Bacillus badius strain NBPM-293 plasmid pPM5, complete sequence.
type: Entry
definition: Bacillus badius strain NBPM-293 plasmid pPM5, complete sequence.
sequence version: NZ_CP082367.1
sequence date: 2023-06-18
sequence: sequence
division: CON
label: NZ_CP082367.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN21156371
keyword: RefSeq
source: Bacillus badius
organism: Bacillus badius
taxonomy: Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP082367.1.\nBacteria and source DNA available from National Biopesticide\nEngineering Technology Research Center.\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 :: Unicycler v. 2.1.2\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 243.5x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 06/18/2023 15:42:49\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) :: 4,391\nCDSs (total) :: 4,254\nGenes (coding) :: 4,207\nCDSs (with protein) :: 4,207\nGenes (RNA) :: 137\nrRNAs :: 11, 11, 11 (5S, 16S, 23S)\ncomplete rRNAs :: 11, 11, 11 (5S, 16S, 23S)\ntRNAs :: 99\nncRNAs :: 5\nPseudo Genes (total) :: 47\nCDSs (without protein) :: 47\nPseudo Genes (ambiguous residues) :: 0 of 47\nPseudo Genes (frameshifted) :: 14 of 47\nPseudo Genes (incomplete) :: 29 of 47\nPseudo Genes (internal stop) :: 9 of 47\nPseudo Genes (multiple problems) :: 5 of 47\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5007
topology: circular
so has quality: SO_0000988
location: 1..5007
location: region:1-5007:1
RO_0002162: 1455

NZ_CP082367
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN21156371
type: BioSample
SIO_000068: biosample

1
title: Complete Genome Sequence of Bacillus badius NBPM-293, a Plant Growth-Promoting Rhizobacterium Isolated from Soil
author: Zhu, L.
author: Min, Y.
author: Zhou, R.
journal: Unpublished

2
title: Direct Submission
author: Zhu, L.
author: Min, Y.
author: Zhou, R.
journal: Submitted (31-AUG-2021) Hubei Biopesticide Engineering Research Center, National Biopesticide Engineering Technology Research Center, Hubei Academy of Agricultural Sciences, No.8,Nanhu Ave.,Hongshan District, Wuhan, Hubei 430064, China

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5007:1
position: 5007
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5007:1:source
so part of: sequence
organism: Bacillus badius
mol type: genomic DNA
strain: NBPM-293
isolation source: soil
plasmid: pPM5
collection date: 2020

1455
type: Taxonomy
SIO_000068: taxonomy

K7T73_RS21855
type: Gene
subclass of: SO_0000704
RO_0002162: 1455
locus tag: K7T73_RS21855
old locus tag: K7T73_21815
so part of: sequence
location: complement(join(4840..5007,1..276))
location: region:1-5007:-1
so has part: feature:1-276:-1:exon
so has part: feature:4840-5007:-1:exon
subclass of: SO_0000010

82148080
type: Gene
SIO_000068: ncbigene

position:1:-1
position: 1
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5007:-1
position: 5007
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-276:-1:exon

position:276:-1
position: 276
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:4840-5007:-1:exon

position:4840:-1
position: 4840
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

K7T73_RS21855
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1455
locus tag: K7T73_RS21855
old locus tag: K7T73_21815
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKKQLIILVIFMGLSLMGCGPMEEKPPKVMIQTEKDNYELTIGSYCWGDTCSDVAGSVEQLLETEEKKPIKVKPGQTISFVMKNGPKPNEISVIQENDNQELDVEVKVKDNQISASMEEGIYYYIYDVRWANGDDAFYPFALEVEVD
SIO_010081: K7T73_RS21855
subclass of: SO_0000673
so part of: K7T73_RS21855
location: complement(join(4840..5007,1..276))
location: region:1-5007:-1
so has part: feature:1-276:-1:exon
so has part: feature:4840-5007:-1:exon

WP_223664331.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-276:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:4840-5007:-1:exon

K7T73_RS21860
type: Gene
subclass of: SO_0000704
RO_0002162: 1455
locus tag: K7T73_RS21860
old locus tag: K7T73_21820
so part of: sequence
location: 470..973
location: region:470-973:1
so has part: feature:470-973:1:exon
subclass of: SO_0000010

82148081
type: Gene
SIO_000068: ncbigene

position:470:1
position: 470
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:973:1
position: 973
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:470-973:1:exon

K7T73_RS21860
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1455
locus tag: K7T73_RS21860
old locus tag: K7T73_21820
inference: COORDINATES: protein motif:HMM:NF013559.2
GO function: GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO process: GO:0006508 - proteolysis [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: M12 family metallopeptidase
translation: MKKGIIFSIIGSLSLLALPSTGDAYVLNSKKIYDTKDAYYWIDPAFTDSQEKNIGSGINTWDVTPEVEFTKKASTPAGANLKIEHSNTSKGTVVGTSFGKGHIILWSGWKKLGSSDKKETVVHEVGHELGLAHTQQEKNSISVMRAKGFNGKPYPLSDDKAGISAKY
SIO_010081: K7T73_RS21860
subclass of: SO_0000673
so part of: K7T73_RS21860
location: 470..973
location: region:470-973:1
so has part: feature:470-973:1:exon

WP_223664333.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:470-973:1:exon

K7T73_RS21865
type: Gene
subclass of: SO_0000704
RO_0002162: 1455
locus tag: K7T73_RS21865
old locus tag: K7T73_21825
so part of: sequence
location: 985..1632
location: region:985-1632:1
so has part: feature:985-1632:1:exon
subclass of: SO_0000010

