Paraburkholderia caffeinilytica strain CF1 plasmid p1, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Paraburkholderia.
Complete genome sequence of Paraburkholderia caffeinilytica CF1, an efficient bacterium for caffeine degradation
Submitted (07-AUG-2018) School of Biological Engineering, Dalian Polytechnic University, No.1 Qing Gongyuan, Gan Jingzi District, Dalian 116034, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP031468.1.\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 :: SMRT portal v. 2.3.0\nExpected Final Version :: yes\nGenome Coverage :: 100x\nSequencing Technology :: Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/23/2023 04:33:05\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 7,395\nCDSs (total) :: 7,308\nGenes (coding) :: 7,196\nCDSs (with protein) :: 7,196\nGenes (RNA) :: 87\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 65\nncRNAs :: 4\nPseudo Genes (total) :: 112\nCDSs (without protein) :: 112\nPseudo Genes (ambiguous residues) :: 0 of 112\nPseudo Genes (frameshifted) :: 25 of 112\nPseudo Genes (incomplete) :: 98 of 112\nPseudo Genes (internal stop) :: 13 of 112\nPseudo Genes (multiple problems) :: 21 of 112\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Paraburkholderia caffeinilytica
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011875643.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018913215.1
COORDINATES: similar to AA sequence:RefSeq:WP_017702358.1
COORDINATES: similar to AA sequence:RefSeq:WP_003894603.1
COORDINATES: similar to AA sequence:RefSeq:WP_018441919.1
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_007182806.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007586026.1
COORDINATES: similar to AA sequence:RefSeq:WP_004434301.1
COORDINATES: similar to AA sequence:RefSeq:WP_012565280.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011382090.1
COORDINATES: similar to AA sequence:RefSeq:WP_008917785.1
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_013089215.1
COORDINATES: similar to AA sequence:RefSeq:WP_012211068.1
COORDINATES: similar to AA sequence:RefSeq:WP_013691818.1
GO:0051782 - negative regulation of cell division [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
translesion DNA synthesis-associated protein ImuA
COORDINATES: similar to AA sequence:RefSeq:WP_007182879.1
GO:0043828 - tRNA 2-selenouridine synthase activity [Evidence IEA]
GO:0002098 - tRNA wobble uridine modification [Evidence IEA]
COORDINATES: protein motif:HMM:NF015437.2
autoinducer binding domain-containing protein
COORDINATES: protein motif:HMM:NF012699.2
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007182883.1
COORDINATES: similar to AA sequence:RefSeq:WP_007731408.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007731410.1
COORDINATES: similar to AA sequence:RefSeq:WP_007731411.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_007731413.1
VirB4 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_007731414.1
COORDINATES: similar to AA sequence:RefSeq:WP_007731416.1
COORDINATES: similar to AA sequence:RefSeq:WP_015004618.1
COORDINATES: similar to AA sequence:RefSeq:WP_007731423.1
COORDINATES: similar to AA sequence:RefSeq:WP_007731429.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_007731431.1
COORDINATES: similar to AA sequence:RefSeq:WP_015004624.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007731438.1
COORDINATES: similar to AA sequence:RefSeq:WP_007731440.1
COORDINATES: similar to AA sequence:RefSeq:WP_007745463.1
COORDINATES: similar to AA sequence:RefSeq:WP_007745464.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007745466.1
COORDINATES: similar to AA sequence:RefSeq:WP_007745467.1
COORDINATES: similar to AA sequence:RefSeq:WP_018441948.1
COORDINATES: similar to AA sequence:RefSeq:WP_007738656.1
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_012406663.1
COORDINATES: similar to AA sequence:RefSeq:WP_006047345.1
COORDINATES: similar to AA sequence:RefSeq:WP_018227590.1
COORDINATES: similar to AA sequence:RefSeq:WP_020562086.1
GO:0008863 - formate dehydrogenase (NAD+) activity [Evidence IEA]; GO:0051287 - NAD binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018268073.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF015431.2
GO:0001216 - DNA-binding transcription activator activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016836.2
COORDINATES: similar to AA sequence:RefSeq:WP_007181842.1
BMP family ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017678248.1
2-oxoglutarate and iron-dependent oxygenase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007835122.1
COORDINATES: similar to AA sequence:RefSeq:WP_011489719.1
GO:0015205 - nucleobase transmembrane transporter activity [Evidence IEA]
nucleobase:cation symporter-2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018312241.1
COORDINATES: similar to AA sequence:RefSeq:WP_007396211.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
aromatic ring-hydroxylating dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_017678253.1
COORDINATES: similar to AA sequence:RefSeq:WP_017340034.1
COORDINATES: similar to AA sequence:RefSeq:WP_018309839.1
COORDINATES: similar to AA sequence:RefSeq:WP_018309840.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0010181 - FMN binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012081511.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
glutathione S-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019451408.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0051903 - S-(hydroxymethyl)glutathione dehydrogenase activity [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]; GO:0009404 - toxin metabolic process [Evidence IEA]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_010101946.1
