Paracoccus liaowanqingii strain 2251 plasmid unnamed2, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Paracoccus.
Paracoccus liaowanqingii sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii)
Submitted (29-MAY-2019) National Institue for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District Changbai Road, No. 155, Beijing, Beijing 102206, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP040762.1.\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 :: SOAPdenovo v. 4.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/23/2022 04:22:22\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) :: 4,759\nCDSs (total) :: 4,694\nGenes (coding) :: 4,486\nCDSs (with protein) :: 4,486\nGenes (RNA) :: 65\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 53\nncRNAs :: 3\nPseudo Genes (total) :: 208\nCDSs (without protein) :: 208\nPseudo Genes (ambiguous residues) :: 0 of 208\nPseudo Genes (frameshifted) :: 104 of 208\nPseudo Genes (incomplete) :: 126 of 208\nPseudo Genes (internal stop) :: 32 of 208\nPseudo Genes (multiple problems) :: 49 of 208\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type material of Paracoccus liaowanqingii
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_003528877.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019996183.1
COORDINATES: similar to AA sequence:RefSeq:WP_019996182.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018633994.1
COORDINATES: similar to AA sequence:RefSeq:WP_010396603.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012652408.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011809194.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024583.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012779057.1
COORDINATES: protein motif:HMM:NF020037.2
COORDINATES: similar to AA sequence:RefSeq:WP_003570724.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011907535.1
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_011930855.1
COORDINATES: similar to AA sequence:RefSeq:WP_007191299.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611116.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013960491.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427422.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611917.1
COORDINATES: similar to AA sequence:RefSeq:WP_007923257.1
COORDINATES: similar to AA sequence:RefSeq:WP_019516101.1
COORDINATES: similar to AA sequence:RefSeq:WP_011746827.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014763569.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007120621.1
COORDINATES: protein motif:HMM:NF015642.2
COORDINATES: protein motif:HMM:NF014825.2
GO:0046872 - metal ion binding [Evidence IEA]
SEC-C metal-binding domain-containing protein
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_015497845.1
COORDINATES: protein motif:HMM:NF019324.2
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF019474.2
COORDINATES: protein motif:HMM:NF014073.2
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_018575427.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013833427.1
COORDINATES: similar to AA sequence:RefSeq:WP_018857986.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012778788.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013634892.1
COORDINATES: similar to AA sequence:RefSeq:WP_011512241.1
frameshifted; 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_012778787.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:TIGR00254.1
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_010967560.1
COORDINATES: similar to AA sequence:RefSeq:WP_008558627.1
COORDINATES: similar to AA sequence:RefSeq:WP_003616132.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827281.1
COORDINATES: similar to AA sequence:RefSeq:WP_009465831.1
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_011053439.1
COORDINATES: similar to AA sequence:RefSeq:WP_008839617.1
COORDINATES: similar to AA sequence:RefSeq:WP_019956495.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011516023.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013625.2
COORDINATES: protein motif:HMM:NF024776.2
COORDINATES: protein motif:HMM:NF012894.2
COORDINATES: similar to AA sequence:RefSeq:WP_011750190.1
COORDINATES: similar to AA sequence:RefSeq:WP_017998513.1
COORDINATES: protein motif:HMM:NF018527.2
COORDINATES: protein motif:HMM:NF013775.2
COORDINATES: similar to AA sequence:RefSeq:WP_008231132.1
COORDINATES: similar to AA sequence:RefSeq:WP_009570964.1
COORDINATES: protein motif:HMM:NF013936.2
COORDINATES: protein motif:HMM:TIGR00369.1
COORDINATES: similar to AA sequence:RefSeq:WP_007817478.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970376.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF012442.2
COORDINATES: protein motif:HMM:NF014035.2
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611946.1
COORDINATES: protein motif:HMM:NF012573.2
COORDINATES: similar to AA sequence:RefSeq:WP_007121444.1
COORDINATES: similar to AA sequence:RefSeq:WP_007589660.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612055.1
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_014529321.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993128.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611977.1
COORDINATES: similar to AA sequence:RefSeq:WP_009867760.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611976.1
COORDINATES: similar to AA sequence:RefSeq:WP_003548916.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
GO:0019619 - 3,4-dihydroxybenzoate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018000586.1
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010394599.1
COORDINATES: similar to AA sequence:RefSeq:WP_018000588.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009465864.1
COORDINATES: protein motif:HMM:NF033545.0
COORDINATES: similar to AA sequence:RefSeq:WP_007600727.1
COORDINATES: similar to AA sequence:RefSeq:WP_018063809.1
COORDINATES: similar to AA sequence:RefSeq:WP_008837255.1
COORDINATES: similar to AA sequence:RefSeq:WP_013382874.1
GO:0055085 - transmembrane transport [Evidence IEA]
TRAP transporter substrate-binding protein DctP
COORDINATES: similar to AA sequence:RefSeq:WP_018856120.1
COORDINATES: protein motif:HMM:NF019349.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014538212.1
COORDINATES: similar to AA sequence:RefSeq:WP_007204692.1
3-keto-5-aminohexanoate cleavage protein
COORDINATES: similar to AA sequence:RefSeq:WP_009817545.1
