Clostridium taeniosporum strain 1/k plasmid pCt1, complete sequence.
type: Entry
definition: Clostridium taeniosporum strain 1/k plasmid pCt1, complete sequence.
sequence version: NZ_CP017254.1
sequence date: 2023-03-13
sequence: sequence
division: CON
label: NZ_CP017254.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN05608059
keyword: RefSeq
source: Clostridium taeniosporum
organism: Clostridium taeniosporum
taxonomy: Bacteria; Bacillota; Clostridia; Eubacteriales; Clostridiaceae; Clostridium.
reference: 1
references: 29293521
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP017254.1.\nSource bacteria are available from James R. Walker, Department of\nMolecular Biosciences, University of Texas, 2506 Speedway Stop\nA5000, Austin, TX 78712.\n\nAnnotation modified by submitter.\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 :: Newbler v. 2.7; Consed v. 22.0\nGenome Coverage :: 56x;900x\nSequencing Technology :: 454; Illumina; Sanger dideoxy sequencing\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/13/2023 10:05:00\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) :: 3,232\nCDSs (total) :: 3,127\nGenes (coding) :: 3,067\nCDSs (with protein) :: 3,067\nGenes (RNA) :: 105\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 78\nncRNAs :: 5\nPseudo Genes (total) :: 60\nCDSs (without protein) :: 60\nPseudo Genes (ambiguous residues) :: 0 of 60\nPseudo Genes (frameshifted) :: 43 of 60\nPseudo Genes (incomplete) :: 17 of 60\nPseudo Genes (internal stop) :: 12 of 60\nPseudo Genes (multiple problems) :: 11 of 60\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5894
topology: circular
so has quality: SO_0000988
location: 1..5894
location: region:1-5894:1
RO_0002162: 394958

NZ_CP017254
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN05608059
type: BioSample
SIO_000068: biosample

1
title: Genomics of Clostridium taeniosporum, an organism which forms endospores with ribbon-like appendages
author: Cambridge, J.M.
author: Blinkova, A.L.
author: Salvador Rocha, E.I.
author: Bode Hernandez, A.
author: Moreno, M.
author: Gines-Candelaria, E.
author: Goetz, B.M.
author: Hunicke-Smith, S.
author: Satterwhite, E.
author: Tucker, H.O.
author: Walker, J.R.
journal: PLoS One 13 (1), e0189673 (2018)
pubmed: 29293521
comments: Publication Status: Online-Only

29293521
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Cambridge, J.M.
author: Blinkova, A.L.
author: Salvador Rocha, E.I.
author: Henandez, A.B.
author: Moreno, M.
author: Gines-Candelaria, E.
author: Goetz, B.M.
author: Hunicke-Smith, S.
author: Satterwhite, E.
author: Tucker, H.O.
author: Walker, J.R.
journal: Submitted (06-SEP-2016) Molecular Biosciences, University of Texas, 2506 Speedway Stop A5000, Austin, TX 78712, USA

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

position:5894:1
position: 5894
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5894:1:source
so part of: sequence
organism: Clostridium taeniosporum
mol type: genomic DNA
strain: 1/k
isolation source: Lake Mainaki silt
plasmid: pCt1
country: Ukraine: Crimean Lake Mainaki silt
collection date: 1964
collected by: N. A. Krasil'nkov
identified by: N. A. Krasil'nikov

394958
type: Taxonomy
SIO_000068: taxonomy

BGI42_RS16290
type: Gene
subclass of: SO_0000704
RO_0002162: 394958
locus tag: BGI42_RS16290
old locus tag: BGI42_14645
so part of: sequence
location: join(5394..5894,1..912)
location: region:1-5894:1
so has part: feature:5394-5894:1:exon
so has part: feature:1-912:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:5394-5894:1:exon

position:5394:1
position: 5394
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-912:1:exon

position:912:1
position: 912
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

