Paracoccus marcusii strain CP157 plasmid pCP157_03, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
High Potential for Secondary Metabolite Production of Paracoccus marcusii CP157, Isolated From the Crustacean Cancer pagurus
Submitted (10-DEC-2020) Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP065895.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP SMRTPortal v. 2.3.0\nGenome Coverage :: 65x\nSequencing Technology :: PacBio; Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 06:10:02\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) :: 4,059\nCDSs (total) :: 3,997\nGenes (coding) :: 3,913\nCDSs (with protein) :: 3,913\nGenes (RNA) :: 62\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 3\nPseudo Genes (total) :: 84\nCDSs (without protein) :: 84\nPseudo Genes (ambiguous residues) :: 0 of 84\nPseudo Genes (frameshifted) :: 47 of 84\nPseudo Genes (incomplete) :: 43 of 84\nPseudo Genes (internal stop) :: 20 of 84\nPseudo Genes (multiple problems) :: 23 of 84\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011331263.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009804006.1
COORDINATES: protein motif:HMM:NF010396.0
COORDINATES: similar to AA sequence:RefSeq:WP_019862816.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019963873.1
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_010969406.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0015556 - C4-dicarboxylate transmembrane transporter activity [Evidence IEA]
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020042051.1
COORDINATES: similar to AA sequence:RefSeq:WP_002938547.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010969401.1
COORDINATES: similar to AA sequence:RefSeq:WP_008226844.1
transketolase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007558611.1
COORDINATES: similar to AA sequence:RefSeq:WP_014529495.1
COORDINATES: similar to AA sequence:RefSeq:WP_018064281.1
GO:0004371 - glycerone kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611977.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011805842.1
COORDINATES: protein motif:HMM:NF020604.2
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: similar to AA sequence:RefSeq:WP_009504423.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_008209717.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]; GO:0003979 - UDP-glucose 6-dehydrogenase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012360.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611905.1
COORDINATES: protein motif:HMM:NF012573.2
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_011970376.1
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_007813144.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612405.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019370852.1
COORDINATES: similar to AA sequence:RefSeq:WP_019998513.1
COORDINATES: similar to AA sequence:RefSeq:WP_004682529.1
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:NF013718.2
COORDINATES: similar to AA sequence:RefSeq:WP_008874627.1
COORDINATES: similar to AA sequence:RefSeq:WP_019998559.1
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012335084.1
COORDINATES: protein motif:HMM:NF021098.2
COORDINATES: protein motif:HMM:NF016807.2
GO:0009882 - blue light photoreceptor activity [Evidence IEA]; GO:0071949 - FAD binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017671507.1
COORDINATES: protein motif:HMM:NF023697.2
COORDINATES: similar to AA sequence:RefSeq:WP_007254235.1
COORDINATES: similar to AA sequence:RefSeq:WP_016736121.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF013736.2
GO:0004673 - protein histidine kinase activity [Evidence IEA]
HWE histidine kinase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002943955.1
COORDINATES: similar to AA sequence:RefSeq:WP_019951735.1
COORDINATES: similar to AA sequence:RefSeq:WP_013648256.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004739226.1
COORDINATES: similar to AA sequence:RefSeq:WP_007881755.1
COORDINATES: protein motif:HMM:NF018381.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611843.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024013.2
COORDINATES: protein motif:HMM:NF014273.2
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010139925.1
COORDINATES: similar to AA sequence:RefSeq:WP_010141449.1
COORDINATES: similar to AA sequence:RefSeq:WP_009762545.1
COORDINATES: similar to AA sequence:RefSeq:WP_017484705.1
COORDINATES: similar to AA sequence:RefSeq:WP_018098185.1
COORDINATES: similar to AA sequence:RefSeq:WP_018719134.1
GO:0009055 - electron transfer activity [Evidence IEA]
cytochrome b/b6 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013721346.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803257.1
COORDINATES: similar to AA sequence:RefSeq:WP_017929788.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012335530.1
COORDINATES: protein motif:HMM:NF014425.2
COORDINATES: similar to AA sequence:RefSeq:WP_019952781.1
lipid-A-disaccharide synthase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003543080.1
COORDINATES: similar to AA sequence:RefSeq:WP_008554250.1