82148082
type: Gene
SIO_000068: ncbigene

position:985:1
position: 985
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1632:1
position: 1632
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:985-1632:1:exon

K7T73_RS21865
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1455
locus tag: K7T73_RS21865
old locus tag: K7T73_21825
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKRLLGGVAAVLAVSTAIGLYINSSSEEEPNKKTIEATSKPKITVIEAKTIDYSSLEELQTELPIAVKGIKTDEKKTELQYSKVDNSLIGGHTVSNFKITEVLQNNNEAAEIKVGNNIPVMEYSFLDKESDTTYTYNGYANMRENEEYILFLLPKEEEVFPIGSTSIGKIPVEKSTEVEIYKEDFEANNDNVDDTEEVIENIEKVYEEVRAEYVE
SIO_010081: K7T73_RS21865
subclass of: SO_0000673
so part of: K7T73_RS21865
location: 985..1632
location: region:985-1632:1
so has part: feature:985-1632:1:exon

WP_223664340.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:985-1632:1:exon

K7T73_RS21870
type: Gene
subclass of: SO_0000704
RO_0002162: 1455
locus tag: K7T73_RS21870
old locus tag: K7T73_21830
so part of: sequence
location: 1915..2259
location: region:1915-2259:1
so has part: feature:1915-2259:1:exon
subclass of: SO_0000010

82148083
type: Gene
SIO_000068: ncbigene

position:1915:1
position: 1915
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2259:1
position: 2259
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1915-2259:1:exon

K7T73_RS21870
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1455
locus tag: K7T73_RS21870
old locus tag: K7T73_21830
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MEGVWGRVPQRVWAAPKGWFLPCVSMVFRLAEKEPRRAYTNEIGIVGYTNFIGSLCPMCYAFPNIYRFKNETVGSVTRKKGRAARGKLRNYSHGEIQDLGRAGDTKAQSKTGEN
SIO_010081: K7T73_RS21870
subclass of: SO_0000673
so part of: K7T73_RS21870
location: 1915..2259
location: region:1915-2259:1
so has part: feature:1915-2259:1:exon

WP_223664348.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1915-2259:1:exon

K7T73_RS21875
type: Gene
subclass of: SO_0000704
RO_0002162: 1455
gene: mobV
locus tag: K7T73_RS21875
old locus tag: K7T73_21835
so part of: sequence
location: 2168..3355
location: region:2168-3355:1
so has part: feature:2168-3355:1:exon
subclass of: SO_0000010

82148084
type: Gene
SIO_000068: ncbigene

position:2168:1
position: 2168
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3355:1
position: 3355
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2168-3355:1:exon

K7T73_RS21875
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1455
gene: mobV
locus tag: K7T73_RS21875
old locus tag: K7T73_21835
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016099255.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0006310 - DNA recombination [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobV family relaxase
translation: MANYAIIRMEKFKISDVQGIQKHNQRQGKIKSNPDIDYERSHLNYDLLNREYLQYERRIKDEISERVKRKPRANSVVLSEFLVTASPEYMQSLTKDEQKRYFERSLDFIKERYGERNTLYAVVHQDEANPHMHVGVLPITEDGRLSAKDIYNRTELRQLQQDFPDELQRQGFEVERGKEGSKEKHLHPNEYKEKQDLEREIAFLEKNLEQKKNQLLAISGNVPEKNVSLKPKRKEIKTLVKPKLIGKPEIIEKETGNYVFSPKQLEKLENVVTAAVTIKRDYERLQSTDLVEENTKLHKELFQQRKENHKLTRENKELRSENMGLKRHISDLQREIGFLYQNTKEFLKERTESVRAFKNVFKDFIGDLRKKITGSEFERLYKRERAQECDRGMER
SIO_010081: K7T73_RS21875
subclass of: SO_0000673
so part of: K7T73_RS21875
location: 2168..3355
location: region:2168-3355:1
so has part: feature:2168-3355:1:exon

WP_223664360.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2168-3355:1:exon

K7T73_RS21880
type: Gene
subclass of: SO_0000704
RO_0002162: 1455
locus tag: K7T73_RS21880
old locus tag: K7T73_21840
so part of: sequence
location: 3688..4743
location: region:3688-4743:1
so has part: feature:3688-4743:1:exon
subclass of: SO_0000010

82148085
type: Gene
SIO_000068: ncbigene

position:3688:1
position: 3688
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4743:1
position: 4743
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3688-4743:1:exon

K7T73_RS21880
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1455
locus tag: K7T73_RS21880
old locus tag: K7T73_21840
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009499497.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0006260 - DNA replication [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: protein rep
translation: MRKKQERSGISPVDDEILGKYAPKKSLNRKAFHFIKKYLGEAAAEYFEECNTFISFLTNGDKSVKRTYKANNCKNRFCPMCAWKKAKKDAMKLGVMLEAIKQKEDKEFLFLTLTAPNCQAEELSDTIDKFNKAYHKLFKRRNVQKAVKGYVRKLEVTTDQELKITRELYHQKREYFDKRGLKMGHDNPQYDTYNPHFHAILVVNKSYFKKNYIRHDEWLNMWRDCMDDPSITQVRVERLKKKGSSNGVLEIAKYAAKHDDLLINEKVFDVFYTSLKGRQLLVYSGVMKDYAQKYESGELDDFKEKDENAYTHLLSAIWAKSKYIQELRALTEHELQEINKTKFVEEVEDII
SIO_010081: K7T73_RS21880
subclass of: SO_0000673
so part of: K7T73_RS21880
location: 3688..4743
location: region:3688-4743:1
so has part: feature:3688-4743:1:exon

WP_223664329.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3688-4743:1:exon