Paracoccus zhejiangensis strain J6 plasmid pPZ02, 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\nCP025432.1.\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+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF015431.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011485221.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006394309.1
COORDINATES: similar to AA sequence:RefSeq:WP_010955159.1
COORDINATES: similar to AA sequence:RefSeq:WP_014189193.1
COORDINATES: similar to AA sequence:RefSeq:WP_010400219.1
COORDINATES: similar to AA sequence:RefSeq:WP_010400220.1
COORDINATES: similar to AA sequence:RefSeq:WP_010400221.1
COORDINATES: protein motif:HMM:NF015905.2
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008336078.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF040249.1
COORDINATES: protein motif:HMM:NF014381.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
NAD/NADP-dependent octopine/nopaline dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009465867.1
COORDINATES: similar to AA sequence:RefSeq:WP_009812249.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009812250.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013382924.1
COORDINATES: similar to AA sequence:RefSeq:WP_006593178.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819806.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803570.1
mercury resistance system transport protein MerF
COORDINATES: similar to AA sequence:RefSeq:WP_009807473.1
COORDINATES: similar to AA sequence:RefSeq:WP_017927535.1
mercuric transporter MerT family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009209168.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015923008.1
COORDINATES: similar to AA sequence:RefSeq:WP_009618209.1
COORDINATES: similar to AA sequence:RefSeq:WP_019956948.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120059.1
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_019404837.1
COORDINATES: similar to AA sequence:RefSeq:WP_005978987.1
electron transfer flavoprotein-ubiquinone oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007197898.1
class I adenylate-forming enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017928481.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007425723.1
COORDINATES: similar to AA sequence:RefSeq:WP_009826243.1
COORDINATES: similar to AA sequence:RefSeq:WP_008547043.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009176753.1
GO:0003985 - acetyl-CoA C-acetyltransferase activity [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008226753.1
GO:0070403 - NAD+ binding [Evidence IEA]
3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017928475.1
COORDINATES: similar to AA sequence:RefSeq:WP_007425717.1
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: similar to AA sequence:RefSeq:WP_007197889.1
C4-dicarboxylate TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008282908.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982795.1
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_008995222.1
COORDINATES: similar to AA sequence:RefSeq:WP_014878829.1
COORDINATES: similar to AA sequence:RefSeq:WP_019863962.1
COORDINATES: similar to AA sequence:RefSeq:WP_019863961.1
COORDINATES: similar to AA sequence:RefSeq:WP_009469622.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF023228.2
COORDINATES: similar to AA sequence:RefSeq:WP_018390217.1
COORDINATES: similar to AA sequence:RefSeq:WP_010400524.1
COORDINATES: similar to AA sequence:RefSeq:WP_014332409.1
COORDINATES: similar to AA sequence:RefSeq:WP_002730641.1
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: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_018009737.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611917.1
COORDINATES: similar to AA sequence:RefSeq:WP_005631495.1
COORDINATES: similar to AA sequence:RefSeq:WP_012641295.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972745.1
COORDINATES: similar to AA sequence:RefSeq:WP_010442288.1
COORDINATES: similar to AA sequence:RefSeq:WP_005631479.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0003674 - molecular_function [Evidence IEA]
GO:0045861 - negative regulation of proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010442286.1
COORDINATES: similar to AA sequence:RefSeq:WP_017276710.1
GO:0015385 - sodium:proton antiporter activity [Evidence IEA]
GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0006814 - sodium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008235597.1
COORDINATES: similar to AA sequence:RefSeq:WP_014880157.1
COORDINATES: similar to AA sequence:RefSeq:WP_010442276.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008556092.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611693.1
COORDINATES: similar to AA sequence:RefSeq:WP_008883091.1
COORDINATES: similar to AA sequence:RefSeq:WP_008883032.1
COORDINATES: similar to AA sequence:RefSeq:WP_008882979.1
COORDINATES: similar to AA sequence:RefSeq:WP_018426265.1
COORDINATES: similar to AA sequence:RefSeq:WP_004118319.1
COORDINATES: similar to AA sequence:RefSeq:WP_008495843.1
COORDINATES: similar to AA sequence:RefSeq:WP_037302177.1
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_002723528.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120715.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612253.1
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_012976042.1
COORDINATES: similar to AA sequence:RefSeq:WP_011746418.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family transposase zinc-finger binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019956188.1
integrase arm-type DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007794245.1
GO:0016020 - membrane [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018234997.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_009570724.1
COORDINATES: similar to AA sequence:RefSeq:WP_008886623.1
COORDINATES: similar to AA sequence:RefSeq:WP_008886663.1
COORDINATES: similar to AA sequence:RefSeq:WP_007794232.1
cyclopropane-fatty-acyl-phospholipid synthase family protein
COORDINATES: protein motif:HMM:NF024742.2
COORDINATES: similar to AA sequence:RefSeq:WP_008886957.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013066444.1
