Clostridium cadaveris strain IFB3C5 plasmid pCCIFB3C5_1, complete sequence.
type: Entry
definition: Clostridium cadaveris strain IFB3C5 plasmid pCCIFB3C5_1, complete sequence.
sequence version: NZ_CP076621.1
sequence date: 2022-12-10
sequence: sequence
division: CON
label: NZ_CP076621.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN19659030
keyword: RefSeq
source: Clostridium cadaveris
organism: Clostridium cadaveris
taxonomy: Bacteria; Bacillota; Clostridia; Eubacteriales; Clostridiaceae; Clostridium.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP076621.1.\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 :: NOV-2020\nAssembly Method :: Microbial assembly v. 1\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 212x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/10/2022 05:46:01\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,525\nCDSs (total) :: 3,413\nGenes (coding) :: 3,361\nCDSs (with protein) :: 3,361\nGenes (RNA) :: 112\nrRNAs :: 9, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 9, 9 (5S, 16S, 23S)\ntRNAs :: 81\nncRNAs :: 4\nPseudo Genes (total) :: 52\nCDSs (without protein) :: 52\nPseudo Genes (ambiguous residues) :: 0 of 52\nPseudo Genes (frameshifted) :: 19 of 52\nPseudo Genes (incomplete) :: 31 of 52\nPseudo Genes (internal stop) :: 14 of 52\nPseudo Genes (multiple problems) :: 10 of 52\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4819
topology: circular
so has quality: SO_0000988
location: 1..4819
location: region:1-4819:1
RO_0002162: 1529

NZ_CP076621
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN19659030
type: BioSample
SIO_000068: biosample

1
title: Genome Resource Announcements Clostridium cadaveris and Morganella morganii
author: Zepeda Rivera, M.A.
author: Jones, D.S.
author: Stepanovica, M.
author: McGlinchey, A.
author: Baryiames, A.
author: LaCourse, K.
author: Johnston, C.D.
author: Bullman, S.
journal: Unpublished

2
title: Direct Submission
author: Zepeda Rivera, M.A.
author: Jones, D.S.
author: Stepanovica, M.
author: McGlinchey, A.
author: Baryiames, A.
author: LaCourse, K.
author: Johnston, C.D.
author: Bullman, S.
journal: Submitted (10-JUN-2021) Vaccine and Infectious Disease, Fred Hutchinson Cancer Research, 1100 Fairview Ave N, E4 Eastlake Building, Seattle, WA 98109, USA

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

position:4819:1
position: 4819
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4819:1:source
so part of: sequence
organism: Clostridium cadaveris
mol type: genomic DNA
strain: IFB3C5
isolation source: adenocarcinoma in distal colon
host: Homo sapiens
plasmid: pCCIFB3C5_1

1529
type: Taxonomy
SIO_000068: taxonomy

KQH81_RS17500
type: Gene
subclass of: SO_0000704
RO_0002162: 1529
locus tag: KQH81_RS17500
old locus tag: KQH81_17485
so part of: sequence
location: complement(join(4637..4819,1..861))
location: region:1-4819:-1
so has part: feature:1-861:-1:exon
so has part: feature:4637-4819:-1:exon
subclass of: SO_0000010

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

position:4819:-1
position: 4819
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-861:-1:exon

position:861:-1
position: 861
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:4637-4819:-1:exon

position:4637:-1
position: 4637
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

KQH81_RS17500
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1529
locus tag: KQH81_RS17500
old locus tag: KQH81_17485
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013913692.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MDKNYLVTKSNYFIMNSSYDLSLEEQKLILTLASMVQPEDEEFKPYIFKISDFMELLGVENQAKYTEIPKITKELMKKVFEIEEGNRLIQTAWLSGAIYEKGTGYVTLKFNPDLKPYMLKLNTMFTQYKLANILSMKSKYSPRIYEILKCNEFKRQGYIEIEVEELRKLLKADNIYPLYADFKRKIIFQTQKELKKISDISFDFEEIKTGRKVTALRFYIHQNRIKSINNTMIIEEVSATVSEDIELEREDINKIIYMMKAENIKELDAIKIYKAANGDINKIQEKYNLSKSMPGIKNIVGWMIKAIQEDYHAIKGKGKIDNFNNFEQRQYDFEDLERKLLGWDNEE
SIO_010081: KQH81_RS17500
subclass of: SO_0000673
so part of: KQH81_RS17500
location: complement(join(4637..4819,1..861))
location: region:1-4819:-1
so has part: feature:1-861:-1:exon
so has part: feature:4637-4819:-1:exon

WP_230029346.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-861:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:4637-4819:-1:exon

KQH81_RS17505
type: Gene
subclass of: SO_0000704
RO_0002162: 1529
locus tag: KQH81_RS17505
old locus tag: KQH81_17490
so part of: sequence
location: complement(1483..2064)
location: region:1483-2064:-1
so has part: feature:1483-2064:-1:exon
subclass of: SO_0000010

position:1483:-1
position: 1483
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2064:-1
position: 2064
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1483-2064:-1:exon