GO:0018578 - protocatechuate 3,4-dioxygenase activity [Evidence IEA]
GO:0046278 - 3,4-dihydroxybenzoate metabolic process [Evidence IEA]
protocatechuate 3,4-dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_007204124.1
protocatechuate 3,4-dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_008531665.1
GO:0047575 - 4-carboxymuconolactone decarboxylase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018633650.1
GO:0047570 - 3-oxoadipate enol-lactonase activity [Evidence IEA]
GO:0042952 - beta-ketoadipate pathway [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013382870.1
sugar phosphate isomerase/epimerase and 4-hydroxyphenylpyruvate domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018301722.1
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019962926.1
COORDINATES: similar to AA sequence:RefSeq:WP_019962927.1
tripartite tricarboxylate transporter TctB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019962928.1
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018633651.1
COORDINATES: similar to AA sequence:RefSeq:WP_007801696.1
COORDINATES: similar to AA sequence:RefSeq:WP_018303842.1
COORDINATES: similar to AA sequence:RefSeq:WP_007801700.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007801702.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007801705.1
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_007801707.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007801708.1
COORDINATES: similar to AA sequence:RefSeq:WP_003550967.1
COORDINATES: similar to AA sequence:RefSeq:WP_007794744.1
GO:0018659 - 4-hydroxybenzoate 3-monooxygenase activity [Evidence IEA]
GO:0018874 - benzoate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008886111.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: similar to AA sequence:RefSeq:WP_043766072.1
COORDINATES: similar to AA sequence:RefSeq:WP_006200010.1
COORDINATES: similar to AA sequence:RefSeq:WP_007815263.1
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: protein motif:HMM:NF022603.2
COORDINATES: similar to AA sequence:RefSeq:WP_007813081.1
COORDINATES: protein motif:HMM:NF016807.2
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: protein motif:HMM:NF014567.2
bifunctional diguanylate cyclase/phosphodiesterase
COORDINATES: similar to AA sequence:RefSeq:WP_014750744.1
COORDINATES: similar to AA sequence:RefSeq:WP_008945290.1
COORDINATES: similar to AA sequence:RefSeq:WP_010916009.1
COORDINATES: similar to AA sequence:RefSeq:WP_014765779.1
COORDINATES: similar to AA sequence:RefSeq:WP_010110397.1
COORDINATES: similar to AA sequence:RefSeq:WP_017993379.1
COORDINATES: similar to AA sequence:RefSeq:WP_018184845.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808286.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273520.1
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: similar to AA sequence:RefSeq:WP_012554517.1
GO:0015074 - DNA integration [Evidence IEA]
frameshifted; internal stop; 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: protein motif:HMM:NF024770.2
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007822136.1
COORDINATES: similar to AA sequence:RefSeq:WP_017969201.1
COORDINATES: similar to AA sequence:RefSeq:WP_018900964.1
COORDINATES: similar to AA sequence:RefSeq:WP_011339535.1
COORDINATES: similar to AA sequence:RefSeq:WP_002723119.1
COORDINATES: similar to AA sequence:RefSeq:WP_007822125.1
COORDINATES: similar to AA sequence:RefSeq:WP_007822123.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002723116.1
COORDINATES: similar to AA sequence:RefSeq:WP_002723115.1
COORDINATES: similar to AA sequence:RefSeq:WP_006083519.1
COORDINATES: similar to AA sequence:RefSeq:WP_004580556.1
COORDINATES: similar to AA sequence:RefSeq:WP_009101040.1
COORDINATES: similar to AA sequence:RefSeq:WP_009101042.1
COORDINATES: protein motif:HMM:NF018979.2
COORDINATES: similar to AA sequence:RefSeq:WP_013651147.1
COORDINATES: similar to AA sequence:RefSeq:WP_010399400.1
TraR/DksA family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017140509.1
COORDINATES: similar to AA sequence:RefSeq:WP_020042153.1
COORDINATES: nucleotide motif:Rfam:14.4:RF03058
sul1 is cis-regulatory element that is thought to sense ions involved in sulfur or methionine metabolism; They are found in Alphaproteobacteria; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF014045.2
COORDINATES: similar to AA sequence:RefSeq:WP_009561829.1
D-alanyl-D-alanine carboxypeptidase family protein
COORDINATES: protein motif:HMM:NF013652.2
COORDINATES: protein motif:HMM:NF016145.2
polysaccharide pyruvyl transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611445.1
COORDINATES: similar to AA sequence:RefSeq:WP_005979685.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930806.1
internal stop; 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_014879059.1
COORDINATES: similar to AA sequence:RefSeq:WP_019590546.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]
GO:0015716 - organic phosphonate transport [Evidence IEA]
phosphonate ABC transporter, permease protein PhnE
COORDINATES: similar to AA sequence:RefSeq:WP_008957042.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
phosphonate ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_016352819.1
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:0043168 - anion binding [Evidence IEA]; GO:0043225 - ATPase-coupled inorganic anion transmembrane transporter activity [Evidence IEA]
phosphate/phosphite/phosphonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_015124236.1
ExeM/NucH family extracellular endonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_086558218.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_015126371.1
WGxxGxxG-CTERM domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011911050.1
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: protein motif:HMM:NF013530.2
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011454646.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005856485.1
COORDINATES: protein motif:HMM:NF017273.2
COORDINATES: similar to AA sequence:RefSeq:WP_008280036.1
COORDINATES: similar to AA sequence:RefSeq:WP_012976929.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009820208.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331390.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011331389.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335662.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611178.1
COORDINATES: similar to AA sequence:RefSeq:WP_013640721.1