GO:0018738 - S-formylglutathione hydrolase activity [Evidence IEA]
GO:0046292 - formaldehyde metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007739081.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_007181597.1
GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020070178.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011488631.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009540109.1
COORDINATES: similar to AA sequence:RefSeq:WP_019403974.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015669427.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845629.1
COORDINATES: similar to AA sequence:RefSeq:WP_018095213.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018260441.1
2,4'-dihydroxyacetophenone dioxygenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009618263.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]; GO:0008483 - transaminase activity [Evidence IEA]
aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_007698406.1
COORDINATES: similar to AA sequence:RefSeq:WP_017903882.1
GO:0004655 - porphobilinogen synthase activity [Evidence IEA]
GO:0033014 - tetrapyrrole biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018012434.1
GO:0004399 - histidinol dehydrogenase activity [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015270266.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013094623.1
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: protein motif:HMM:NF028172.2
glycosyl hydrolase family 79 C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012338315.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004633984.1
COORDINATES: similar to AA sequence:RefSeq:WP_014752041.1
GO:0008484 - sulfuric ester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004190401.1
COORDINATES: similar to AA sequence:RefSeq:WP_012405979.1
COORDINATES: similar to AA sequence:RefSeq:WP_014330970.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273717.1
COORDINATES: protein motif:HMM:NF025694.2
COORDINATES: similar to AA sequence:RefSeq:WP_010693870.1
COORDINATES: similar to AA sequence:RefSeq:WP_014330973.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014330974.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018273721.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008140051.1
aminotransferase class V-fold PLP-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_019566996.1
amino acid ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_004129474.1
GO:0006865 - amino acid transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017130929.1
COORDINATES: similar to AA sequence:RefSeq:WP_012335797.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611812.1
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_020497728.1
COORDINATES: similar to AA sequence:RefSeq:WP_007752188.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017777135.1
COORDINATES: similar to AA sequence:RefSeq:WP_015003499.1
COORDINATES: similar to AA sequence:RefSeq:WP_009762400.1
COORDINATES: similar to AA sequence:RefSeq:WP_020812347.1
carbon-nitrogen hydrolase family protein
COORDINATES: protein motif:HMM:NF026057.2
COORDINATES: similar to AA sequence:RefSeq:WP_007737903.1
COORDINATES: similar to AA sequence:RefSeq:WP_006999305.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0015658 - branched-chain amino acid transmembrane transporter activity [Evidence IEA]; GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0015803 - branched-chain amino acid transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
branched-chain amino acid ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013690101.1
COORDINATES: similar to AA sequence:RefSeq:WP_017702855.1
COORDINATES: protein motif:HMM:NF019342.2
GO:0016787 - hydrolase activity [Evidence IEA]
Members of this family of hydrolases with an active site Cys residue belong to MEROPS family C26; Derived by automated computational analysis using gene prediction method: Protein Homology.
gamma-glutamyl-gamma-aminobutyrate hydrolase family protein
COORDINATES: protein motif:HMM:NF025885.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
sigma 54-interacting transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017772343.1
COORDINATES: protein motif:HMM:NF024242.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008965242.1
COORDINATES: similar to AA sequence:RefSeq:WP_006408120.1
GO:0015171 - amino acid transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017539.2
COORDINATES: similar to AA sequence:RefSeq:WP_007584281.1
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018441940.1
COORDINATES: similar to AA sequence:RefSeq:WP_012406648.1
COORDINATES: similar to AA sequence:RefSeq:WP_009771287.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_007731354.1
COORDINATES: similar to AA sequence:RefSeq:WP_007731361.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_007731363.1
COORDINATES: similar to AA sequence:RefSeq:WP_012406643.1
COORDINATES: similar to AA sequence:RefSeq:WP_007731368.1
COORDINATES: similar to AA sequence:RefSeq:WP_007731370.1
COORDINATES: similar to AA sequence:RefSeq:WP_007731376.1
COORDINATES: similar to AA sequence:RefSeq:WP_009913959.1
COORDINATES: similar to AA sequence:RefSeq:WP_015004267.1
COORDINATES: similar to AA sequence:RefSeq:WP_015004266.1
COORDINATES: similar to AA sequence:RefSeq:WP_018310260.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007182612.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182613.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012734044.1