Clostridium butyricum strain CDC_51208 plasmid pNPD4_1, complete sequence.
type: Entry
definition: Clostridium butyricum strain CDC_51208 plasmid pNPD4_1, complete sequence.
sequence version: NZ_CP013240.1
sequence date: 2023-02-06
sequence: sequence
division: CON
label: NZ_CP013240.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN04262337
keyword: RefSeq
source: Clostridium butyricum
organism: Clostridium butyricum
taxonomy: Bacteria; Bacillota; Clostridia; Eubacteriales; Clostridiaceae; Clostridium.
reference: 1
references: 28729254
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP013240.1.\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 :: Velvet v. 1.2.08; HGAP v. 3; Phrap SPS4.24\nGenome Coverage :: 319x; 52.6x\nSequencing Technology :: Illumina NextSeq; PacBio RS\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 02:58:52\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) :: 4,231\nCDSs (total) :: 4,103\nGenes (coding) :: 4,056\nCDSs (with protein) :: 4,056\nGenes (RNA) :: 128\nrRNAs :: 12, 12, 12 (5S, 16S, 23S)\ncomplete rRNAs :: 12, 12, 12 (5S, 16S, 23S)\ntRNAs :: 88\nncRNAs :: 4\nPseudo Genes (total) :: 47\nCDSs (without protein) :: 47\nPseudo Genes (ambiguous residues) :: 0 of 47\nPseudo Genes (frameshifted) :: 11 of 47\nPseudo Genes (incomplete) :: 33 of 47\nPseudo Genes (internal stop) :: 9 of 47\nPseudo Genes (multiple problems) :: 6 of 47\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 9567
topology: circular
so has quality: SO_0000988
location: 1..9567
location: region:1-9567:1
RO_0002162: 1492

NZ_CP013240
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN04262337
type: BioSample
SIO_000068: biosample

1
title: Finished Whole-Genome Sequences of Clostridium butyricum Toxin Subtype E4 and Clostridium baratii Toxin Subtype F7 Strains
author: Halpin, J.L.
author: Hill, K.
author: Johnson, S.L.
author: Bruce, D.C.
author: Shirey, T.B.
author: Dykes, J.K.
author: Luquez, C.
journal: Genome Announc 5 (29), e00375-17 (2017)
pubmed: 28729254
comments: Erratum:[Genome Announc. 2017 Sep 21;5(38):. PMID: 28935752] Publication Status: Online-Only

28729254
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Hill, K.K.
author: Shirey, T.B.
author: Raphael, B.
author: Daligault, H.E.
author: Bruce, D.C.
author: Johnson, S.L.
author: Foley, B.T.
journal: Submitted (17-NOV-2015) BioScience B11, Los Alamos National Laboratory, PO Box 1663 M888, Los Alamos, NM 87545, USA

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

position:9567:1
position: 9567
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9567:1:source
so part of: sequence
organism: Clostridium butyricum
mol type: genomic DNA
strain: CDC_51208
plasmid: pNPD4_1
note: Botulism neurotoxin type E subtype E4

1492
type: Taxonomy
SIO_000068: taxonomy

NPD4_RS21150
type: Gene
subclass of: SO_0000704
RO_0002162: 1492
locus tag: NPD4_RS21150
old locus tag: NPD4_4234
so part of: sequence
location: join(8645..9567,1..1963)
location: region:1-9567:1
so has part: feature:8645-9567:1:exon
so has part: feature:1-1963:1:exon
subclass of: SO_0000010

66383018
type: Gene
SIO_000068: ncbigene

urn:…
SIO_000300: 1
SIO_000628: feature:8645-9567:1:exon

position:8645:1
position: 8645
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-1963:1:exon

position:1963:1
position: 1963
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

