Planococcus lenghuensis strain Y42 plasmid unnamed1, complete sequence.
Bacteria; Bacillota; Bacilli; Bacillales; Planococcaceae; Planococcus.
The complete genomic sequence of a novel cold adapted crude oil-degrading bacterium Planococcus qaidamina Y42
Submitted (07-FEB-2017) Key Laboratory of Extreme Environmental Microbiol Resources and Engineering, Northwest Institute of Eco-Environment and Resources,CAS, NO. 320 chengguan donggang West Road, Lanzhou, Gansu 730030, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP019641.1.\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 :: SPAdes v. 3.5.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 300.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/29/2022 04:32:02\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) :: 4,188\nCDSs (total) :: 4,087\nGenes (coding) :: 4,002\nCDSs (with protein) :: 4,002\nGenes (RNA) :: 101\nrRNAs :: 9, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 9, 9 (5S, 16S, 23S)\ntRNAs :: 70\nncRNAs :: 4\nPseudo Genes (total) :: 85\nCDSs (without protein) :: 85\nPseudo Genes (ambiguous residues) :: 0 of 85\nPseudo Genes (frameshifted) :: 40 of 85\nPseudo Genes (incomplete) :: 39 of 85\nPseudo Genes (internal stop) :: 18 of 85\nPseudo Genes (multiple problems) :: 12 of 85\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF013540.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF012772.2
bifunctional diguanylate cyclase/phosphodiesterase
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008428702.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008178876.1
COORDINATES: similar to AA sequence:RefSeq:WP_006829828.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015660830.1
COORDINATES: similar to AA sequence:RefSeq:WP_009792073.1
COORDINATES: similar to AA sequence:RefSeq:WP_003726066.1
COORDINATES: protein motif:HMM:NF013068.2
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_019377767.1
GO:0015572 - N-acetylglucosamine transmembrane transporter activity [Evidence IEA]
N-acetylglucosamine-specific PTS transporter subunit IIBC
COORDINATES: similar to AA sequence:RefSeq:WP_014641991.1
GO:0008448 - N-acetylglucosamine-6-phosphate deacetylase activity [Evidence IEA]
GO:0006040 - amino sugar metabolic process [Evidence IEA]
N-acetylglucosamine-6-phosphate deacetylase
COORDINATES: similar to AA sequence:RefSeq:WP_006828619.1
GO:0004342 - glucosamine-6-phosphate deaminase activity [Evidence IEA]
GO:0006046 - N-acetylglucosamine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008640171.1
COORDINATES: similar to AA sequence:RefSeq:WP_008497349.1
COORDINATES: similar to AA sequence:RefSeq:WP_008498846.1
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF015354.2
COORDINATES: similar to AA sequence:RefSeq:WP_000680007.1
COORDINATES: protein motif:HMM:NF021981.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF017760.2
COORDINATES: similar to AA sequence:RefSeq:WP_002358276.1
COORDINATES: protein motif:HMM:NF024252.2
COORDINATES: protein motif:HMM:NF033550.5
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF020442.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000116125.1
COORDINATES: similar to AA sequence:RefSeq:WP_019392797.1
COORDINATES: protein motif:HMM:NF019500.2
COORDINATES: protein motif:HMM:NF021524.2
COORDINATES: protein motif:HMM:NF013206.2
COORDINATES: similar to AA sequence:RefSeq:WP_006831544.1
COORDINATES: similar to AA sequence:RefSeq:WP_018398193.1
COORDINATES: protein motif:HMM:NF016119.2
COORDINATES: protein motif:HMM:NF017832.2
COORDINATES: protein motif:HMM:NF020438.2
COORDINATES: protein motif:HMM:NF003462.0
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF025471.2
COORDINATES: similar to AA sequence:RefSeq:WP_006440399.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019414673.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004890083.1
GO:0005507 - copper ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024919.2
COORDINATES: similar to AA sequence:RefSeq:WP_016764803.1
COORDINATES: protein motif:HMM:NF012787.2
GO:0016209 - antioxidant activity [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008428957.1
GO:0046872 - metal ion binding [Evidence IEA]
zinc ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_004436770.1
COORDINATES: similar to AA sequence:RefSeq:WP_006828613.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_009362331.1
