Candidatus Endomicrobium trichonymphae plasmid pTGRD3, complete sequence.
type: Entry
definition: Candidatus Endomicrobium trichonymphae plasmid pTGRD3, complete sequence.
sequence version: NC_020422.1
sequence date: 2022-12-30
sequence: sequence
division: CON
label: NC_020422.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMD00232923
keyword: RefSeq
source: Candidatus Endomicrobium trichonymphae
organism: Candidatus Endomicrobium trichonymphae
taxonomy: Bacteria; Elusimicrobiota; Endomicrobiia; Endomicrobiales; Endomicrobiaceae; Endomicrobium.
reference: 1
references: 18391199
reference: 2
reference: 3
comment: REFSEQ INFORMATION: The reference sequence is identical to\nAP009513.1.\n\nOn Feb 28, 2013 this sequence version replaced NS_000194.1.\nThe wood-feeding termite Reticulitermes speratus (Isoptera;\nRhinotermitidae) was collected in Saitama, Japan. The entire gut\nwas removed from a worker termite, and a single cell of the\ncellulolytic protist Trichonympha agilis (Parabasalia;\nTrichonymphida) in the gut was physically isolated by using a\nmicromanipulator. In order to collect the intracellular symbionts\nof T. agilis, as-yet-uncultivated bacteria designated phylotype\nRs-D17 belonging to the candidate division Termite Group 1, the\nhost T. agilis cell was ruptured in buffer and bacterial cells\nwhich leaked out were collected with a glass capillary. These\ncollected cells were directly subjected to isothermal whole genome\namplification. After checking their purity by clone analysis of 16S\nrRNA gene and its adjacent ITS, the complete genome sequence was\ndetermined using ABI 3730 capillary sequencers and a GS20 system.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/30/2022 00:47:37\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) :: 1,200\nCDSs (total) :: 1,150\nGenes (coding) :: 1,141\nCDSs (with protein) :: 1,141\nGenes (RNA) :: 50\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 2\nPseudo Genes (total) :: 9\nCDSs (without protein) :: 9\nPseudo Genes (ambiguous residues) :: 0 of 9\nPseudo Genes (frameshifted) :: 2 of 9\nPseudo Genes (incomplete) :: 4 of 9\nPseudo Genes (internal stop) :: …

sequence
subclass of: SO_0000155
sequence length: 5362
topology: circular
so has quality: SO_0000988
location: 1..5362
location: region:1-5362:1
RO_0002162: 1408204

NC_020422
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMD00232923
type: BioSample
SIO_000068: biosample

1
title: Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell
author: Hongoh, Y.
author: Sharma, V.K.
author: Prakash, T.
author: Noda, S.
author: Taylor, T.D.
author: Kudo, T.
author: Sakaki, Y.
author: Toyoda, A.
author: Hattori, M.
author: Ohkuma, M.
journal: Proc Natl Acad Sci U S A
volume: 105
issue: 14
pages: 5555-5560
year: 2008
pubmed: 18391199

18391199
type: PubMed
SIO_000068: pubmed

2
title: Revised annotation of the genome of 'Ca. Endomicrobium trichonymphae' phylotype Rs-D17
author: Hongoh, Y.
author: Yoshioka, T.
author: Izawa, K.
journal: Unpublished

3
title: Direct Submission
author: Toyoda, A.
author: Hongoh, Y.
author: Sharma, V.K.
author: Hattori, M.
author: Ohkuma, M.
author: Sakaki, Y.
author: Izawa, K.
author: Yoshioka, T.
journal: Submitted (01-OCT-2007) Contact:Yuichi Hongoh Tokyo Institute of Technology, Department of Life Science and Technology; 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan

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

position:5362:1
position: 5362
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5362:1:source
so part of: sequence
organism: Candidatus Endomicrobium trichonymphae
mol type: genomic DNA
strain: Rs-D17 genomovar Ri2008
isolation source: a single cell of termite (Reticulitermes speratus) gut protist
host: Trichonympha agilis
plasmid: pTGRD3

1408204
type: Taxonomy
SIO_000068: taxonomy

H0I88_RS05845
type: Gene
subclass of: SO_0000704
RO_0002162: 1408204
locus tag: H0I88_RS05845
old locus tag: TGRD_P3-1
so part of: sequence
location: 1..1275
location: region:1-1275:1
so has part: feature:1-1275:1:exon
subclass of: SO_0000010

position:1275:1
position: 1275
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-1275:1:exon

