Clostridioides difficile strain S-0253 plasmid unnamed, complete sequence.
type: Entry
definition: Clostridioides difficile strain S-0253 plasmid unnamed, complete sequence.
sequence version: NZ_CP076402.1
sequence date: 2023-03-26
sequence: sequence
division: CON
label: NZ_CP076402.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN19491759
keyword: RefSeq
source: Clostridioides difficile (Clostridium difficile)
organism: Clostridioides difficile
taxonomy: Bacteria; Bacillota; Clostridia; Eubacteriales; Peptostreptococcaceae; Clostridioides.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP076402.1.\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 Date :: 21-JAN-2021\nAssembly Method :: Unicycler v. v0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 563x MinION +\n 130x Illuminax\nSequencing Technology :: MinION Mk1c and Illumina NovaSeq 6000\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/26/2023 06:15:58\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) :: 3,732\nCDSs (total) :: 3,603\nGenes (coding) :: 3,567\nCDSs (with protein) :: 3,567\nGenes (RNA) :: 129\nrRNAs :: 11, 12, 12 (5S, 16S, 23S)\ncomplete rRNAs :: 11, 12, 12 (5S, 16S, 23S)\ntRNAs :: 90\nncRNAs :: 4\nPseudo Genes (total) :: 36\nCDSs (without protein) :: 36\nPseudo Genes (ambiguous residues) :: 0 of 36\nPseudo Genes (frameshifted) :: 8 of 36\nPseudo Genes (incomplete) :: 24 of 36\nPseudo Genes (internal stop) :: 13 of 36\nPseudo Genes (multiple problems) :: 7 of 36\nCRISPR Arrays :: 4\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 6760
topology: circular
so has quality: SO_0000988
location: 1..6760
location: region:1-6760:1
RO_0002162: 1496

NZ_CP076402
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN19491759
type: BioSample
SIO_000068: biosample

1
title: Complete genome assembly of three Australian C. difficile strains
author: O'Grady, K.I.
journal: Unpublished

2
title: Direct Submission
author: O'Grady, K.I.
journal: Submitted (02-JUN-2021) Riley C. difficile Research Group, University of Western Australia, Hospital Ave, Perth, WA 6009, Australia

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

position:6760:1
position: 6760
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6760:1:source
so part of: sequence
organism: Clostridioides difficile
mol type: genomic DNA
strain: S-0253
isolation source: clinical, PCR+ stool swab
host: Homo sapiens
plasmid: unnamed
country: Australia: South Australia
collection date: 2014-04-02
collected by: South Australia Pathology
note: Ribotype 002, Sequence type 8

1496
type: Taxonomy
SIO_000068: taxonomy

KNZ77_RS18580
type: Gene
subclass of: SO_0000704
RO_0002162: 1496
gene: repA
locus tag: KNZ77_RS18580
old locus tag: KNZ77_18580
so part of: sequence
location: 1..1638
location: region:1-1638:1
so has part: feature:1-1638:1:exon
subclass of: SO_0000010

66356154
type: Gene
SIO_000068: ncbigene

position:1638:1
position: 1638
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-1638:1:exon

KNZ77_RS18580
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1496
gene: repA
locus tag: KNZ77_RS18580
old locus tag: KNZ77_18580
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011161239.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication protein RepA
translation: MEQLDSKYKLKKFLMAVFRDGIGQGNNLIDNEYVRVFQNNKSNSKQLELGEEFKEYSKTTFFKNIDDIVEFTFAKNIYYENTFFNLCTTDGKAGTNENLINRYALGFDFDKKELGQGFNYKDIINLFTKIGLHYHILVDSGNGFHVYVLINKTNNIKLVSEVTNTLINKLGADKQANLSTQVLRVPYTYNIKNTTKQVKIIHQDKNIYRYDIEKLAKKYCKDVKTVGNTNTKYILDSKLPNCIVDILKNGSKDGHKNLDLQKIVVTLRLRNKSLSQVISVAREWNYISQNSLSNSELEYQVKYMYEKLKTVNFGCTGCEFNSDCWNKIESDFIYSDEDTLFNMPHKHSKDLKYKNRKGVKIMTGNQLFIYNVLLNNKDRELNIDDIMELITYKRKKKVKNIVMSEKTLRETLKELQHNDYITKTKGVTKLGIKDTYNVKEVRCNIDKQYTISYFVTMAVIWGIISTEELRLYTHMRYKQDLLVKDDKIKGNILRINQEELAKDLGVTQQRISNMIESLLDTKILDVWETKINDRGFMYYTYRLNK
SIO_010081: KNZ77_RS18580
subclass of: SO_0000673
so part of: KNZ77_RS18580
location: 1..1638
location: region:1-1638:1
so has part: feature:1-1638:1:exon

WP_011161239.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-1638:1:exon

KNZ77_RS18585
type: Gene
subclass of: SO_0000704
RO_0002162: 1496
locus tag: KNZ77_RS18585
old locus tag: KNZ77_18585
so part of: sequence
location: complement(2632..3192)
location: region:2632-3192:-1
so has part: feature:2632-3192:-1:exon
subclass of: SO_0000010

66356155
type: Gene
SIO_000068: ncbigene

position:2632:-1
position: 2632
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3192:-1
position: 3192
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2632-3192:-1:exon