NPD4_RS21150
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1492
locus tag: NPD4_RS21150
old locus tag: NPD4_4234
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: MDNKKKQIGRLILVCALIALVLVVGINPSISAYASSTTSSATYVETNINNAYARITSNKTDYNWKFKVYKVIDPNNKKEPSYENGIFKLQGKEVIIDTEYLATVYSKIYVNVDGVYVGEDSERCENYRFNQLDNAYYAAYKLKNLHTGINTIKVRAFKPYTVNLDPNYYGPEYIDNTIRVMVTSTIDESIKNINLGTAAIADFELLGITTVTSSNIRDVRNAIIVAREKKGSDLIQAEIEQVVEHASNEKETAFKEIIDGKGTISDYQIIGITNVKEENLEDVNWYLKEKGTSNENEIKNNVNIIVNALSNINNGTMTLSYYQTLGITTVTSSNVRDVRDVIIVAKEKKESNLTRTEIGKIAENAANIREAAVKEIVDGKGTISDYQIIGITNVKEENLEDVNWYLKEKGTSNEAQIKTNVSNIVNTLNNVNAGTTTLSGYQILGITTVTSSNVRNVKESIIAAKKEKGSNLTRTEIGKIAENAANIREAAVKEIVDGKGTISDYQIIGITNVKEENLEDVNWYLKEKGTSNEAQIKTNVSNIVNALSNINNGTMTLSYYQTLGITTVTSSNVRDVRDVIIVAKEKKESNLTRTEIGKIAENAANIREAAVKEIVDGKGTISDYQIIGITNVKEENLEDVNWYLKEKGTSNEAQIKTNVSNIVNTLNNVNAGTTTLSGYQILGITTVTSSNVRNVKESIIAAKKEKGSNLTRTEIGKIAENAANIREAAVKEIVDGKGTISDYQIIGITNVKEENLEDVNWYLKEKGTSNEAQIKTNVSNIVNTLNNVNAGTTTLSGYQILGITTVTSSNVRNVKDAIIAAKKEKGSNLTRTEIGKIAENAANIREAAVKEIVDGKGTISDYQIIGITNVKEENLEDINWYLKEKGTSNEAQIKTNVSNIVNTLNNVNAGTTTLSCYQTLGITTVTSSNVRNVKDAIIAAKKEKGSNLTRTEIKSIVLNII
SIO_010081: NPD4_RS21150
subclass of: SO_0000673
so part of: NPD4_RS21150
location: join(8645..9567,1..1963)
location: region:1-9567:1
so has part: feature:8645-9567:1:exon
so has part: feature:1-1963:1:exon

WP_236901044.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8645-9567:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-1963:1:exon

NPD4_RS20860
type: Gene
subclass of: SO_0000704
RO_0002162: 1492
locus tag: NPD4_RS20860
old locus tag: NPD4_4235
so part of: sequence
location: complement(1987..2250)
location: region:1987-2250:-1
so has part: feature:1987-2250:-1:exon
subclass of: SO_0000010

66382984
type: Gene
SIO_000068: ncbigene

position:1987:-1
position: 1987
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2250:-1
position: 2250
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1987-2250:-1:exon

NPD4_RS20860
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1492
locus tag: NPD4_RS20860
old locus tag: NPD4_4235
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003406525.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MTDNKEKINKLDEKIKQLQAQKNSLIAREKEKERKARTKRLIEIGAIFDSIGIDTVEKANTLKSGFNNDDSFKSCINKIIIQNNKKE
SIO_010081: NPD4_RS20860
subclass of: SO_0000673
so part of: NPD4_RS20860
location: complement(1987..2250)
location: region:1987-2250:-1
so has part: feature:1987-2250:-1:exon

WP_003406525.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1987-2250:-1:exon

NPD4_RS20865
type: Gene
subclass of: SO_0000704
RO_0002162: 1492
locus tag: NPD4_RS20865
old locus tag: NPD4_4236
so part of: sequence
location: 2518..4161
location: region:2518-4161:1
so has part: feature:2518-4161:1:exon
subclass of: SO_0000010

66382985
type: Gene
SIO_000068: ncbigene

position:2518:1
position: 2518
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4161:1
position: 4161
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2518-4161:1:exon

