Eggerthella lenta strain APC055-529-1D plasmid p529-1D_1, complete sequence.
type: Entry
definition: Eggerthella lenta strain APC055-529-1D plasmid p529-1D_1, complete sequence.
sequence version: NZ_CP089332.1
sequence date: 2023-02-16
sequence: sequence
division: CON
label: NZ_CP089332.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN23789010
keyword: RefSeq
source: Eggerthella lenta
organism: Eggerthella lenta
taxonomy: Bacteria; Actinomycetota; Coriobacteriia; Eggerthellales; Eggerthellaceae; Eggerthella.
reference: 1
references: 35056644
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP089332.1.\nBacteria and source DNA available from Colin Hill.\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 :: 2008\nAssembly Method :: Unicycler v. v0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 30.0x\nSequencing Technology :: Illumina; Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/13/2023 21:55:18\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) :: 3,038\nCDSs (total) :: 2,978\nGenes (coding) :: 2,963\nCDSs (with protein) :: 2,963\nGenes (RNA) :: 60\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 3\nPseudo Genes (total) :: 15\nCDSs (without protein) :: 15\nPseudo Genes (ambiguous residues) :: 0 of 15\nPseudo Genes (frameshifted) :: 3 of 15\nPseudo Genes (incomplete) :: 13 of 15\nPseudo Genes (internal stop) :: 0 of 15\nPseudo Genes (multiple problems) :: 1 of 15\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 3844
topology: circular
so has quality: SO_0000988
location: 1..3844
location: region:1-3844:1
RO_0002162: 84112

NZ_CP089332
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN23789010
type: BioSample
SIO_000068: biosample

1
title: Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity
author: Buttimer, C.
author: Bottacini, F.
author: Shkoporov, A.N.
author: Draper, L.A.
author: Ross, P.
author: Hill, C.
journal: Microorganisms 10 (1), 195 (2022)
pubmed: 35056644
comments: Publication Status: Online-Only

35056644
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Buttimer, C.T.H.
journal: Submitted (08-DEC-2021) APC microbiome, Unversity College Cork, College Road, Cork, Co. Cork T12 YT20, Ireland

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

position:3844:1
position: 3844
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-3844:1:source
so part of: sequence
organism: Eggerthella lenta
mol type: genomic DNA
strain: APC055-529-1D
isolation source: feaces
host: Homo sapiens
plasmid: p529-1D_1
country: Ireland
lat lon: 51.8985 N 8.4756 W
collection date: 2020-12-08

84112
type: Taxonomy
SIO_000068: taxonomy

LUA64_RS15170
type: Gene
subclass of: SO_0000704
RO_0002162: 84112
locus tag: LUA64_RS15170
so part of: sequence
location: complement(join(3694..3844,1..212))
location: region:1-3844:-1
so has part: feature:1-212:-1:exon
so has part: feature:3694-3844:-1:exon
subclass of: SO_0000010

69512517
type: Gene
SIO_000068: ncbigene

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

position:3844:-1
position: 3844
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-212:-1:exon

position:212:-1
position: 212
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:3694-3844:-1:exon

position:3694:-1
position: 3694
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

LUA64_RS15170
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 84112
locus tag: LUA64_RS15170
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: MKVKKTYRLEQETIEELEKLCSDSGKSATEVIEGAIHDAIHVPDVERIGDGWAQTVAALTDQLAVKDDQIASLGRALEAAQETAKAAQALHAANVQERALESSEQKESRRWRWPWDRQDG
SIO_010081: LUA64_RS15170
subclass of: SO_0000673
so part of: LUA64_RS15170
location: complement(join(3694..3844,1..212))
location: region:1-3844:-1
so has part: feature:1-212:-1:exon
so has part: feature:3694-3844:-1:exon

WP_114516736.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-212:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:3694-3844:-1:exon

LUA64_RS15175
type: Gene
subclass of: SO_0000704
RO_0002162: 84112
locus tag: LUA64_RS15175
so part of: sequence
location: complement(209..940)
location: region:209-940:-1
so has part: feature:209-940:-1:exon
subclass of: SO_0000010

69512518
type: Gene
SIO_000068: ncbigene

position:209:-1
position: 209
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:940:-1
position: 940
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:209-940:-1:exon

