Paracoccus liaowanqingii strain 2251 plasmid unnamed5, 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\nCP040761.1.\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: protein motif:HMM:NF019128.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF018604.2
COORDINATES: similar to AA sequence:RefSeq:WP_013331893.1
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_003518829.1
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]
GO:0015716 - organic phosphonate transport [Evidence IEA]
phosphonate ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006726474.1
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]
phosphonate ABC transporter, permease protein PhnE
COORDINATES: similar to AA sequence:RefSeq:WP_019953399.1
COORDINATES: similar to AA sequence:RefSeq:WP_018245377.1
COORDINATES: similar to AA sequence:RefSeq:WP_020188210.1
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_014750213.1
COORDINATES: similar to AA sequence:RefSeq:WP_011750837.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008234418.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013384559.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803780.1
COORDINATES: similar to AA sequence:RefSeq:WP_018064057.1
COORDINATES: similar to AA sequence:RefSeq:WP_019950017.1
COORDINATES: similar to AA sequence:RefSeq:WP_019950016.1
COORDINATES: similar to AA sequence:RefSeq:WP_013651873.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011969407.1
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007803782.1
four-carbon acid sugar kinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007803767.1
GO:0000287 - magnesium ion binding [Evidence IEA]
RuBisCO large subunit C-terminal-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019565735.1
COORDINATES: similar to AA sequence:RefSeq:WP_017979727.1
GO:0003905 - alkylbase DNA N-glycosylase activity [Evidence IEA]
GO:0006284 - base-excision repair [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017929948.1
alpha-1,4-glucan--maltose-1-phosphate maltosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014240599.1
GO:0047471 - maltose alpha-D-glucosyltransferase activity [Evidence IEA]
GO:0005991 - trehalose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018301031.1
GO:0003844 - 1,4-alpha-glucan branching enzyme activity [Evidence IEA]; GO:0043169 - cation binding [Evidence IEA]; GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]; GO:0005978 - glycogen biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012643952.1
GO:0004134 - 4-alpha-glucanotransferase activity [Evidence IEA]
GO:0005980 - glycogen catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011842661.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007421814.1
COORDINATES: similar to AA sequence:RefSeq:WP_007197297.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001346.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887428.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008887548.1
GO:0003868 - 4-hydroxyphenylpyruvate dioxygenase activity [Evidence IEA]
GO:0006559 - L-phenylalanine catabolic process [Evidence IEA]; GO:0006572 - tyrosine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008887448.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010394709.1
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008874619.1
COORDINATES: similar to AA sequence:RefSeq:WP_014876578.1
COORDINATES: similar to AA sequence:RefSeq:WP_007257001.1
COORDINATES: similar to AA sequence:RefSeq:WP_007257000.1
COORDINATES: protein motif:HMM:NF010396.0
COORDINATES: similar to AA sequence:RefSeq:WP_018301935.1
COORDINATES: similar to AA sequence:RefSeq:WP_009176891.1
COORDINATES: similar to AA sequence:RefSeq:WP_018425975.1
COORDINATES: similar to AA sequence:RefSeq:WP_018633801.1
COORDINATES: similar to AA sequence:RefSeq:WP_018633803.1
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018425972.1
COORDINATES: similar to AA sequence:RefSeq:WP_007256859.1
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013918.2
COORDINATES: similar to AA sequence:RefSeq:WP_007004273.1
COORDINATES: similar to AA sequence:RefSeq:WP_016970921.1
COORDINATES: similar to AA sequence:RefSeq:WP_014744260.1
COORDINATES: similar to AA sequence:RefSeq:WP_004706967.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331467.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
organoarsenical effux MFS transporter ArsJ
COORDINATES: similar to AA sequence:RefSeq:WP_011908443.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]; GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Evidence IEA]
GO:0006006 - glucose metabolic process [Evidence IEA]
ArsJ-associated glyceraldehyde-3-phosphate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_014747562.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_018328346.1
COORDINATES: similar to AA sequence:RefSeq:WP_011336896.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819877.1
COORDINATES: protein motif:HMM:TIGR02292.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_007692755.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF019324.2
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018575427.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015449381.1
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_013833427.1
COORDINATES: protein motif:HMM:NF018691.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005859685.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017999106.1
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: similar to AA sequence:RefSeq:WP_009820228.1
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: similar to AA sequence:RefSeq:WP_018065941.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_009803689.1
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007068955.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_010138154.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820237.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282965.1
