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Organism name:
Pyrococcus horikoshii OT3 (euryarchaeotes)
Taxonomy check:
Infraspecific name:
Strain: OT3
Assembly type:
Assembly level:
Complete Genome
Genome representation:
RefSeq category:
representative genome
Relation to type material:
assembly from type material
GenBank assembly accession:
GCA_000011105.1 (latest)
RefSeq assembly accession:
GCF_000011105.1 (latest)
RefSeq assembly and GenBank assembly identical:

IDs: 32268 [UID] 11908 [GenBank] 32268 [RefSeq]

See Genome Information for Pyrococcus horikoshii

There are 2 assemblies for this organism

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History (Show revision history)


Kawarabayasi, Y. is officially affiliated with the National Institute of Bioscience and Human-Technology, Tsukuba, Ibaraki 305-0046, Japan.
Robb, T. F. is at the Center of Marine Biotechnology, University of Maryland, Baltimore, MD, USA.
Horikoshi, K. is at the Japan Marine Science ... and Technology Center, Yokosuka, Kanagawa 237-0061, Japan.
Masuchi, Y. is at the University of Tokyo, Meguro, Tokyo 153-0041, Japan.
Shizuya, H. is at the California Institute of Technology, Pasadena, CA, USA.
The other authors are at the National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya, Tokyo 151-0066, Japan. All the sequence with length 100 codons or more between ATG or GTG and stop codon are defined as CDS
Homology analysis is performed by Smith-Waterman algorithm against GenBank and GenPept release 103; EMBL release 52.0; SwissProt release 34.0; PIR-Protein release 54.0; and OWL release 29.5. E-mail address for comments and questions: genomeOT3@nite.go.jp Restriction map, ORF organization, sequence alignment and more information are available at W.W.W. site of Biotechnology Center, URL: http://www.bio.nite.go.jp/
The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/  more


Annotation Provider::NCBI RefSeq
Annotation Date::02/11/2024 00:43:07
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::6.6
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA
Genes (total)::1,940
CDSs (total)::1,870
Genes (coding)::1,853
CDSs (with protein)::1,853
Genes (RNA)::70
rRNAs::2, 1, 1 (5S, 16S, 23S)
complete rRNAs::2, 1, 1 (5S, 16S, 23S)
Pseudo Genes (total)::17
CDSs (without protein)::17
Pseudo Genes (ambiguous residues)::0 of 17
Pseudo Genes (frameshifted)::11 of 17
Pseudo Genes (incomplete)::5 of 17
Pseudo Genes (internal stop)::4 of 17
Pseudo Genes (multiple problems)::2 of 17
CRISPR Arrays::6

Global statistics

Total sequence length1,738,505
Total ungapped length1,738,505
Total number of chromosomes and plasmids1

Supplemental Content

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
Assembly Unit: Primary Assembly (GCF_000011115.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome BA000001.2=NC_000961.1

Assembly statistics

Chromosome 1,738,505

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Pyrococcus horikoshii OT3Pyrococcus horikoshii

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000007305.1Pyrococcus furiosustype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type81.5611.4110.40

ANI result

Taxonomy check statusBest match statusComment
OKbelow-threshold-mismatchAssembly is the type-strain, mismatch is within genus and expected