BGI42_RS16290
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 394958
locus tag: BGI42_RS16290
old locus tag: BGI42_14645
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: relaxase/mobilization nuclease domain-containing protein
translation: MAIVKVTNSKASIGKAINYVTKEEKTEDKLVSGINCTPETVLHEMKATKEQFRKTDGRQYAHYIHSFKPGEQITHEKAHKLALEISEKQFKGYEVLVATHKDKDHIHSHIIVNSVSYEDGRKLHSSKKDLAEVKELSNKICEREGLSIIKPQKDVLTSFNAKKYKSLEKGLEGTYKSYMLDLWKNVNIFKKVATCKEQFIQNMNNKGYQVNWSDTRKYITYTTPEGKRVRDSNLVKTFKNEKLSKEELLNEFSRNGEKLGGTYRAKGDIGKSILFGRNEVSSGRDDKLINVDKTEQRQTEPNNRPVEERKTDTRARADREHTEIKQGSPSITFGNGGSEERQQSKDRGINPDNTENSRSNTGYIHEVSRDTVRDKQLREGENLEGQSNPILNTTRSDNRIDIDDSRSLSTNNPLDELVKKFDKTLQKAEEREKEKKAFAELQAKAREERKLKLEQKPKVKYKSMDRGWER
SIO_010081: BGI42_RS16290
subclass of: SO_0000673
so part of: BGI42_RS16290
location: join(5394..5894,1..912)
location: region:1-5894:1
so has part: feature:5394-5894:1:exon
so has part: feature:1-912:1:exon

WP_069681105.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5394-5894:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-912:1:exon

BGI42_RS14775
type: Gene
subclass of: SO_0000704
RO_0002162: 394958
locus tag: BGI42_RS14775
old locus tag: BGI42_14650
so part of: sequence
location: 1026..2258
location: region:1026-2258:1
so has part: feature:1026-2258:1:exon
subclass of: SO_0000010

position:1026:1
position: 1026
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2258:1
position: 2258
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1026-2258:1:exon

BGI42_RS14775
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 394958
locus tag: BGI42_RS14775
old locus tag: BGI42_14650
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017352643.1
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: MGQVLRQQEYNEPIEYLNTVHGTSKGWITRAEISGSFNQWHYKYNDLVKQDFIGENNYISLNTFYSTYRRLEYLKELKAHFIDLDIYKTKFTKEQVLMRLDEEYFNKSIPRPNLIIDSGRGLYLIWLINSVPSQALPLWKAVEEYLYKELKVFGADRQALDATRVLRVPGSINSKSNTVVEVLEQYEYVYDLREIQEGYLPELDKNKPKKKGRPSKTVFIHRERSLYYARIQDIIKLCELRNYDLKGQRELILFLYRYWLCYFTEDTQKALEDTLELNNQFILPLSETEVIRATRSAERVFLNKDKKYKYKNQTLIDLLEITGLEETYMKTIISDREYKRRKRMRNNISYQEQLKAKGKISEKDKISQRRAKIKDLLEQGLKQKDICLHLDISKRTYIRDINYIKEQGLA
SIO_010081: BGI42_RS14775
subclass of: SO_0000673
so part of: BGI42_RS14775
location: 1026..2258
location: region:1026-2258:1
so has part: feature:1026-2258:1:exon

WP_069681101.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1026-2258:1:exon

BGI42_RS14780
type: Gene
subclass of: SO_0000704
RO_0002162: 394958
locus tag: BGI42_RS14780
old locus tag: BGI42_14655
so part of: sequence
location: complement(2683..3681)
location: region:2683-3681:-1
so has part: feature:2683-3681:-1:exon
subclass of: SO_0000010

position:2683:-1
position: 2683
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3681:-1
position: 3681
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2683-3681:-1:exon

BGI42_RS14780
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 394958
locus tag: BGI42_RS14780
old locus tag: BGI42_14655
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015392433.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: M28 family peptidase
translation: MINIKSIFKLGIILILVINFIGCSKNINTKKIGDTKQNNKIEQESQIEIPNTKDIINTLCSDDFGGRLTGSDGDNKTRDYIEGIIKNLKLEPLFDEEYYEPYTQDVYKKLSLFEDNGEPENKEVQNLVGVINGSDNTKAVVISAHFDHIGCQDGKIIRGALDNASGVATLIQIAKNLKIKSQRKPFNRDIIFAFFDGEETGLQGSKAFVKDIKDTYSDLYNINIDCVGGKNSGKISLYNKSKISDKLTAAMKETFRNNNMDFSKIYEQGVISDERRFEQNNIPNIYIKQENIKPYIHKETDIPDSLDYAEILKIANVLSNFVEINDGKTFKN
SIO_010081: BGI42_RS14780
subclass of: SO_0000673
so part of: BGI42_RS14780
location: complement(2683..3681)
location: region:2683-3681:-1
so has part: feature:2683-3681:-1:exon

