Paracoccus zhejiangensis strain J6 plasmid pPZ03, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
Paracoccus zhejiangensis sp. nov., isolated from activated sludge in wastewater-treatment system
Submitted (16-DEC-2017) Dept. of biology, Kyung Hee University, 1 HoeGi-Dong, Dongdaemun-gu, Seoul 02447, Korea, Republic of
REFSEQ INFORMATION: The reference sequence is identical to\nCP025433.1.\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 :: 09-NOV-2017\nAssembly Method :: RS HGAP Assembly v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 237.0x\nSequencing Technology :: PacBio; Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 01/01/2023 02:50:49\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) :: 4,516\nCDSs (total) :: 4,460\nGenes (coding) :: 4,382\nCDSs (with protein) :: 4,382\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 78\nCDSs (without protein) :: 78\nPseudo Genes (ambiguous residues) :: 0 of 78\nPseudo Genes (frameshifted) :: 33 of 78\nPseudo Genes (incomplete) :: 64 of 78\nPseudo Genes (internal stop) :: 17 of 78\nPseudo Genes (multiple problems) :: 28 of 78\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
cytochrome-c oxidase, cbb3-type subunit III
COORDINATES: similar to AA sequence:RefSeq:WP_006952789.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
cbb3-type cytochrome c oxidase subunit 3
COORDINATES: similar to AA sequence:RefSeq:WP_019403445.1
cytochrome-c oxidase, cbb3-type subunit II
COORDINATES: similar to AA sequence:RefSeq:WP_019198786.1
cytochrome-c oxidase, cbb3-type subunit I
COORDINATES: similar to AA sequence:RefSeq:WP_010126909.1
GO:0008535 - respiratory chain complex IV assembly [Evidence IEA]
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
cbb3-type cytochrome oxidase assembly protein CcoS
COORDINATES: protein motif:HMM:TIGR01511.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819775.1
COORDINATES: similar to AA sequence:RefSeq:WP_008549269.1
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005855106.1
COORDINATES: similar to AA sequence:RefSeq:WP_002720931.1
GO:0018454 - acetoacetyl-CoA reductase activity [Evidence IEA]
GO:0042619 - poly-hydroxybutyrate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007425269.1
GO:0045250 - cytosolic pyruvate dehydrogenase complex [Evidence IEA]
GO:0004738 - pyruvate dehydrogenase activity [Evidence IEA]
GO:0006086 - acetyl-CoA biosynthetic process from pyruvate [Evidence IEA]
pyruvate dehydrogenase (acetyl-transferring), homodimeric type
COORDINATES: similar to AA sequence:RefSeq:WP_018263482.1
GO:0045254 - pyruvate dehydrogenase complex [Evidence IEA]
GO:0004742 - dihydrolipoyllysine-residue acetyltransferase activity [Evidence IEA]
dihydrolipoyllysine-residue acetyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_005858184.1
GO:0004148 - dihydrolipoyl dehydrogenase activity [Evidence IEA]
GO:0045454 - cell redox homeostasis [Evidence IEA]; GO:0051068 - dihydrolipoamide metabolic process [Evidence IEA]; GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019994825.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749200.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749199.1
COORDINATES: similar to AA sequence:RefSeq:WP_010398807.1
COORDINATES: protein motif:HMM:TIGR01838.1
GO:0016746 - acyltransferase activity [Evidence IEA]
class I poly(R)-hydroxyalkanoic acid synthase
COORDINATES: protein motif:HMM:NF013677.2
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_014189972.1
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_011749336.1
COORDINATES: protein motif:HMM:NF024795.2
COORDINATES: similar to AA sequence:RefSeq:WP_015914912.1
COORDINATES: similar to AA sequence:RefSeq:WP_014878829.1
COORDINATES: similar to AA sequence:RefSeq:WP_003044989.1
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006699254.1
winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006728065.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011647461.1
COORDINATES: similar to AA sequence:RefSeq:WP_011647460.1
GO:0004096 - catalase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019461712.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019956294.1
internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
Arm DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011655426.1
COORDINATES: similar to AA sequence:RefSeq:WP_005619553.1
COORDINATES: protein motif:HMM:NF033580.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003464978.1
DDE-type integrase/transposase/recombinase
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]
COORDINATES: similar to AA sequence:RefSeq:WP_007256465.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: similar to AA sequence:RefSeq:WP_017929223.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007255097.1
