Paenibacillus polymyxa strain ZF129 plasmid pAP1, complete sequence.
Bacteria; Bacillota; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus.
Complete genome sequence of biocontrol strain Paenibacillus polymyxa ZF129 and further analysis of its biocontrol mechanism
Submitted (04-JUN-2019) Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing 100081, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP040830.1.\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 :: HGAP v. 2.3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 1092.65x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 12:34:44\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) :: 5,147\nCDSs (total) :: 4,990\nGenes (coding) :: 4,939\nCDSs (with protein) :: 4,939\nGenes (RNA) :: 157\nrRNAs :: 14, 14, 14 (5S, 16S, 23S)\ncomplete rRNAs :: 14, 14, 14 (5S, 16S, 23S)\ntRNAs :: 111\nncRNAs :: 4\nPseudo Genes (total) :: 51\nCDSs (without protein) :: 51\nPseudo Genes (ambiguous residues) :: 0 of 51\nPseudo Genes (frameshifted) :: 29 of 51\nPseudo Genes (incomplete) :: 24 of 51\nPseudo Genes (internal stop) :: 8 of 51\nPseudo Genes (multiple problems) :: 9 of 51\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019005919.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012372.2
GO:0003886 - DNA (cytosine-5-)-methyltransferase activity [Evidence IEA]; GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: protein motif:HMM:NF025390.2
COORDINATES: similar to AA sequence:RefSeq:WP_013311014.1
GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0032775 - DNA methylation on adenine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018887104.1
COORDINATES: protein motif:HMM:NF013855.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005545867.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: protein motif:HMM:NF013632.2
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019325.2
COORDINATES: protein motif:HMM:NF019450.2
copper amine oxidase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010345272.1
GO:0005515 - protein binding [Evidence IEA]
fibronectin type III domain-containing protein
COORDINATES: protein motif:HMM:NF014069.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF028286.2
COORDINATES: protein motif:HMM:NF025571.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: similar to AA sequence:RefSeq:WP_006287825.1
COORDINATES: protein motif:HMM:NF013727.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF013700.2
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF040179.1
CpsD/CapB family tyrosine-protein kinase
COORDINATES: protein motif:HMM:NF016214.2
COORDINATES: protein motif:HMM:NF033832.1
COORDINATES: protein motif:HMM:NF015414.2
COORDINATES: similar to AA sequence:RefSeq:WP_014600178.1
COORDINATES: similar to AA sequence:RefSeq:WP_016204193.1
GO:0003886 - DNA (cytosine-5-)-methyltransferase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006675363.1
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009674523.1
GO:0000166 - nucleotide binding [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009674519.1
COORDINATES: protein motif:HMM:NF025107.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF016296.2
LytTR family transcriptional regulator DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF016526.2
GO:0008233 - peptidase activity [Evidence IEA]
GO:0009372 - quorum sensing [Evidence IEA]
accessory gene regulator B family protein
COORDINATES: protein motif:HMM:NF020945.2
aspartyl-phosphate phosphatase Spo0E family protein
COORDINATES: protein motif:HMM:NF021759.2
COORDINATES: protein motif:HMM:NF015947.2
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF015935.2
COORDINATES: protein motif:HMM:NF016232.2
COORDINATES: similar to AA sequence:RefSeq:WP_019635922.1
COORDINATES: similar to AA sequence:RefSeq:WP_000947592.1
COORDINATES: protein motif:HMM:NF033630.1
COORDINATES: similar to AA sequence:RefSeq:WP_010345676.1
COORDINATES: similar to AA sequence:RefSeq:WP_016819375.1
COORDINATES: similar to AA sequence:RefSeq:WP_015846227.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017756288.1
COORDINATES: similar to AA sequence:RefSeq:WP_013370807.1
COORDINATES: protein motif:HMM:NF013252.2
COORDINATES: similar to AA sequence:RefSeq:WP_010349904.1
COORDINATES: similar to AA sequence:RefSeq:WP_016324577.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006211192.1
COORDINATES: similar to AA sequence:RefSeq:WP_005552490.1