Pacificitalea manganoxidans strain DY25 plasmid pDY25-A, 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\nCP021405.1.\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_014880613.1
GO:0016746 - acyltransferase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013651784.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_019954967.1
COORDINATES: similar to AA sequence:RefSeq:WP_014880610.1
alpha-ketoacid dehydrogenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_006933718.1
thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_005619409.1
COORDINATES: similar to AA sequence:RefSeq:WP_020043338.1
COORDINATES: similar to AA sequence:RefSeq:WP_020043337.1
COORDINATES: similar to AA sequence:RefSeq:WP_014880605.1
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005625633.1
COORDINATES: similar to AA sequence:RefSeq:WP_018700527.1
COORDINATES: similar to AA sequence:RefSeq:WP_005625641.1
COORDINATES: similar to AA sequence:RefSeq:WP_014880601.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014880600.1
COORDINATES: similar to AA sequence:RefSeq:WP_006933708.1
COORDINATES: similar to AA sequence:RefSeq:WP_008182062.1
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012179200.1
COORDINATES: similar to AA sequence:RefSeq:WP_014954550.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017971427.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014954552.1
COORDINATES: similar to AA sequence:RefSeq:WP_018389727.1
COORDINATES: similar to AA sequence:RefSeq:WP_003507823.1
sulfite exporter TauE/SafE family protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF020090.2
COORDINATES: similar to AA sequence:RefSeq:WP_005614078.1
COORDINATES: similar to AA sequence:RefSeq:WP_009811305.1
COORDINATES: similar to AA sequence:RefSeq:WP_006470719.1
COORDINATES: similar to AA sequence:RefSeq:WP_020590959.1
COORDINATES: similar to AA sequence:RefSeq:WP_018697967.1
COORDINATES: protein motif:HMM:NF012698.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005980316.1
TRAP transporter substrate-binding protein DctP
COORDINATES: similar to AA sequence:RefSeq:WP_017928965.1
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: similar to AA sequence:RefSeq:WP_019296588.1
GO:0008832 - dGTPase activity [Evidence IEA]
GO:0015949 - nucleobase-containing small molecule interconversion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009507223.1
COORDINATES: similar to AA sequence:RefSeq:WP_009507222.1
COORDINATES: protein motif:HMM:NF013438.2
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012515.2
COORDINATES: similar to AA sequence:RefSeq:WP_007253648.1
COORDINATES: similar to AA sequence:RefSeq:WP_007253649.1
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]
isocitrate/isopropylmalate family dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_018389967.1
COORDINATES: similar to AA sequence:RefSeq:WP_007253651.1
COORDINATES: similar to AA sequence:RefSeq:WP_007253652.1
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007253655.1
COORDINATES: similar to AA sequence:RefSeq:WP_007253656.1
COORDINATES: protein motif:HMM:NF015905.2
COORDINATES: similar to AA sequence:RefSeq:WP_007253658.1
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_007253660.1
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_012085581.1
COORDINATES: similar to AA sequence:RefSeq:WP_008967546.1
4-hydroxythreonine-4-phosphate dehydrogenase PdxA
COORDINATES: similar to AA sequence:RefSeq:WP_007253663.1
GO:0009027 - tartrate dehydrogenase activity [Evidence IEA]
GO:0046395 - carboxylic acid catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009359948.1
COORDINATES: protein motif:HMM:NF015366.2
COORDINATES: similar to AA sequence:RefSeq:WP_019956973.1
COORDINATES: similar to AA sequence:RefSeq:WP_008883013.1
phosphatidylcholine/phosphatidylserine synthase
COORDINATES: similar to AA sequence:RefSeq:WP_019956971.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011908248.1
COORDINATES: similar to AA sequence:RefSeq:WP_010137915.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887859.1
TRAP transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF012958.2
COORDINATES: similar to AA sequence:RefSeq:WP_010137912.1
COORDINATES: similar to AA sequence:RefSeq:WP_019462237.1
COORDINATES: protein motif:HMM:NF012873.2
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:TIGR01733.1
amino acid adenylation domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020211059.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015344 - siderophore uptake transmembrane transporter activity [Evidence IEA]
GO:0015891 - siderophore transport [Evidence IEA]
FepA family TonB-dependent siderophore receptor
COORDINATES: similar to AA sequence:RefSeq:WP_009819378.1
COORDINATES: similar to AA sequence:RefSeq:WP_020043718.1
MotA/TolQ/ExbB proton channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009504294.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009812874.1
COORDINATES: protein motif:HMM:NF024503.2
GO:0015291 - secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010141858.1
COORDINATES: similar to AA sequence:RefSeq:WP_008963627.1
COORDINATES: similar to AA sequence:RefSeq:WP_009572516.1
COORDINATES: similar to AA sequence:RefSeq:WP_020142514.1
D-2-hydroxyacid dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009825639.1
type 1 glutamine amidotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005864124.1
COORDINATES: similar to AA sequence:RefSeq:WP_002724987.1
COORDINATES: similar to AA sequence:RefSeq:WP_012643364.1
