.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:TIGR02123.1
COORDINATES: protein motif:HMM:TIGR02122.1
GO:0005215 - transporter activity [Evidence IEA]
TAXI family TRAP transporter solute-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_014131800.1
COORDINATES: similar to AA sequence:RefSeq:WP_017537005.1
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: protein motif:HMM:NF024989.2
COORDINATES: protein motif:HMM:TIGR02118.1
COORDINATES: protein motif:HMM:NF015325.2
COORDINATES: similar to AA sequence:RefSeq:WP_006019156.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014131797.1
aromatic-ring-hydroxylating dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_017134361.1
4-hydroxythreonine-4-phosphate dehydrogenase PdxA
COORDINATES: similar to AA sequence:RefSeq:WP_014131795.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574118.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
IclR family transcriptional regulator C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF019421.2
HipA N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: similar to AA sequence:RefSeq:WP_014104098.1
frameshifted; 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:NF033517.1
COORDINATES: similar to AA sequence:RefSeq:WP_007812393.1
COORDINATES: protein motif:HMM:NF024904.2
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014332409.1
COORDINATES: similar to AA sequence:RefSeq:WP_015493510.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_013961422.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335641.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503789.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807938.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120663.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011536569.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820257.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501438.1
COORDINATES: similar to AA sequence:RefSeq:WP_016869180.1
COORDINATES: similar to AA sequence:RefSeq:WP_016869179.1
multiubiquitin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005878692.1
COORDINATES: similar to AA sequence:RefSeq:WP_009797786.1
COORDINATES: similar to AA sequence:RefSeq:WP_009797785.1
COORDINATES: protein motif:HMM:NF025120.2
COORDINATES: similar to AA sequence:RefSeq:WP_010517587.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187346.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819680.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187348.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503768.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824414.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009807491.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_009805280.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241702.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120648.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012187077.1
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010308590.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807537.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187356.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807539.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187358.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120641.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807542.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327455.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820102.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819700.1
COORDINATES: similar to AA sequence:RefSeq:WP_007284652.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_008031971.1
COORDINATES: protein motif:HMM:NF024118.2
COORDINATES: similar to AA sequence:RefSeq:WP_009453051.1
COORDINATES: similar to AA sequence:RefSeq:WP_007257056.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807962.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807963.1
COORDINATES: similar to AA sequence:RefSeq:WP_005617061.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574209.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187244.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803223.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803221.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803220.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065890.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808024.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009573575.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808026.1
COORDINATES: protein motif:HMM:NF019157.2
tannase/feruloyl esterase family alpha/beta hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_003523969.1
COORDINATES: protein motif:HMM:NF019349.2
COORDINATES: similar to AA sequence:RefSeq:WP_009819810.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573583.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573584.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824502.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503854.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138178.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807971.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503851.1
COORDINATES: similar to AA sequence:RefSeq:WP_008889351.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009815494.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815493.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0017000 - antibiotic biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009503847.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815491.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009573591.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803463.1
COORDINATES: similar to AA sequence:RefSeq:WP_013959872.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807977.1
COORDINATES: similar to AA sequence:RefSeq:WP_008889345.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503840.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001721.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803474.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009827282.1
COORDINATES: similar to AA sequence:RefSeq:WP_018303599.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573601.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815479.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138164.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121400.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503821.1
COORDINATES: similar to AA sequence:RefSeq:WP_007796189.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820197.1
COORDINATES: similar to AA sequence:RefSeq:WP_013959912.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Cu(I)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007120890.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503816.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008282876.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820147.1
COORDINATES: similar to AA sequence:RefSeq:WP_010968681.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120885.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503811.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011427422.1
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_004213009.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824440.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611129.1
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: protein motif:HMM:NF013077.2
COORDINATES: protein motif:HMM:NF012596.2
COORDINATES: similar to AA sequence:RefSeq:WP_008089196.1