Paracoccus alcaliphilus strain TK 1015 = DSM 8512 plasmid p77023, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
Biogeographic distribution of Paracoccus
Submitted (05-JAN-2021) Genomic and Applied Microbiology & Goettingen Genomics Laboratory, Georg-August-University Goettingen, Grisebachstr. 8, Goettingen, Lower Saxony 37077, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP067128.1.\nBacteria and source DNA available from Prof. Dr. Thorsten\nBrinkhoff, ICMB, University Oldenburg.\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 :: 26-NOV-2020\nAssembly Method :: Unicycler v. 0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 148.0x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/09/2023 17:10:06\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) :: 4,800\nCDSs (total) :: 4,744\nGenes (coding) :: 4,523\nCDSs (with protein) :: 4,523\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) :: 221\nCDSs (without protein) :: 221\nPseudo Genes (ambiguous residues) :: 0 of 221\nPseudo Genes (frameshifted) :: 75 of 221\nPseudo Genes (incomplete) :: 180 of 221\nPseudo Genes (internal stop) :: 34 of 221\nPseudo Genes (multiple problems) :: 61 of 221\nCRISPR Arrays :: 1\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:NF040974.1
COORDINATES: protein motif:HMM:NF023228.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611905.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009450125.1
COORDINATES: protein motif:HMM:NF013434.2
COORDINATES: protein motif:HMM:NF019604.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024900.2
COORDINATES: protein motif:HMM:NF015445.2
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009813180.1
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: protein motif:HMM:NF012742.2
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009820019.1
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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
programmed frameshift; 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_020952554.1
COORDINATES: similar to AA sequence:RefSeq:WP_014531097.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF017528.2
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.; 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_076612018.1
COORDINATES: similar to AA sequence:RefSeq:WP_013654839.1
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.
COORDINATES: similar to AA sequence:RefSeq:WP_011510447.1
COORDINATES: protein motif:HMM:NF015431.2
LysR family substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011567122.1
putative sulfate exporter family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_008279508.1
COORDINATES: similar to AA sequence:RefSeq:WP_011046350.1
GO:0004399 - histidinol dehydrogenase activity [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019860816.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018387323.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018064344.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0015411 - ABC-type taurine transporter transporter activity [Evidence IEA]; GO:0030977 - taurine binding [Evidence IEA]
GO:0015734 - taurine transport [Evidence IEA]
taurine ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014881428.1
GO:0047689 - aspartate racemase activity [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010141420.1
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_008207772.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006199508.1
COORDINATES: similar to AA sequence:RefSeq:WP_007792048.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018387324.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009814339.1
COORDINATES: similar to AA sequence:RefSeq:WP_009828096.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611865.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008562047.1
COORDINATES: similar to AA sequence:RefSeq:WP_009178320.1
COORDINATES: similar to AA sequence:RefSeq:WP_005981106.1
COORDINATES: similar to AA sequence:RefSeq:WP_009178592.1
GO:0030638 - polyketide metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005981100.1
COORDINATES: similar to AA sequence:RefSeq:WP_005981098.1
COORDINATES: similar to AA sequence:RefSeq:WP_009178398.1
COORDINATES: similar to AA sequence:RefSeq:WP_014875635.1
COORDINATES: similar to AA sequence:RefSeq:WP_010442387.1
COORDINATES: similar to AA sequence:RefSeq:WP_005981089.1
COORDINATES: similar to AA sequence:RefSeq:WP_005981088.1
COORDINATES: similar to AA sequence:RefSeq:WP_005981086.1
COORDINATES: similar to AA sequence:RefSeq:WP_010442382.1
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_008187203.1
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013041277.1
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011911250.1
COORDINATES: similar to AA sequence:RefSeq:WP_010399435.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827397.1
COORDINATES: similar to AA sequence:RefSeq:WP_010399431.1
GO:0009294 - DNA-mediated transformation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010399429.1
COORDINATES: similar to AA sequence:RefSeq:WP_012757137.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_010399477.1
COORDINATES: protein motif:HMM:NF020419.2
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_086558226.1
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_009809990.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011909670.1
COORDINATES: similar to AA sequence:RefSeq:WP_019956757.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007812573.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO:0001558 - regulation of cell growth [Evidence IEA]
type II toxin-antitoxin system PrlF family antitoxin