NPD4_RS20865
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1492
locus tag: NPD4_RS20865
old locus tag: NPD4_4236
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003406527.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobQ family relaxase
translation: MSIYHFGQMKVISRGTGRSVIASSAYISGEKLYNEYDGLTHDYTRKQGVVFSEVMLPENAKDEWKNRQILWNEVEKIEKSKVSQLARSFEVGLQTEFTLEENIKLIKEYVKDNFIDKGMCADICIHDKSDGNPHAHVMLTMRKIDEQGKFLPKAEKQYLCRNDKGDEKYLRSNDLKEDRNFEKVYKCKYKNDYRELTNRELKMEEYKNYKKISKYPLDKKIDMCADWNNNNNVELWREDWARVNNKLFKEKGLNIRVDHRSYERQEINRVPTIHEGYGARLRAKNGKECDRIDINRYITNLNEKIKGYENDIHKLKNEMIELNRDIDIKIKSGIEAMSLGLPKSSYKTTDSDIKEMLKELKEKLSDKANKNLGVDRALKYIDKREIKTNDDVKVIRYQLSTIRTDYGNRIDAIDDYINRMNSIYDNILRKSREVNSLEKEVEELGIFKFKQKKYLNERIEELKNEINEFKESEFYQKNLKYTDKLEELKRERKECLEVLKKCDNENSILYDIETLSKDKNKLIGNLNNDKKNDINFKVKRHSNELEL
SIO_010081: NPD4_RS20865
subclass of: SO_0000673
so part of: NPD4_RS20865
location: 2518..4161
location: region:2518-4161:1
so has part: feature:2518-4161:1:exon

WP_003406527.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2518-4161:1:exon

NPD4_RS20870
type: Gene
subclass of: SO_0000704
RO_0002162: 1492
locus tag: NPD4_RS20870
old locus tag: NPD4_4237
so part of: sequence
location: 4711..5382
location: region:4711-5382:1
so has part: feature:4711-5382:1:exon
subclass of: SO_0000010

66382986
type: Gene
SIO_000068: ncbigene

position:4711:1
position: 4711
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5382:1
position: 5382
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4711-5382:1:exon

NPD4_RS20870
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1492
locus tag: NPD4_RS20870
old locus tag: NPD4_4237
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003406523.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MNLAFIKILGQIDKVLKEDENGSATVLFKIDPESKNLNTSIAMVEFKKKHWDKIKNSPKDLLKVTLYGRYDLRLKNNKPFMYVRCESIRKIKQKNIEIETQQLELMLKDKVKKKKKKKIEKENFNNKWYECIPKEEFKEIDISKVKLVEEIHLEAIIPIFNIKKLSKYEEVNPIAVRRLENGEYGLVTGVRSFLVGKIFDKNLRAYITDLDRQTFKEKYSLEI
SIO_010081: NPD4_RS20870
subclass of: SO_0000673
so part of: NPD4_RS20870
location: 4711..5382
location: region:4711-5382:1
so has part: feature:4711-5382:1:exon

WP_003406523.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4711-5382:1:exon

NPD4_RS20875
type: Gene
subclass of: SO_0000704
RO_0002162: 1492
locus tag: NPD4_RS20875
old locus tag: NPD4_4238
so part of: sequence
location: 6227..6475
location: region:6227-6475:1
so has part: feature:6227-6475:1:exon
subclass of: SO_0000010

66382987
type: Gene
SIO_000068: ncbigene

position:6227:1
position: 6227
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6475:1
position: 6475
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6227-6475:1:exon

NPD4_RS20875
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1492
locus tag: NPD4_RS20875
old locus tag: NPD4_4238
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003406516.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid stabilization protein
translation: MFKLDKEILELLKLIQSDIADIKQEQSETNERLDSIEKKIDITYEQVARTAEDITSIKDDINTVETITAKNWQDITKLKSIK
SIO_010081: NPD4_RS20875
subclass of: SO_0000673
so part of: NPD4_RS20875
location: 6227..6475
location: region:6227-6475:1
so has part: feature:6227-6475:1:exon