LUA64_RS15175
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 84112
locus tag: LUA64_RS15175
inference: COORDINATES: protein motif:HMM:NF013849.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication protein
translation: MPYADPEKRREVKRKYEQEKRKQRRTNWMLVFYEDQCPEWREELDELGMPTLVSPSHDADEWTERDEKKNPKHKAGTLKEPHRHLLAMYDNPVSYDQVVKDFAFLKSKNVKYVKSLPAMARYLTHMDSPDKAQYDPEGVCEFGGADWRDLCATTSDKHLALREMRAFIRENNVVDFYLFWDWCDEHNDEWSRLLDDSCCYAIEHYMRSFRAAQVVTQEDREALRAKRGDDGCHTDCQTGAIRE
SIO_010081: LUA64_RS15175
subclass of: SO_0000673
so part of: LUA64_RS15175
location: complement(209..940)
location: region:209-940:-1
so has part: feature:209-940:-1:exon

WP_114516737.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:209-940:-1:exon

LUA64_RS15180
type: Gene
subclass of: SO_0000704
RO_0002162: 84112
locus tag: LUA64_RS15180
so part of: sequence
location: complement(1536..1916)
location: region:1536-1916:-1
so has part: feature:1536-1916:-1:exon
subclass of: SO_0000010

69512519
type: Gene
SIO_000068: ncbigene

position:1536:-1
position: 1536
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1916:-1
position: 1916
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1536-1916:-1:exon

LUA64_RS15180
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 84112
locus tag: LUA64_RS15180
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: MDYRMLYEKLVAEAEENGLGGEFVDWGISISKWRADPVALALYGWLLENEPEGMAAKSERQIDWEMGIVGMASSRRREEAVKSWRRSPGAAERENGGFLVALGLSNAERSAANEAMIAEIPEVAFF
SIO_010081: LUA64_RS15180
subclass of: SO_0000673
so part of: LUA64_RS15180
location: complement(1536..1916)
location: region:1536-1916:-1
so has part: feature:1536-1916:-1:exon

WP_195996248.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1536-1916:-1:exon

LUA64_RS15185
type: Gene
subclass of: SO_0000704
RO_0002162: 84112
locus tag: LUA64_RS15185
so part of: sequence
location: complement(2714..2920)
location: region:2714-2920:-1
so has part: feature:2714-2920:-1:exon
subclass of: SO_0000010

69512520
type: Gene
SIO_000068: ncbigene

position:2714:-1
position: 2714
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2920:-1
position: 2920
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2714-2920:-1:exon

LUA64_RS15185
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 84112
locus tag: LUA64_RS15185
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009608402.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix transcriptional regulator
translation: MAIVIELDEIMEDRGVSLNKLSHRVGITNVNLSRIKTGKVRAVRFSTLAAICDALECQPGDILKNVEP
SIO_010081: LUA64_RS15185
subclass of: SO_0000673
so part of: LUA64_RS15185
location: complement(2714..2920)
location: region:2714-2920:-1
so has part: feature:2714-2920:-1:exon

WP_114516733.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2714-2920:-1:exon

LUA64_RS15190
type: Gene
subclass of: SO_0000704
RO_0002162: 84112
locus tag: LUA64_RS15190
so part of: sequence
location: 3028..3243
location: region:3028-3243:1
so has part: feature:3028-3243:1:exon
subclass of: SO_0000010

69512521
type: Gene
SIO_000068: ncbigene

position:3028:1
position: 3028
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3243:1
position: 3243
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3028-3243:1:exon

LUA64_RS15190
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 84112
locus tag: LUA64_RS15190
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009608401.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix transcriptional regulator
translation: MSTIRVQYGLRIKDLRDERGLSQRGFAALIGMSPTYLADIERDARNVSIDNMKRIADGFGVTFHEMTEGME
SIO_010081: LUA64_RS15190
subclass of: SO_0000673
so part of: LUA64_RS15190
location: 3028..3243
location: region:3028-3243:1
so has part: feature:3028-3243:1:exon

WP_233861728.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3028-3243:1:exon

LUA64_RS15195
type: Gene
subclass of: SO_0000704
RO_0002162: 84112
locus tag: LUA64_RS15195
so part of: sequence
location: complement(3390..3590)
location: region:3390-3590:-1
so has part: feature:3390-3590:-1:exon
subclass of: SO_0000010

69512522
type: Gene
SIO_000068: ncbigene

position:3390:-1
position: 3390
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3590:-1
position: 3590
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3390-3590:-1:exon

LUA64_RS15195
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 84112
locus tag: LUA64_RS15195
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: MAERIKVEYFEEPPVVLEVGGRRSWQAQTTDPFCNVWHEITEGSDHVTRWVKSSFDGRMVRESDEV
SIO_010081: LUA64_RS15195
subclass of: SO_0000673
so part of: LUA64_RS15195
location: complement(3390..3590)
location: region:3390-3590:-1
so has part: feature:3390-3590:-1:exon

WP_195528923.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3390-3590:-1:exon