Paracoccus jeotgali strain CBA4604 plasmid pCBA4604-01, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Paracoccus.
Genomic analysis of Paracoccus sp. CBA4604
Submitted (20-DEC-2017) Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, Gwangju, Gwangju 61755, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP025584.1.\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 :: RS HGAP Assembly v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 146.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/26/2022 04:14:26\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 3,224\nCDSs (total) :: 3,168\nGenes (coding) :: 3,081\nCDSs (with protein) :: 3,081\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) :: 87\nCDSs (without protein) :: 87\nPseudo Genes (ambiguous residues) :: 0 of 87\nPseudo Genes (frameshifted) :: 54 of 87\nPseudo Genes (incomplete) :: 38 of 87\nPseudo Genes (internal stop) :: 14 of 87\nPseudo Genes (multiple problems) :: 16 of 87\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF021098.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005617050.1
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_005617048.1
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015821555.1
COORDINATES: similar to AA sequence:RefSeq:WP_019339649.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014994517.1
COORDINATES: similar to AA sequence:RefSeq:WP_011466160.1
COORDINATES: similar to AA sequence:RefSeq:WP_020703957.1
COORDINATES: similar to AA sequence:RefSeq:WP_012206962.1
COORDINATES: similar to AA sequence:RefSeq:WP_012416771.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_019139953.1
COORDINATES: similar to AA sequence:RefSeq:WP_009241152.1
COORDINATES: protein motif:HMM:NF014430.2
COORDINATES: similar to AA sequence:RefSeq:WP_086558307.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_007558556.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015235792.1
COORDINATES: similar to AA sequence:RefSeq:WP_017956946.1
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF012596.2
enoyl-CoA hydratase/isomerase family protein
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012398.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012589.2
GO:0016773 - phosphotransferase activity, alcohol group as acceptor [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF014910.2
COORDINATES: protein motif:HMM:NF013434.2
glycerol-3-phosphate dehydrogenase/oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_011501457.1
COORDINATES: protein motif:HMM:NF012738.2
COORDINATES: protein motif:HMM:NF024808.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF024994.2
COORDINATES: protein motif:HMM:NF013540.2
COORDINATES: protein motif:HMM:NF012656.2
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_036759113.1
COORDINATES: similar to AA sequence:RefSeq:WP_052096176.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008228918.1
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_009824650.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0051049 - regulation of transport [Evidence IEA]
phosphate signaling complex protein PhoU
COORDINATES: similar to AA sequence:RefSeq:WP_007205896.1
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_009160029.1
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_009158756.1
phosphate ABC transporter permease subunit PstC
COORDINATES: similar to AA sequence:RefSeq:WP_011047679.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007119652.1
COORDINATES: similar to AA sequence:RefSeq:WP_017932647.1
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: similar to AA sequence:RefSeq:WP_013368485.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335790.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335786.1
COORDINATES: similar to AA sequence:RefSeq:WP_013368488.1
YkoF family thiamine/hydroxymethylpyrimidine-binding protein
COORDINATES: nucleotide motif:Rfam:14.4:RF00059
TPP riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF022019.2
COORDINATES: similar to AA sequence:RefSeq:WP_006724000.1
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_007396258.1
COORDINATES: similar to AA sequence:RefSeq:WP_011750687.1
GO:0004356 - glutamate-ammonia ligase activity [Evidence IEA]
GO:0006542 - glutamine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009563189.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0015930 - glutamate synthase activity [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0006537 - glutamate biosynthetic process [Evidence IEA]; GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009157910.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827091.1
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_009175392.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002721993.1
COORDINATES: similar to AA sequence:RefSeq:WP_014529321.1
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF017826.2
COORDINATES: protein motif:HMM:NF013561.2
COORDINATES: similar to AA sequence:RefSeq:WP_005632315.1
COORDINATES: protein motif:HMM:NF012573.2
COORDINATES: similar to AA sequence:RefSeq:WP_005852463.1
23S rRNA (adenine(2030)-N(6))-methyltransferase RlmJ
COORDINATES: similar to AA sequence:RefSeq:WP_011337232.1
COORDINATES: similar to AA sequence:RefSeq:WP_011907535.1
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_009503866.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011331447.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807920.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749831.1
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.; frameshifted; 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_018000155.1
COORDINATES: similar to AA sequence:RefSeq:WP_017998127.1
PLP-dependent aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013960746.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018067671.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331270.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331271.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010396018.1
COORDINATES: similar to AA sequence:RefSeq:WP_010396019.1
GO:0050487 - sulfoacetaldehyde acetyltransferase activity [Evidence IEA]
GO:0019529 - taurine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002724852.1
putative sulfate exporter family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_011747936.1
GO:0008959 - phosphate acetyltransferase activity [Evidence IEA]
GO:0006086 - acetyl-CoA biosynthetic process from pyruvate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009816756.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007787782.1
COORDINATES: similar to AA sequence:RefSeq:WP_013963214.1
GO:0004053 - arginase activity [Evidence IEA]
GO:0019547 - arginine catabolic process to ornithine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007427948.1
COORDINATES: similar to AA sequence:RefSeq:WP_017430898.1
COORDINATES: similar to AA sequence:RefSeq:WP_000965522.1
GO:0015837 - amine transport [Evidence IEA]
The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc.; The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011975737.1
COORDINATES: similar to AA sequence:RefSeq:WP_019933496.1
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF037640.2
COORDINATES: protein motif:HMM:NF019604.2
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_013963211.1
COORDINATES: similar to AA sequence:RefSeq:WP_008033775.1
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF025939.2
COORDINATES: protein motif:HMM:TIGR02123.1
COORDINATES: protein motif:HMM:TIGR02122.1
TAXI family TRAP transporter solute-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003441301.1
COORDINATES: similar to AA sequence:RefSeq:WP_014852738.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887339.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_008887440.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011749186.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011242083.1
COORDINATES: similar to AA sequence:RefSeq:WP_013984640.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138187.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187243.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611845.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611976.1
COORDINATES: similar to AA sequence:RefSeq:WP_012330183.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612068.1
COORDINATES: similar to AA sequence:RefSeq:WP_007564078.1
COORDINATES: similar to AA sequence:RefSeq:WP_009812250.1
COORDINATES: similar to AA sequence:RefSeq:WP_016395069.1
GO:0070403 - NAD+ binding [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016500612.1
GO:0003985 - acetyl-CoA C-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018318967.1
COORDINATES: similar to AA sequence:RefSeq:WP_011049065.1
COORDINATES: similar to AA sequence:RefSeq:WP_019140934.1
GO:0016874 - ligase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012079404.1
branched-chain amino acid ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009666737.1
COORDINATES: similar to AA sequence:RefSeq:WP_009666738.1
COORDINATES: similar to AA sequence:RefSeq:WP_009666739.1
COORDINATES: similar to AA sequence:RefSeq:WP_006576136.1
COORDINATES: protein motif:HMM:NF024844.2
MaoC family dehydratase N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF036525.2
COORDINATES: similar to AA sequence:RefSeq:WP_019718581.1
COORDINATES: similar to AA sequence:RefSeq:WP_006763850.1