COORDINATES: similar to AA sequence:RefSeq:WP_018010293.1
COORDINATES: similar to AA sequence:RefSeq:WP_012559875.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120602.1
COORDINATES: similar to AA sequence:RefSeq:WP_011199106.1
COORDINATES: similar to AA sequence:RefSeq:WP_008231132.1
COORDINATES: similar to AA sequence:RefSeq:WP_015495989.1
GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011338607.1
COORDINATES: similar to AA sequence:RefSeq:WP_011504940.1
COORDINATES: similar to AA sequence:RefSeq:WP_017928897.1
COORDINATES: similar to AA sequence:RefSeq:WP_008279258.1
NCS1 family nucleobase:cation symporter-1
COORDINATES: similar to AA sequence:RefSeq:WP_019564624.1
COORDINATES: similar to AA sequence:RefSeq:WP_016736809.1
COORDINATES: similar to AA sequence:RefSeq:WP_009208055.1
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004677489.1
COORDINATES: similar to AA sequence:RefSeq:WP_019339080.1
tripartite tricarboxylate transporter permease
COORDINATES: protein motif:HMM:NF018979.2
tripartite tricarboxylate transporter TctB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019339082.1
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011578906.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578907.1
COORDINATES: protein motif:HMM:NF014430.2
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_007848035.1
mandelate racemase/muconate lactonizing enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007597941.1
COORDINATES: similar to AA sequence:RefSeq:WP_003591317.1
COORDINATES: similar to AA sequence:RefSeq:WP_018067163.1
COORDINATES: similar to AA sequence:RefSeq:WP_005862560.1
COORDINATES: similar to AA sequence:RefSeq:WP_018480299.1
COORDINATES: similar to AA sequence:RefSeq:WP_018493595.1
COORDINATES: similar to AA sequence:RefSeq:WP_018444772.1
COORDINATES: similar to AA sequence:RefSeq:WP_007767294.1
COORDINATES: similar to AA sequence:RefSeq:WP_018480302.1
COORDINATES: similar to AA sequence:RefSeq:WP_006725353.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003572717.1
COORDINATES: similar to AA sequence:RefSeq:WP_018632554.1
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018632562.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326100.1
COORDINATES: similar to AA sequence:RefSeq:WP_018632558.1
COORDINATES: similar to AA sequence:RefSeq:WP_007606599.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326097.1
COORDINATES: similar to AA sequence:RefSeq:WP_018858159.1
COORDINATES: similar to AA sequence:RefSeq:WP_020203533.1
COORDINATES: similar to AA sequence:RefSeq:WP_007801514.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008081891.1
COORDINATES: similar to AA sequence:RefSeq:WP_019848268.1
COORDINATES: similar to AA sequence:RefSeq:WP_009210708.1
GO:0009982 - pseudouridine synthase activity [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
GO:0001522 - pseudouridine synthesis [Evidence IEA]; GO:0009451 - RNA modification [Evidence IEA]
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_011331267.1
GO:0009975 - cyclase activity [Evidence IEA]
GO:0009966 - regulation of signal transduction [Evidence IEA]
sensor domain-containing diguanylate cyclase
COORDINATES: protein motif:HMM:NF018980.2
COORDINATES: similar to AA sequence:RefSeq:WP_011911050.1
GO:0004803 - transposase activity [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_076612055.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF017088.2
COORDINATES: similar to AA sequence:RefSeq:WP_007426906.1
COORDINATES: protein motif:HMM:NF013117.2
mechanosensitive ion channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013634892.1
COORDINATES: protein motif:HMM:NF017373.2
COORDINATES: similar to AA sequence:RefSeq:WP_007256665.1
COORDINATES: similar to AA sequence:RefSeq:WP_015824003.1
COORDINATES: similar to AA sequence:RefSeq:WP_008518798.1
COORDINATES: protein motif:HMM:NF016807.2
COORDINATES: similar to AA sequence:RefSeq:WP_007817478.1
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_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: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_011665038.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405493.1
COORDINATES: protein motif:HMM:NF023697.2
COORDINATES: similar to AA sequence:RefSeq:WP_011455331.1
COORDINATES: similar to AA sequence:RefSeq:WP_014529321.1
COORDINATES: protein motif:HMM:NF013431.2
COORDINATES: similar to AA sequence:RefSeq:WP_003579213.1
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_006939373.1
COORDINATES: similar to AA sequence:RefSeq:WP_010975871.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018001540.1
COORDINATES: similar to AA sequence:RefSeq:WP_007801517.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001542.1
COORDINATES: similar to AA sequence:RefSeq:WP_008886522.1
COORDINATES: similar to AA sequence:RefSeq:WP_014129413.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006939354.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005857581.1
COORDINATES: similar to AA sequence:RefSeq:WP_005857582.1
COORDINATES: similar to AA sequence:RefSeq:WP_011750477.1
COORDINATES: similar to AA sequence:RefSeq:WP_015501553.1
COORDINATES: similar to AA sequence:RefSeq:WP_019955981.1
COORDINATES: similar to AA sequence:RefSeq:WP_017927912.1
COORDINATES: similar to AA sequence:RefSeq:WP_007204055.1
COORDINATES: similar to AA sequence:RefSeq:WP_019954687.1
COORDINATES: similar to AA sequence:RefSeq:WP_019956741.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019955699.1
COORDINATES: similar to AA sequence:RefSeq:WP_007816262.1
COORDINATES: similar to AA sequence:RefSeq:WP_008279516.1
COORDINATES: similar to AA sequence:RefSeq:WP_020043513.1
esterase-like activity of phytase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007426077.1
TRAP transporter substrate-binding protein DctP
COORDINATES: similar to AA sequence:RefSeq:WP_007426078.1
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_008887844.1
COORDINATES: similar to AA sequence:RefSeq:WP_010913699.1