WP_069681102.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2683-3681:-1:exon

BGI42_RS14785
type: Gene
subclass of: SO_0000704
RO_0002162: 394958
locus tag: BGI42_RS14785
old locus tag: BGI42_14660
so part of: sequence
location: complement(3772..4140)
location: region:3772-4140:-1
so has part: feature:3772-4140:-1:exon
subclass of: SO_0000010

position:3772:-1
position: 3772
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4140:-1
position: 4140
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3772-4140:-1:exon

BGI42_RS14785
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 394958
locus tag: BGI42_RS14785
old locus tag: BGI42_14660
inference: COORDINATES: protein motif:HMM:NF019844.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: SH3 domain-containing protein
translation: MKSKKVLSLLLATCIVGTSIEVFSVAVNAKVRDSITIEESNTVTDENNEVSHRRVPRSVGSIVVTARSGANIRKGPGTNYKKIGAIAWGEDTPYAYEKKNGWYKIEWGDSYGWISASTCELQ
SIO_010081: BGI42_RS14785
subclass of: SO_0000673
so part of: BGI42_RS14785
location: complement(3772..4140)
location: region:3772-4140:-1
so has part: feature:3772-4140:-1:exon

WP_069681103.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3772-4140:-1:exon

BGI42_RS14790
type: Gene
subclass of: SO_0000704
RO_0002162: 394958
locus tag: BGI42_RS14790
old locus tag: BGI42_14665
so part of: sequence
location: 4279..4782
location: region:4279-4782:1
so has part: feature:4279-4782:1:exon
subclass of: SO_0000010

position:4279:1
position: 4279
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4782:1
position: 4782
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4279-4782:1:exon

BGI42_RS14790
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 394958
locus tag: BGI42_RS14790
old locus tag: BGI42_14665
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: MYTVEEVSKQLKVSKVTIYSKLKKFDTLVVLKQGKKYITDDLFKLIQDDLKIRNADNNNLNSNNNINLNDEMAMDTDNLINLNKDLVNTLIEQLREKDRQISELHKLIENNQVLLKQEKEVNQIQLEEHIRELDIKLNDVKENMEKRKGEQQEKRKGLLKKCMFWVG
SIO_010081: BGI42_RS14790
subclass of: SO_0000673
so part of: BGI42_RS14790
location: 4279..4782
location: region:4279-4782:1
so has part: feature:4279-4782:1:exon

WP_069681104.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4279-4782:1:exon

BGI42_RS14795
type: Gene
subclass of: SO_0000704
RO_0002162: 394958
gene: mobC
locus tag: BGI42_RS14795
old locus tag: BGI42_14670
so part of: sequence
location: 5116..5433
location: region:5116-5433:1
so has part: feature:5116-5433:1:exon
subclass of: SO_0000010

position:5116:1
position: 5116
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5433:1
position: 5433
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5116-5433:1:exon

BGI42_RS14795
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 394958
gene: mobC
locus tag: BGI42_RS14795
old locus tag: BGI42_14670
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006002000.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid mobilization relaxosome protein MobC
translation: MNKSRPKQMIFRVNEKEKEQILKKVKRSKLNQNKYLLKCALDKEIHVIDGLHDMTIELKRIGNNLNQLTRAVNEGQANCSKELESIKGELSETWQLLRSLIQRQV
SIO_010081: BGI42_RS14795
subclass of: SO_0000673
so part of: BGI42_RS14795
location: 5116..5433
location: region:5116-5433:1
so has part: feature:5116-5433:1:exon

WP_084023917.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5116-5433:1:exon