KQH81_RS17505
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1529
locus tag: KQH81_RS17505
old locus tag: KQH81_17490
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: MKKCKILSLILSLCIISTSTSIVAFASPTKTSSNNLYESETLNSKKSIINELYKLGFTDKEIEELFEEFPYDESIPLIDNTISSNKIYNILRTSPGDTKNSTYYISTNWVKGLGYSISIGSAGLGLSKAEWAKILVKKMGWKVTVLVGAIASAVADMAMGPNGVRIEMTYTWSYGDTSMAWYWAPTAFDTYKY
SIO_010081: KQH81_RS17505
subclass of: SO_0000673
so part of: KQH81_RS17505
location: complement(1483..2064)
location: region:1483-2064:-1
so has part: feature:1483-2064:-1:exon

WP_230029348.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1483-2064:-1:exon

KQH81_RS17510
type: Gene
subclass of: SO_0000704
RO_0002162: 1529
locus tag: KQH81_RS17510
old locus tag: KQH81_17495
so part of: sequence
location: 3069..3293
location: region:3069-3293:1
so has part: feature:3069-3293:1:exon
subclass of: SO_0000010

position:3069:1
position: 3069
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3293:1
position: 3293
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3069-3293:1:exon

KQH81_RS17510
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1529
locus tag: KQH81_RS17510
old locus tag: KQH81_17495
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: plasmid recombination protein
translation: MEFAWNTQKNNMSDIKGLENEQERKGKISNEEIDLSKTYLNYDLVQSDLNLYQRVKRREELMKFVQFHEYKKIQ
SIO_010081: KQH81_RS17510
subclass of: SO_0000673
so part of: KQH81_RS17510
location: 3069..3293
location: region:3069-3293:1
so has part: feature:3069-3293:1:exon

WP_230029341.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3069-3293:1:exon

KQH81_RS17515
type: Gene
subclass of: SO_0000704
RO_0002162: 1529
locus tag: KQH81_RS17515
old locus tag: KQH81_17500
so part of: sequence
location: 3311..4111
location: region:3311-4111:1
so has part: feature:3311-4111:1:exon
subclass of: SO_0000010

position:3311:1
position: 3311
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4111:1
position: 4111
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3311-4111:1:exon

KQH81_RS17515
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1529
locus tag: KQH81_RS17515
old locus tag: KQH81_17500
inference: COORDINATES: protein motif:HMM:NF013258.2
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: plasmid recombination protein
translation: MTVPQDQFKEWGIDRSKRYLEEVYNYFCKEIGKENVVSAKVHLDETTPHMHLHFVPVSQDGKLQARVLMTPAKINKIHNDAPEYLREKGFDVVRGVGKTKKSLDIHQYKAEKLKEEIKLLENKLKALEGDLKALDSIESSFTRIDSIKAKKSPIGSKISISEEDYRLLVDLSKKSFMLSSKVDTLQDKITGLEERLHDKQLRVDERLELNNLRSENKDLKQKINKANKIINGLSSDFKEEFLKAKEEFEKPVETREMNYNSLDWER
SIO_010081: KQH81_RS17515
subclass of: SO_0000673
so part of: KQH81_RS17515
location: 3311..4111
location: region:3311-4111:1
so has part: feature:3311-4111:1:exon

WP_230029350.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3311-4111:1:exon

KQH81_RS17520
type: Gene
subclass of: SO_0000704
RO_0002162: 1529
locus tag: KQH81_RS17520
old locus tag: KQH81_17505
so part of: sequence
location: complement(4142..4339)
location: region:4142-4339:-1
so has part: feature:4142-4339:-1:exon
subclass of: SO_0000010

position:4142:-1
position: 4142
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4339:-1
position: 4339
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4142-4339:-1:exon

KQH81_RS17520
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1529
locus tag: KQH81_RS17520
old locus tag: KQH81_17505
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002590767.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MINQPDYGEVSFISGDSKNIELLNKSLGDIELTEGEEKSLVWLSGWESSTVKNIISAFKKAKINL
SIO_010081: KQH81_RS17520
subclass of: SO_0000673
so part of: KQH81_RS17520
location: complement(4142..4339)
location: region:4142-4339:-1
so has part: feature:4142-4339:-1:exon

WP_230029343.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4142-4339:-1:exon

KQH81_RS17525
type: Gene
subclass of: SO_0000704
RO_0002162: 1529
locus tag: KQH81_RS17525
old locus tag: KQH81_17510
so part of: sequence
location: complement(4359..4586)
location: region:4359-4586:-1
so has part: feature:4359-4586:-1:exon
subclass of: SO_0000010

position:4359:-1
position: 4359
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4586:-1
position: 4586
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4359-4586:-1:exon

KQH81_RS17525
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1529
locus tag: KQH81_RS17525
old locus tag: KQH81_17510
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003458984.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid stabilization protein
translation: MDKEILEILKSLQEDTKEIKSALKEIDRKLDGVVEQTADLTEFRTSVISRLDELKEVEEVTKANCYEIAKLKIIK
SIO_010081: KQH81_RS17525
subclass of: SO_0000673
so part of: KQH81_RS17525
location: complement(4359..4586)
location: region:4359-4586:-1
so has part: feature:4359-4586:-1:exon

WP_230029345.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4359-4586:-1:exon