COORDINATES: similar to AA sequence:RefSeq:WP_015735029.1
COORDINATES: similar to AA sequence:RefSeq:WP_010650451.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016874 - ligase activity [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]; GO:0051301 - cell division [Evidence IEA]; GO:0008360 - regulation of cell shape [Evidence IEA]
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase
COORDINATES: similar to AA sequence:RefSeq:WP_010650494.1
COORDINATES: protein motif:HMM:NF013434.2
COORDINATES: protein motif:HMM:NF020893.2
COORDINATES: similar to AA sequence:RefSeq:WP_010288812.1
COORDINATES: similar to AA sequence:RefSeq:WP_019414266.1
COORDINATES: similar to AA sequence:RefSeq:WP_012727303.1
COORDINATES: protein motif:HMM:NF016154.2
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: similar to AA sequence:RefSeq:WP_017380438.1
GO:0004066 - asparagine synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0006529 - asparagine biosynthetic process [Evidence IEA]
asparagine synthase (glutamine-hydrolyzing)
COORDINATES: similar to AA sequence:RefSeq:WP_006829040.1
COORDINATES: protein motif:HMM:NF024420.2
COORDINATES: protein motif:HMM:NF033517.1
COORDINATES: protein motif:HMM:NF013700.2
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009336130.1
COORDINATES: protein motif:HMM:NF024078.2
COORDINATES: protein motif:HMM:NF039493.1
COORDINATES: protein motif:HMM:NF024367.2
COORDINATES: protein motif:HMM:NF025442.2
COORDINATES: protein motif:HMM:NF016024.2
COORDINATES: protein motif:HMM:TIGR00663.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF025815.2
COORDINATES: similar to AA sequence:RefSeq:WP_002114363.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_009336109.1
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014898.2
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: protein motif:HMM:NF012320.2
COORDINATES: protein motif:HMM:NF025186.2
COORDINATES: protein motif:HMM:NF024108.2
COORDINATES: protein motif:HMM:NF012652.2
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013176026.1
COORDINATES: similar to AA sequence:RefSeq:WP_012584637.1
COORDINATES: protein motif:HMM:TIGR04416.1
COORDINATES: similar to AA sequence:RefSeq:WP_014096622.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF024359.2
COORDINATES: protein motif:HMM:NF039653.1
COORDINATES: similar to AA sequence:RefSeq:WP_009790726.1
COORDINATES: similar to AA sequence:RefSeq:WP_000654328.1
COORDINATES: protein motif:HMM:NF012493.2
COORDINATES: similar to AA sequence:RefSeq:WP_019379899.1
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: protein motif:HMM:NF013980.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
SprT family zinc-dependent metalloprotease
COORDINATES: protein motif:HMM:NF020419.2
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: protein motif:HMM:NF024758.2
trypsin-like peptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006831665.1
COORDINATES: protein motif:HMM:NF024803.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
MerR family DNA-binding transcriptional regulator
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF024550.2
COORDINATES: similar to AA sequence:RefSeq:WP_003322310.1
GO:0001228 - DNA-binding transcription activator activity, RNA polymerase II-specific [Evidence IEA]
Hg(II)-responsive transcriptional regulator
COORDINATES: protein motif:HMM:NF012621.2
heavy metal-associated domain-containing protein
COORDINATES: protein motif:HMM:NF014713.2
cytochrome c biogenesis CcdA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004635122.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000163428.1
COORDINATES: similar to AA sequence:RefSeq:WP_006828672.1
COORDINATES: similar to AA sequence:RefSeq:WP_006828671.1
COORDINATES: protein motif:HMM:NF012955.2
COORDINATES: protein motif:HMM:NF012546.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611651.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012298.2
GO:0004672 - protein kinase activity [Evidence IEA]
GO:0006468 - protein phosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF040103.1
COORDINATES: similar to AA sequence:RefSeq:WP_014096191.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_017695326.1
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: protein motif:HMM:NF013245.2
COORDINATES: protein motif:HMM:NF026041.2