WP_236901042.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6227-6475:1:exon

NPD4_RS20880
type: Gene
subclass of: SO_0000704
RO_0002162: 1492
locus tag: NPD4_RS20880
old locus tag: NPD4_4239
so part of: sequence
location: 6611..7147
location: region:6611-7147:1
so has part: feature:6611-7147:1:exon
subclass of: SO_0000010

66382988
type: Gene
SIO_000068: ncbigene

position:6611:1
position: 6611
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7147:1
position: 7147
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6611-7147:1:exon

NPD4_RS20880
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1492
locus tag: NPD4_RS20880
old locus tag: NPD4_4239
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003406529.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix domain-containing protein
translation: MSKETQKAKIERLEKELKQAQEIIKTQNSEINEMIDKADNSFENSSTYIQMHRRIEDLELKVKVITDSVEHNKRMYVSELKKNSELIKEIYQLRDIKVVQKLNMNNDKDMQKELEKLNKENEELKGKLNAGRKEKFTKQQQEEIKRLRLDGKSMQDIADILKCSKATIFNYLKRLNKN
SIO_010081: NPD4_RS20880
subclass of: SO_0000673
so part of: NPD4_RS20880
location: 6611..7147
location: region:6611-7147:1
so has part: feature:6611-7147:1:exon

WP_236901043.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6611-7147:1:exon

NPD4_RS20885
type: Gene
subclass of: SO_0000704
RO_0002162: 1492
locus tag: NPD4_RS20885
old locus tag: NPD4_4240
so part of: sequence
location: 7251..7841
location: region:7251-7841:1
so has part: feature:7251-7841:1:exon
subclass of: SO_0000010

66382989
type: Gene
SIO_000068: ncbigene

position:7251:1
position: 7251
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7841:1
position: 7841
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7251-7841:1:exon

NPD4_RS20885
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1492
locus tag: NPD4_RS20885
old locus tag: NPD4_4240
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: MDYKSMELDDLAGYINLQLEKGRNFTEVAVEDFSCNESTLRKRLTGKKLYKRIGNKYVRQCQTIDDKNQNSNEINDVRQSVRQDVTDGNSTQIINETKAQSIMVSPSDNEKFLGLISNYELIMKMLDNYKNNEDSFNKSNGLVVELPVEKKKDFRVTLRLNDVIYEEFKEFADRNKQFTVKELVSQALKEFIQKYK
SIO_010081: NPD4_RS20885
subclass of: SO_0000673
so part of: NPD4_RS20885
location: 7251..7841
location: region:7251-7841:1
so has part: feature:7251-7841:1:exon

WP_003406522.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7251-7841:1:exon

NPD4_RS20890
type: Gene
subclass of: SO_0000704
RO_0002162: 1492
locus tag: NPD4_RS20890
old locus tag: NPD4_4241
so part of: sequence
location: complement(8029..8502)
location: region:8029-8502:-1
so has part: feature:8029-8502:-1:exon
subclass of: SO_0000010

66382990
type: Gene
SIO_000068: ncbigene

position:8029:-1
position: 8029
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:8502:-1
position: 8502
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8029-8502:-1:exon

NPD4_RS20890
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1492
locus tag: NPD4_RS20890
old locus tag: NPD4_4241
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003406520.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DNA-binding protein
translation: MNNFTINNSINYTNTDLINVYSNNKISNENSDFKNTTPILNDSLELDSDKKNIINKINANEAFKKTSEDMELSKEEEIDLRLEYARISQQMRHHGYNVPDFDLNNSDPKTSSFLPFLSEMKEFSKTYFSSGDHLVSSDFLGNFCDKFEENLKKYDCF
SIO_010081: NPD4_RS20890
subclass of: SO_0000673
so part of: NPD4_RS20890
location: complement(8029..8502)
location: region:8029-8502:-1
so has part: feature:8029-8502:-1:exon

WP_071983128.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8029-8502:-1:exon