KNZ77_RS18585
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1496
locus tag: KNZ77_RS18585
old locus tag: KNZ77_18585
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003430816.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: peptidoglycan-binding domain-containing protein
translation: MLKKLKKMLLITCCLFMMSSTAFAETQNSEGKSFTISGYTFMYENAPQEIKDKYKENCLDIGVEPQPNDEIFITPSELKTYSNIDMYSARSSSFTVTYHYSYYKVTGDKNYTVNTSTIVKYGNSGNPVHLVQLLLKKVGYALEVDSQFGNTTLSKVKSFQGSYGLTVDGIVGSATWKKFASATNLD
SIO_010081: KNZ77_RS18585
subclass of: SO_0000673
so part of: KNZ77_RS18585
location: complement(2632..3192)
location: region:2632-3192:-1
so has part: feature:2632-3192:-1:exon

WP_011161240.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2632-3192:-1:exon

KNZ77_RS18590
type: Gene
subclass of: SO_0000704
RO_0002162: 1496
locus tag: KNZ77_RS18590
old locus tag: KNZ77_18590
so part of: sequence
location: complement(3238..4221)
location: region:3238-4221:-1
so has part: feature:3238-4221:-1:exon
subclass of: SO_0000010

66356156
type: Gene
SIO_000068: ncbigene

position:3238:-1
position: 3238
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4221:-1
position: 4221
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3238-4221:-1:exon

KNZ77_RS18590
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1496
locus tag: KNZ77_RS18590
old locus tag: KNZ77_18590
inference: COORDINATES: protein motif:HMM:NF017390.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: M56 family metallopeptidase
translation: MSNLILTDILRTSITSSLVICFLLLLRTTIFRIFNKGFNYYIWLIVIVRLLFPFSYFTYTISDSKFQYKPILNEVDYSNTVLIIYLTIVILLAIYRFIKYLKFKSLVIDLSYDIENLEINNLYNNLLKELNIEKHIKLKYTYEINTPSFFGLFDNYILLPPHNYNLNELHWILKHELIHYKSKDLYIRYLVLFLKCVYFFNPFIYLLDRIIYHSCELHCDEVVLKGCSLENIKSYANTILDSIERSSRDSNNYTTGLHRKSNFEKRVYDMFKNKGKSGILIALILCLLSSFTYFKFDSIISKPINHSLDAPLPVNTGKEKSFTITID
SIO_010081: KNZ77_RS18590
subclass of: SO_0000673
so part of: KNZ77_RS18590
location: complement(3238..4221)
location: region:3238-4221:-1
so has part: feature:3238-4221:-1:exon

WP_021363141.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3238-4221:-1:exon

KNZ77_RS18595
type: Gene
subclass of: SO_0000704
RO_0002162: 1496
locus tag: KNZ77_RS18595
old locus tag: KNZ77_18595
so part of: sequence
location: complement(4234..4596)
location: region:4234-4596:-1
so has part: feature:4234-4596:-1:exon
subclass of: SO_0000010

66356157
type: Gene
SIO_000068: ncbigene

position:4234:-1
position: 4234
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4596:-1
position: 4596
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4234-4596:-1:exon

KNZ77_RS18595
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1496
locus tag: KNZ77_RS18595
old locus tag: KNZ77_18595
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009903180.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: BlaI/MecI/CopY family transcriptional regulator
translation: MIEKIPRAELKVMMLFWDTDKVLTSRDIVNIMSEEWKQTTTLTLLSRLSKRGFLEPTKKPTHTTYKILIDKKSYLEFATSDFVKNVHNDSIVSLVDSVNKEKIGKDELASLRAFIKKLKK
SIO_010081: KNZ77_RS18595
subclass of: SO_0000673
so part of: KNZ77_RS18595
location: complement(4234..4596)
location: region:4234-4596:-1
so has part: feature:4234-4596:-1:exon

WP_021363140.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4234-4596:-1:exon

KNZ77_RS18600
type: Gene
subclass of: SO_0000704
RO_0002162: 1496
locus tag: KNZ77_RS18600
old locus tag: KNZ77_18600
so part of: sequence
location: 5839..6486
location: region:5839-6486:1
so has part: feature:5839-6486:1:exon
subclass of: SO_0000010

66356158
type: Gene
SIO_000068: ncbigene

position:5839:1
position: 5839
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6486:1
position: 6486
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5839-6486:1:exon

KNZ77_RS18600
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1496
locus tag: KNZ77_RS18600
old locus tag: KNZ77_18600
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: MNKKLEKPFVYKREYDLTGYDVEILQKYELEQAIYVYVGSSCAYNMRARSSKWRYHIRTNNKSICCNIKNFIHNLELFYKMELKLSDNIINDKLYYSNIAEFEEFETLEKAREVESTIISQYQFLDSINHMLKQKIILLSNKDSVLNITKNGNTNYLKVKNKYIEKHKNKPIMRYHINCQFNTDGSVKSITQEFEPILELNKKNTLSRPSRVFLK
SIO_010081: KNZ77_RS18600
subclass of: SO_0000673
so part of: KNZ77_RS18600
location: 5839..6486
location: region:5839-6486:1
so has part: feature:5839-6486:1:exon

WP_011161238.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5839-6486:1:exon