COORDINATES: similar to AA sequence:RefSeq:WP_006828293.1
COORDINATES: similar to AA sequence:RefSeq:WP_019380939.1
nucleotidyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020618995.1
COORDINATES: protein motif:HMM:NF024098.2
COORDINATES: similar to AA sequence:RefSeq:WP_008432008.1
COORDINATES: protein motif:HMM:NF033592.1
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: similar to AA sequence:RefSeq:WP_003475155.1
iron-siderophore ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008826744.1
COORDINATES: similar to AA sequence:RefSeq:WP_015327918.1
COORDINATES: protein motif:HMM:NF024729.2
COORDINATES: similar to AA sequence:RefSeq:WP_018665538.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008592102.1
COORDINATES: protein motif:HMM:NF033746.1
COORDINATES: similar to AA sequence:RefSeq:WP_008633936.1
COORDINATES: similar to AA sequence:RefSeq:WP_016203014.1
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_003396749.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0051049 - regulation of transport [Evidence IEA]
phosphate signaling complex protein PhoU
COORDINATES: protein motif:HMM:NF012698.2
COORDINATES: similar to AA sequence:RefSeq:WP_008636973.1
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_008879874.1
phosphate ABC transporter permease subunit PstC
COORDINATES: similar to AA sequence:RefSeq:WP_008636967.1
PstS family phosphate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009499520.1
COORDINATES: protein motif:HMM:NF012481.2
COORDINATES: similar to AA sequence:RefSeq:WP_004434614.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612034.1
COORDINATES: similar to AA sequence:RefSeq:WP_012094141.1
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_008429917.1
GO:0008705 - methionine synthase activity [Evidence IEA]
GO:0009086 - methionine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008429916.1
bifunctional homocysteine S-methyltransferase/methylenetetrahydrofolate reductase
COORDINATES: nucleotide motif:Rfam:14.4:RF00162
SAM riboswitch class I; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_001039247.1
COORDINATES: similar to AA sequence:RefSeq:WP_018933209.1
COORDINATES: similar to AA sequence:RefSeq:WP_017434251.1
COORDINATES: similar to AA sequence:RefSeq:WP_017434252.1
N-acyl homoserine lactonase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014643231.1
COORDINATES: protein motif:HMM:NF013694.2
magnesium transporter CorA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006831327.1
COORDINATES: protein motif:HMM:TIGR04383.1
GO:0010339 - external side of cell wall [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008408654.1
COORDINATES: protein motif:HMM:NF033545.0
COORDINATES: protein motif:HMM:NF025652.2
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:NF013884.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009795175.1
GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA]
GO:0006629 - lipid metabolic process [Evidence IEA]
glycerophosphodiester phosphodiesterase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015254552.1
COORDINATES: similar to AA sequence:RefSeq:WP_007127504.1
COORDINATES: similar to AA sequence:RefSeq:WP_018130289.1
COORDINATES: protein motif:HMM:NF024811.2
COORDINATES: similar to AA sequence:RefSeq:WP_009795170.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009795169.1
glycerol-3-phosphate responsive antiterminator
COORDINATES: protein motif:HMM:NF012376.2
COORDINATES: similar to AA sequence:RefSeq:WP_006835696.1
GO:0006750 - glutathione biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019414385.1
COORDINATES: similar to AA sequence:RefSeq:WP_009172889.1
COORDINATES: similar to AA sequence:RefSeq:WP_010896456.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001033506.1
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_016098251.1
COORDINATES: similar to AA sequence:RefSeq:WP_019156897.1
COORDINATES: similar to AA sequence:RefSeq:WP_013488526.1
COORDINATES: similar to AA sequence:RefSeq:WP_015263579.1
COORDINATES: similar to AA sequence:RefSeq:WP_004903016.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006830712.1
COORDINATES: similar to AA sequence:RefSeq:WP_018768165.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF019850.2
GO:0009058 - biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009374089.1
D-alanyl-D-alanine carboxypeptidase family protein