COORDINATES: similar to AA sequence:RefSeq:WP_014130119.1
COORDINATES: similar to AA sequence:RefSeq:WP_007814133.1
GO:0004474 - malate synthase activity [Evidence IEA]
GO:0006097 - glyoxylate cycle [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009572536.1
COORDINATES: similar to AA sequence:RefSeq:WP_008551148.1
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_007799719.1
COORDINATES: similar to AA sequence:RefSeq:WP_020039574.1
COORDINATES: similar to AA sequence:RefSeq:WP_019016699.1
COORDINATES: protein motif:HMM:NF024854.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005614094.1
COORDINATES: similar to AA sequence:RefSeq:WP_014875497.1
COORDINATES: similar to AA sequence:RefSeq:WP_012177247.1
COORDINATES: similar to AA sequence:RefSeq:WP_005978533.1
COORDINATES: similar to AA sequence:RefSeq:WP_007206343.1
COORDINATES: similar to AA sequence:RefSeq:WP_018390217.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913785.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187500.1
DNA starvation/stationary phase protection protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187501.1
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF015823.2
COORDINATES: similar to AA sequence:RefSeq:WP_013385065.1
COORDINATES: similar to AA sequence:RefSeq:WP_009158830.1
COORDINATES: similar to AA sequence:RefSeq:WP_013984601.1
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_011567779.1
COORDINATES: similar to AA sequence:RefSeq:WP_009814995.1
GO:0004514 - nicotinate-nucleotide diphosphorylase (carboxylating) activity [Evidence IEA]
GO:0019363 - pyridine nucleotide biosynthetic process [Evidence IEA]
carboxylating nicotinate-nucleotide diphosphorylase
COORDINATES: similar to AA sequence:RefSeq:WP_009814996.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0019634 - organic phosphonate metabolic process [Evidence IEA]
phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN
COORDINATES: similar to AA sequence:RefSeq:WP_006727879.1
COORDINATES: similar to AA sequence:RefSeq:WP_013067823.1
GO:0004053 - arginase activity [Evidence IEA]
GO:0019547 - arginine catabolic process to ornithine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020286831.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014744464.1
GO:0000286 - alanine dehydrogenase activity [Evidence IEA]
GO:0006522 - alanine metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013775.2
COORDINATES: similar to AA sequence:RefSeq:WP_008495462.1
aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014880791.1
COORDINATES: similar to AA sequence:RefSeq:WP_010139369.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120397.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0015837 - amine transport [Evidence IEA]
Members of the family are the ATP-binding subunit of ABC transporters for substrates such as betaine, L-proline or other amino acids, choline, carnitine, etc. The substrate specificity is best determined from the substrate-binding subunit, rather than this subunit, as it interacts with the permease subunit and not with substrate directly; Derived by automated computational analysis using gene prediction method: Protein Homology.
betaine/proline/choline family ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006299189.1
COORDINATES: protein motif:HMM:NF013700.2
COORDINATES: similar to AA sequence:RefSeq:WP_013165040.1
COORDINATES: protein motif:HMM:NF012707.2
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008554002.1
COORDINATES: similar to AA sequence:RefSeq:WP_017928797.1
COORDINATES: similar to AA sequence:RefSeq:WP_007906520.1
COORDINATES: similar to AA sequence:RefSeq:WP_013744412.1
COORDINATES: protein motif:HMM:NF012382.2
pyridoxal phosphate-dependent aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_015493500.1
COORDINATES: protein motif:HMM:NF019349.2
COORDINATES: similar to AA sequence:RefSeq:WP_015493499.1
COORDINATES: similar to AA sequence:RefSeq:WP_015493498.1
COORDINATES: similar to AA sequence:RefSeq:WP_015493497.1
COORDINATES: protein motif:HMM:NF014653.2
COORDINATES: similar to AA sequence:RefSeq:WP_019020287.1
COORDINATES: similar to AA sequence:RefSeq:WP_017232980.1
COORDINATES: similar to AA sequence:RefSeq:WP_008959374.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824631.1
COORDINATES: similar to AA sequence:RefSeq:WP_020038213.1
COORDINATES: similar to AA sequence:RefSeq:WP_020038212.1
COORDINATES: similar to AA sequence:RefSeq:WP_009178093.1
COORDINATES: similar to AA sequence:RefSeq:WP_007798944.1
COORDINATES: similar to AA sequence:RefSeq:WP_005620945.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018067170.1
COORDINATES: similar to AA sequence:RefSeq:WP_009287148.1
COORDINATES: similar to AA sequence:RefSeq:WP_020053766.1
COORDINATES: similar to AA sequence:RefSeq:WP_018067163.1
COORDINATES: similar to AA sequence:RefSeq:WP_013046875.1
GO:0004588 - orotate phosphoribosyltransferase activity [Evidence IEA]
GO:0009116 - nucleoside metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007010757.1
COORDINATES: similar to AA sequence:RefSeq:WP_016151337.1
GO:0004152 - dihydroorotate dehydrogenase activity [Evidence IEA]
GO:0006221 - pyrimidine nucleotide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019400627.1
dihydroorotate dehydrogenase electron transfer subunit
COORDINATES: similar to AA sequence:RefSeq:WP_008887047.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887189.1
COORDINATES: similar to AA sequence:RefSeq:WP_009756214.1
COORDINATES: similar to AA sequence:RefSeq:WP_007010751.1
helix-turn-helix transcriptional regulator