COORDINATES: similar to AA sequence:RefSeq:WP_007256466.1
GO:0015144 - carbohydrate transmembrane transporter activity [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
maltose/maltodextrin ABC transporter substrate-binding protein MalE
COORDINATES: similar to AA sequence:RefSeq:WP_014129614.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001252048.1
COORDINATES: protein motif:HMM:NF014335.2
COORDINATES: similar to AA sequence:RefSeq:WP_013068428.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024997.2
COORDINATES: protein motif:HMM:NF013094.2
COORDINATES: protein motif:HMM:NF018381.2
COORDINATES: protein motif:HMM:NF019324.2
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018897447.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF014442.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015497206.1
COORDINATES: similar to AA sequence:RefSeq:WP_020041040.1
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: similar to AA sequence:RefSeq:WP_011536569.1
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009157880.1
frameshifted; internal stop; 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:NF012311.2
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_007118835.1
COORDINATES: similar to AA sequence:RefSeq:WP_002722056.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954973.1
COORDINATES: similar to AA sequence:RefSeq:WP_010400437.1
COORDINATES: similar to AA sequence:RefSeq:WP_013368425.1
COORDINATES: similar to AA sequence:RefSeq:WP_012978187.1
COORDINATES: similar to AA sequence:RefSeq:WP_016844143.1
COORDINATES: similar to AA sequence:RefSeq:WP_010442294.1
COORDINATES: similar to AA sequence:RefSeq:WP_007114042.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006938334.1
COORDINATES: similar to AA sequence:RefSeq:WP_010441780.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010185299.1
COORDINATES: similar to AA sequence:RefSeq:WP_008876097.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF013561.2
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_006725160.1
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_011536558.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011579025.1
COORDINATES: similar to AA sequence:RefSeq:WP_009208650.1
COORDINATES: similar to AA sequence:RefSeq:WP_008758647.1
COORDINATES: similar to AA sequence:RefSeq:WP_012555754.1
COORDINATES: similar to AA sequence:RefSeq:WP_014131750.1
COORDINATES: similar to AA sequence:RefSeq:WP_007596235.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_016556294.1
COORDINATES: similar to AA sequence:RefSeq:WP_013600192.1
COORDINATES: similar to AA sequence:RefSeq:WP_014132988.1
sugar phosphate isomerase/epimerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007596246.1
COORDINATES: similar to AA sequence:RefSeq:WP_014132986.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611129.1
COORDINATES: similar to AA sequence:RefSeq:WP_011046377.1
COORDINATES: protein motif:HMM:NF024809.2
glutathione S-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009819858.1
COORDINATES: protein motif:HMM:NF015649.2
BTAD domain-containing putative transcriptional regulator
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF023568.2
COORDINATES: similar to AA sequence:RefSeq:WP_020040569.1
COORDINATES: similar to AA sequence:RefSeq:WP_008558591.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861669.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187059.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009819734.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009574265.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF018841.2
COORDINATES: similar to AA sequence:RefSeq:WP_009827051.1
GO:0051304 - chromosome separation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011911078.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611905.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS5-like element ISPso2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_008336062.1
COORDINATES: similar to AA sequence:RefSeq:WP_012226833.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017503026.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007406876.1
zinc-dependent alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015497729.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749203.1
COORDINATES: similar to AA sequence:RefSeq:WP_004424460.1
GO:0016901 - oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor [Evidence IEA]
GO:0006089 - lactate metabolic process [Evidence IEA]; GO:0019516 - lactate oxidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012207634.1
COORDINATES: protein motif:HMM:NF013646.2
COORDINATES: protein motif:HMM:NF024776.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913776.1