COORDINATES: similar to AA sequence:RefSeq:WP_013761022.1
COORDINATES: similar to AA sequence:RefSeq:WP_011579025.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536558.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187342.1
COORDINATES: similar to AA sequence:RefSeq:WP_013382981.1
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008876097.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010185299.1
COORDINATES: similar to AA sequence:RefSeq:WP_009450595.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749562.1
COORDINATES: similar to AA sequence:RefSeq:WP_008613283.1
COORDINATES: similar to AA sequence:RefSeq:WP_009450592.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_008033018.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010397533.1
COORDINATES: similar to AA sequence:RefSeq:WP_008280728.1
COORDINATES: similar to AA sequence:RefSeq:WP_012178972.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819773.1
COORDINATES: similar to AA sequence:RefSeq:WP_009817689.1
GO:0030272 - 5-formyltetrahydrofolate cyclo-ligase activity [Evidence IEA]
GO:0006730 - one-carbon metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011567937.1
COORDINATES: similar to AA sequence:RefSeq:WP_007425913.1
COORDINATES: similar to AA sequence:RefSeq:WP_011568621.1
COORDINATES: similar to AA sequence:RefSeq:WP_009505383.1
COORDINATES: similar to AA sequence:RefSeq:WP_009809078.1
GO:0009325 - nitrate reductase complex [Evidence IEA]
GO:0008940 - nitrate reductase activity [Evidence IEA]
GO:0009061 - anaerobic respiration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009505381.1
COORDINATES: similar to AA sequence:RefSeq:WP_009505380.1
GO:0051082 - unfolded protein binding [Evidence IEA]
GO:0051131 - chaperone-mediated protein complex assembly [Evidence IEA]
nitrate reductase molybdenum cofactor assembly chaperone
COORDINATES: similar to AA sequence:RefSeq:WP_009505379.1
GO:0019645 - anaerobic electron transport chain [Evidence IEA]
respiratory nitrate reductase subunit gamma
COORDINATES: similar to AA sequence:RefSeq:WP_009505378.1
GO:0003755 - peptidyl-prolyl cis-trans isomerase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013936.2
COORDINATES: similar to AA sequence:RefSeq:WP_009505376.1
COORDINATES: similar to AA sequence:RefSeq:WP_009505375.1
COORDINATES: similar to AA sequence:RefSeq:WP_005612629.1
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011536569.1
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF015118.2
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: similar to AA sequence:RefSeq:WP_009807908.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF012967.2
COORDINATES: protein motif:HMM:NF015437.2
COORDINATES: protein motif:HMM:NF015393.2
COORDINATES: similar to AA sequence:RefSeq:WP_009859433.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820102.1
COORDINATES: similar to AA sequence:RefSeq:WP_008996399.1
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_013168886.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF019324.2
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: protein motif:HMM:NF018381.2
COORDINATES: similar to AA sequence:RefSeq:WP_003592430.1
winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015316619.1
COORDINATES: similar to AA sequence:RefSeq:WP_009175406.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010660181.1
COORDINATES: similar to AA sequence:RefSeq:WP_018575427.1
COORDINATES: similar to AA sequence:RefSeq:WP_015599814.1
COORDINATES: similar to AA sequence:RefSeq:WP_019404651.1
COORDINATES: similar to AA sequence:RefSeq:WP_011266187.1
COORDINATES: similar to AA sequence:RefSeq:WP_011266186.1
COORDINATES: similar to AA sequence:RefSeq:WP_015914891.1
COORDINATES: similar to AA sequence:RefSeq:WP_018238875.1
COORDINATES: similar to AA sequence:RefSeq:WP_015495979.1
COORDINATES: similar to AA sequence:RefSeq:WP_019466075.1
COORDINATES: similar to AA sequence:RefSeq:WP_013131850.1
ADP-ribosylglycohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019954137.1
COORDINATES: similar to AA sequence:RefSeq:WP_019954138.1
COORDINATES: similar to AA sequence:RefSeq:WP_009452585.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807501.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_009807500.1
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_009807499.1
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_003517228.1
GO:0016639 - oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012573.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612408.1
COORDINATES: protein motif:HMM:NF023398.2
COORDINATES: similar to AA sequence:RefSeq:WP_010915931.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015341809.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_015860163.1
COORDINATES: similar to AA sequence:RefSeq:WP_007514452.1
COORDINATES: similar to AA sequence:RefSeq:WP_018095603.1
COORDINATES: similar to AA sequence:RefSeq:WP_006468204.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017929909.1
COORDINATES: similar to AA sequence:RefSeq:WP_009179448.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121137.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF013970.2
COORDINATES: similar to AA sequence:RefSeq:WP_011883461.1
COORDINATES: similar to AA sequence:RefSeq:WP_011242081.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574268.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574267.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574266.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611129.1
COORDINATES: similar to AA sequence:RefSeq:WP_011046377.1
COORDINATES: protein motif:HMM:NF012382.2
PLP-dependent aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009819864.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819858.1
COORDINATES: protein motif:HMM:NF024809.2
glutathione S-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011910452.1
COORDINATES: similar to AA sequence:RefSeq:WP_004085610.1
type I restriction-modification system subunit M N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF024257.2
substrate-binding domain-containing protein