COORDINATES: similar to AA sequence:RefSeq:WP_020820237.1
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: similar to AA sequence:RefSeq:WP_008034243.1
COORDINATES: similar to AA sequence:RefSeq:WP_007198211.1
Lrp/AsnC family transcriptional regulator
COORDINATES: protein motif:HMM:NF024811.2
COORDINATES: similar to AA sequence:RefSeq:WP_013896367.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011655434.1
COORDINATES: similar to AA sequence:RefSeq:WP_007635327.1
COORDINATES: similar to AA sequence:RefSeq:WP_016735668.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007068625.1
COORDINATES: protein motif:HMM:NF022072.2
COORDINATES: similar to AA sequence:RefSeq:WP_013656968.1
COORDINATES: similar to AA sequence:RefSeq:WP_047389784.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_076611960.1
GO:0015074 - DNA integration [Evidence IEA]
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_007255052.1
COORDINATES: similar to AA sequence:RefSeq:WP_007403880.1
COORDINATES: similar to AA sequence:RefSeq:WP_018449313.1
COORDINATES: similar to AA sequence:RefSeq:WP_017963087.1
PAS domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_012456232.1
GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0008984 - protein-glutamate methylesterase activity [Evidence IEA]
GO:0006935 - chemotaxis [Evidence IEA]; GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012709985.1
COORDINATES: similar to AA sequence:RefSeq:WP_014531211.1
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_013504359.1
COORDINATES: similar to AA sequence:RefSeq:WP_019997779.1
COORDINATES: similar to AA sequence:RefSeq:WP_015824003.1
COORDINATES: similar to AA sequence:RefSeq:WP_007283797.1
COORDINATES: protein motif:HMM:NF039524.1
COORDINATES: similar to AA sequence:RefSeq:WP_010237328.1
COORDINATES: protein motif:HMM:NF013862.2
GO:0006629 - lipid metabolic process [Evidence IEA]
patatin-like phospholipase family protein
COORDINATES: protein motif:HMM:NF025013.2
COORDINATES: similar to AA sequence:RefSeq:WP_012760461.1
COORDINATES: similar to AA sequence:RefSeq:WP_006724510.1
COORDINATES: similar to AA sequence:RefSeq:WP_002725081.1
COORDINATES: similar to AA sequence:RefSeq:WP_018098814.1
COORDINATES: similar to AA sequence:RefSeq:WP_011456702.1
COORDINATES: similar to AA sequence:RefSeq:WP_007812558.1
COORDINATES: similar to AA sequence:RefSeq:WP_013651621.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007686455.1
GO:0046855 - inositol phosphate dephosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF012515.2
COORDINATES: similar to AA sequence:RefSeq:WP_052642793.1
COORDINATES: protein motif:HMM:NF019128.2
COORDINATES: protein motif:HMM:NF016701.2
COORDINATES: similar to AA sequence:RefSeq:WP_020058784.1
COORDINATES: similar to AA sequence:RefSeq:WP_018329185.1
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: protein motif:HMM:NF012955.2
COORDINATES: protein motif:HMM:NF012521.2
COORDINATES: similar to AA sequence:RefSeq:WP_006724941.1
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF012738.2
COORDINATES: protein motif:HMM:NF014997.2
COORDINATES: protein motif:HMM:NF013395.2
COORDINATES: protein motif:HMM:NF014038.2
COORDINATES: protein motif:HMM:NF012514.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013043234.1
COORDINATES: similar to AA sequence:RefSeq:WP_019956279.1
COORDINATES: protein motif:HMM:NF017085.2
COORDINATES: similar to AA sequence:RefSeq:WP_013043237.1
COORDINATES: similar to AA sequence:RefSeq:WP_017997802.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]
GO:0006796 - phosphate-containing compound metabolic process [Evidence IEA]; GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
phosphate regulon transcriptional regulator PhoB
COORDINATES: similar to AA sequence:RefSeq:WP_008280908.1
GO:0051049 - regulation of transport [Evidence IEA]
phosphate signaling complex protein PhoU
COORDINATES: similar to AA sequence:RefSeq:WP_009818866.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0015415 - ATPase-coupled phosphate ion transmembrane transporter activity [Evidence IEA]
phosphate ABC transporter ATP-binding protein PstB
COORDINATES: similar to AA sequence:RefSeq:WP_017997799.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015415 - ATPase-coupled phosphate ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009564363.1
phosphate ABC transporter permease subunit PstC
COORDINATES: similar to AA sequence:RefSeq:WP_020040304.1
substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF017758.2
COORDINATES: protein motif:HMM:NF025605.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009564419.1
COORDINATES: similar to AA sequence:RefSeq:WP_011339001.1
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_015918694.1
COORDINATES: similar to AA sequence:RefSeq:WP_012362803.1
COORDINATES: protein motif:HMM:NF023398.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018065891.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331447.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503866.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein