Candidatus Nitrosoglobus terrae strain TAO100 plasmid pTAO100.
type: Entry
definition: Candidatus Nitrosoglobus terrae strain TAO100 plasmid pTAO100.
sequence version: NZ_AP014837.1
sequence date: 2022-12-25
sequence: sequence
division: CON
label: NZ_AP014837.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMD00027389
keyword: RefSeq
source: Candidatus Nitrosoglobus terrae
organism: Candidatus Nitrosoglobus terrae
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales; Chromatiaceae; Candidatus Nitrosoglobus.
reference: 1
references: 28072419
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nAP014837.1.\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 Method :: Hierarchical Genome Assembly Process v. 3\nGenome Coverage :: 60x\nSequencing Technology :: PacBio RS II; Illumina MiSeq; ABI 3730\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/25/2022 01:51:25\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) :: 1,931\nCDSs (total) :: 1,877\nGenes (coding) :: 1,859\nCDSs (with protein) :: 1,859\nGenes (RNA) :: 54\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 44\nncRNAs :: 4\nPseudo Genes (total) :: 18\nCDSs (without protein) :: 18\nPseudo Genes (ambiguous residues) :: 0 of 18\nPseudo Genes (frameshifted) :: 4 of 18\nPseudo Genes (incomplete) :: 15 of 18\nPseudo Genes (internal stop) :: 4 of 18\nPseudo Genes (multiple problems) :: 4 of 18\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##

sequence
subclass of: SO_0000155
sequence length: 6436
topology: linear
so has quality: SO_0000987
location: 1..6436
location: region:1-6436:1
RO_0002162: 1630141

NZ_AP014837
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMD00027389
type: BioSample
SIO_000068: biosample

1
title: An acid-tolerant ammonia-oxidizing gamma-proteobacterium from soil
author: Hayatsu, M.
author: Tago, K.
author: Uchiyama, I.
author: Toyoda, A.
author: Wang, Y.
author: Shimomura, Y.
author: Okubo, T.
author: Kurisu, F.
author: Hirono, Y.
author: Nonaka, K.
author: Akiyama, H.
author: Itoh, T.
author: Takami, H.
journal: ISME J
volume: 11
issue: 5
pages: 1130-1141
year: 2017
pubmed: 28072419
comments: DOI:10.1038/ismej.2016.191

28072419
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Hayatsu, M.
author: Okubo, T.
journal: Submitted (06-APR-2015) Contact:Masahito Hayatsu National Institute for Agro-Environmental Sciences, Environmental Biofunction Division; Kannondai 3-1-3, Tsukuba, Ibaraki 305-8604, Japan

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

position:6436:1
position: 6436
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6436:1:source
so part of: sequence
organism: Candidatus Nitrosoglobus terrae
mol type: genomic DNA
strain: TAO100
isolation source: soil
plasmid: pTAO100
country: Japan:Shizuoka
lat lon: 34.81 N 138.13 E
collection date: 2012

1630141
type: Taxonomy
SIO_000068: taxonomy

TAO_RS09485
type: Gene
subclass of: SO_0000704
RO_0002162: 1630141
gene: repM
locus tag: TAO_RS09485
old locus tag: TAO_p0001
so part of: sequence
location: complement(756..1568)
location: region:756-1568:-1
so has part: feature:756-1568:-1:exon
subclass of: SO_0000010

position:756:-1
position: 756
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1568:-1
position: 1568
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:756-1568:-1:exon

TAO_RS09485
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1630141
gene: repM
locus tag: TAO_RS09485
old locus tag: TAO_p0001
inference: COORDINATES: protein motif:HMM:NF038290.1
GO function: GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO process: GO:0006270 - DNA replication initiation [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein RepM
translation: MKEKQLVVKDNTLINAAYTLDLVEQRLILLAIVSARKAQQGIDASHTITIRGEDYAKSFNVSRQAAYIALNEAAKSLFKRQFSYEKLTPKGNIEKVTSRWVSDISYINKEGAVMITFTRCVIPLITKLEKHFTSYELQEVAHLRSIYAIRLYELLMAWRSTGKTPKYKLQDFRKKLGLLDDEYERADNFKTRVLDTATTQINQHTDINISWEQYKEGRRVAGFQFTITSKKEPLKKGRKQITKKEAERLAKTGETYTELYGRLAQEYIIG
SIO_010081: TAO_RS09485
subclass of: SO_0000673
so part of: TAO_RS09485
location: complement(756..1568)
location: region:756-1568:-1
so has part: feature:756-1568:-1:exon

WP_096527824.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:756-1568:-1:exon

TAO_RS09490
type: Gene
subclass of: SO_0000704
RO_0002162: 1630141
locus tag: TAO_RS09490
old locus tag: TAO_p0002
so part of: sequence
location: 2203..2643
location: region:2203-2643:1
so has part: feature:2203-2643:1:exon
subclass of: SO_0000010

position:2203:1
position: 2203
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2643:1
position: 2643
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2203-2643:1:exon

TAO_RS09490
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1630141
locus tag: TAO_RS09490
old locus tag: TAO_p0002
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005372028.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF29 domain-containing protein
translation: MSTYETDFYGWTQETAALLKQGRFSEVDMEALIEEVEDMGKSEHRELRNRIAVLLTHLLKWQYQPEQRGNSWQATIEEQRLRVTLLVKENPSLKPRFVESTLEAYPIAVLRAVQETNLAKKTFPMSFELTGWSMEQVLDDGFYPPA
SIO_010081: TAO_RS09490
subclass of: SO_0000673
so part of: TAO_RS09490
location: 2203..2643
location: region:2203-2643:1
so has part: feature:2203-2643:1:exon

WP_096527825.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2203-2643:1:exon

TAO_RS09495
type: Gene
subclass of: SO_0000704
RO_0002162: 1630141
locus tag: TAO_RS09495
old locus tag: TAO_p0003
so part of: sequence
location: complement(2804..4780)
location: region:2804-4780:-1
so has part: feature:2804-4780:-1:exon
subclass of: SO_0000010

position:2804:-1
position: 2804
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4780:-1
position: 4780
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2804-4780:-1:exon

TAO_RS09495
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1630141
locus tag: TAO_RS09495
old locus tag: TAO_p0003
inference: COORDINATES: protein motif:HMM:NF017826.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF927 domain-containing protein
translation: MNDLNQKEKPLNTKSFNNTQEQPTEEIIARAMPSSNTELQGNYELDQLLSKAGNTDNVVPFSNSTQSEAQTDKYRNRWPAEGERPCYTMIDDRDFVKAHKVRLGLYHCTMTKGTKEKDPEPVDRWICSPFEILAITYDDSRNNHGRLMEFMDVESKKRKWAMPMEVLAGDRELQRILLSMGMMMDNPRDSKDICKYINTQHPKARALAVSATGWAADGSNNFVFPDKVIGDNPSSVILQTLDAPRSDFKTLGSFKQWQQQIAAKAIDNPLLVFAISLAFVGPLLKKLHLKAAGFHLVGNSSTGKTTALCVACSVWGSEEFSRTWNSTANGLEKTAADFSDTFLALDEMGECDPRSIGNVIYFLGNGVGKQRMTKMMTTRPQLRWQIGVLSTGERTIADFINEGGKQAKAGQEMRMIDIPVVGTYGIFDELHGSKDGAAFSDQLKQVSSQHYGHAGVAFIEQLIEHTQPDGLAGDLDLMGLYNDCKLSKCFQTEGDDGQPKRVAAHFALVAFAGDLATKFGITGWEEGAAIEAAAFLFQRWRADKGKGNKEGKDVIEALADFIDRHENSRFLSVANTEPQLLVRDLAGYTRIAPEGHNKQFLFVPSGLREALKGLDFKRALDALIEKGILPPARADGKTSRLERINGKMTRVYIRYYRK
SIO_010081: TAO_RS09495
subclass of: SO_0000673
so part of: TAO_RS09495
location: complement(2804..4780)
location: region:2804-4780:-1
so has part: feature:2804-4780:-1:exon

WP_096527826.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2804-4780:-1:exon

TAO_RS09500
type: Gene
subclass of: SO_0000704
RO_0002162: 1630141
locus tag: TAO_RS09500
old locus tag: TAO_p0004
so part of: sequence
location: complement(4777..5748)
location: region:4777-5748:-1
so has part: feature:4777-5748:-1:exon
subclass of: SO_0000010

position:4777:-1
position: 4777
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5748:-1
position: 5748
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4777-5748:-1:exon

TAO_RS09500
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1630141
locus tag: TAO_RS09500
old locus tag: TAO_p0004
inference: COORDINATES: protein motif:HMM:NF024755.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: toprim domain-containing protein
translation: MTLHRWEGNSLDANQAFIQAIEQVGLTPPRKIIADGKIHRFSANGKASNHSGWYVLHDNIHSYVGKFGDWGTGLKVDWHDKAKPLTHQQVKEAQQIQHRNRPQQEAEKARLRALAGVRIKSNWFDAVPANEDHPYLVKKGIKPHNAKQLGEKLIIPVWKSKKLISLQYINEQGVKYFHKGSSYQGGFGIIGNLICPTSNRICIVEGFATAASIHEATGCPVVIAFSAGNLMTVSKRVSDWADSLIGNKWRAVICGDDDRGNEINVGREIALAAGKELGLTVVFPFFSNPNSTGSDFNDLHVSEGIEAVKACIHSQLNNGGYQS
SIO_010081: TAO_RS09500
subclass of: SO_0000673
so part of: TAO_RS09500
location: complement(4777..5748)
location: region:4777-5748:-1
so has part: feature:4777-5748:-1:exon

WP_096527827.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4777-5748:-1:exon

TAO_RS09580
type: Gene
subclass of: SO_0000704
RO_0002162: 1630141
locus tag: TAO_RS09580
old locus tag: TAO_p0005
so part of: sequence
location: complement(5720..5917)
location: region:5720-5917:-1
so has part: feature:5720-5917:-1:exon
subclass of: SO_0000010

position:5720:-1
position: 5720
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5917:-1
position: 5917
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5720-5917:-1:exon

TAO_RS09580
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1630141
locus tag: TAO_RS09580
old locus tag: TAO_p0005
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: MKSQLIGVTQLSRLTGIPRTTIYFWLDQNRSQIPSPVPNSKPMKWLYSDVVSFFKLDDTTQMGGQ
SIO_010081: TAO_RS09580
subclass of: SO_0000673
so part of: TAO_RS09580
location: complement(5720..5917)
location: region:5720-5917:-1
so has part: feature:5720-5917:-1:exon

WP_145955163.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5720-5917:-1:exon