H0I88_RS05845
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1408204
locus tag: H0I88_RS05845
old locus tag: TGRD_P3-1
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: MWNEIKTELTEKIPTIWLEPVKEESFKDDILMLNVPNRYYAEKYKTDFKELIQSVIKTKIGKDIGLQCQIELLPEPITKDKKPKTTSKTPLIKETKFNGKPYFESPAELTEISKEISQAKEIDVDNTKLTSMPVKYSIKDVVSFSLLNSKMFTYPNDKRKKTKVEINIRFNNGTIKPLDLYRGQLDFNDEGYGQLTTTHAKIFLAITHIWQKQGCKFANNSYLAVVDISIRELAKQLGYQKFSGADYKRLLRKTKELADFPMILADMYEAHTFTLLYDVSNHKLKKSRNNKNMLRILINPFIAKQLYERKVILRNPQCYKIKNPTAIKFLICYDKRIIKGNNLRLNIFEIANDLEVNINNITSVAENLKNAFQELNGYELNDSYSLHVELIKENKEWIVVADRVLKEKQQSLKVNCRTDIECEA
SIO_010081: H0I88_RS05845
subclass of: SO_0000673
so part of: H0I88_RS05845
location: 1..1275
location: region:1-1275:1
so has part: feature:1-1275:1:exon

WP_015423777.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-1275:1:exon

H0I88_RS05850
type: Gene
subclass of: SO_0000704
RO_0002162: 1408204
locus tag: H0I88_RS05850
old locus tag: TGRD_P3-2
old locus tag: TGRD_RS05640
so part of: sequence
location: 1470..1769
location: region:1470-1769:1
so has part: feature:1470-1769:1:exon
subclass of: SO_0000010

position:1470:1
position: 1470
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1769:1
position: 1769
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1470-1769:1:exon

H0I88_RS05850
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1408204
locus tag: H0I88_RS05850
old locus tag: TGRD_P3-2
old locus tag: TGRD_RS05640
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: MLSLKDNKKSFFSLMCLFFLVVCGCHSAKEFRDGYITGLADGYALSVNEFKYNAELAKIKDEFDWSKVDFKSEMKMYLDENKDIEKKVYDDYVKNGRKV
SIO_010081: H0I88_RS05850
subclass of: SO_0000673
so part of: H0I88_RS05850
location: 1470..1769
location: region:1470-1769:1
so has part: feature:1470-1769:1:exon

WP_015423778.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1470-1769:1:exon

H0I88_RS05855
type: Gene
subclass of: SO_0000704
RO_0002162: 1408204
locus tag: H0I88_RS05855
old locus tag: TGRD_RS06180
so part of: sequence
location: 1917..2093
location: region:1917-2093:1
so has part: feature:1917-2093:1:exon
subclass of: SO_0000010

position:1917:1
position: 1917
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2093:1
position: 2093
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1917-2093:1:exon

H0I88_RS05855
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1408204
locus tag: H0I88_RS05855
old locus tag: TGRD_RS06180
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: MKSQLNITSKEKDKEPLKNCYKCDVKRVYTDNPYYAPVDYQLDLFDNNNILPVKSCVR
SIO_010081: H0I88_RS05855
subclass of: SO_0000673
so part of: H0I88_RS05855
location: 1917..2093
location: region:1917-2093:1
so has part: feature:1917-2093:1:exon

WP_158302870.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1917-2093:1:exon

H0I88_RS06335
type: Gene
subclass of: SO_0000704
RO_0002162: 1408204
locus tag: H0I88_RS06335
so part of: sequence
location: 3926..4210
location: region:3926-4210:1
so has part: feature:3926-4210:1:exon
subclass of: SO_0000010

position:3926:1
position: 3926
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4210:1
position: 4210
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3926-4210:1:exon

H0I88_RS06335
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1408204
locus tag: H0I88_RS06335
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: MKYRKEFDCCGNDMRHTADAPKLEKRLKKSLNVFDLVLLTAYLFGLLLLTSCSRVNTFGYKIYGRQELLDEVCRLKHIVMKLEGEGKVSSTIVL
SIO_010081: H0I88_RS06335
subclass of: SO_0000673
so part of: H0I88_RS06335
location: 3926..4210
location: region:3926-4210:1
so has part: feature:3926-4210:1:exon

WP_095558999.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3926-4210:1:exon

H0I88_RS06170
type: Gene
subclass of: SO_0000704
RO_0002162: 1408204
locus tag: H0I88_RS06170
old locus tag: TGRD_P3-3
so part of: sequence
location: 4355..4915
location: region:4355-4915:1
so has part: feature:4355-4915:1:exon
subclass of: SO_0000010

position:4355:1
position: 4355
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4915:1
position: 4915
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4355-4915:1:exon

H0I88_RS06170
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1408204
locus tag: H0I88_RS06170
old locus tag: TGRD_P3-3
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: MKFKKIFAVILMLSVFLSGCHRKVITGISKNENDVSTSTNTPASEPTPTPTPTSTPMPTPTPPLTPASPEPASQDKLKKIALFCPPLTQLMFIYGLGLVEGAIQASLPYLFSSPTIISTLSIMFANMPIVGAMWFALFAYRSEVSTLSNVLDWSLPALLVFGEFLYFCGVGAVSPFSHWLWSIDPV
SIO_010081: H0I88_RS06170
subclass of: SO_0000673
so part of: H0I88_RS06170
location: 4355..4915
location: region:4355-4915:1
so has part: feature:4355-4915:1:exon

WP_095559000.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4355-4915:1:exon