PROJECT INFORMATION
GOLD Project ID
Gp0005629  
Project Name
Porphyromonas sp. 31_2  
Other Names
  
Legacy ER Project ID
15062  
Legacy GOLD ID
Gi04556  
NCBI BioProject Name Porphyromonas sp. 31_2
NCBI BioProject ID 39411
NCBI BioProject Accession PRJNA39411
NCBI Locus Tag
HMPREF1002  
NCBI BioSample Accession SAMN00103275
PI Birren, B
Added By Nikos Kyrpides on 2009-07-26
Last Modified By JGI automated process on 2014-08-18
Project Comments
  
Project Status
Permanent Draft  
Project Relevance Human Microbiome Project (HMP)
Medical
Sequencing Center Broad Institute (USA)
Collaborating Institute
  
Funding Agency NIH (USA)
Project Description
Reference genome for the Human Microbiome Project  
Is JGI Project
  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
Project Information
  
Database
  
Genome Publications
  
Other Publications
  
SRA Experiment
 
SRA Experiment Id SRX008307
Experiment Title Genome sequencing of Porphyromonas sp. 31_2 on 454 for the HMP Pilot project.
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name 454-3226
Library Layout SINGLE
Library Instrument 454 GS FLX Titanium
 
SRA Experiment Id SRX011578
Experiment Title Genome sequencing of Porphyromonas sp. 31_2 on 454 for the HMP Pilot project.
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name 454-3314
Library Layout PAIRED
Library Instrument 454 GS FLX Titanium
 
SRA Experiment Id SRX011342
Experiment Title Genome sequencing of Porphyromonas sp. 31_2 on 454 for the HMP Pilot project.
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name 454-3226
Library Layout SINGLE
Library Instrument 454 GS FLX Titanium
 
SRA Experiment Id SRX008445
Experiment Title Genome sequencing of Porphyromonas sp. 31_2 on 454 for the HMP Pilot project.
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name 454-3252
Library Layout SINGLE
Library Instrument 454 GS FLX Titanium
PROJECT COMPOSITION
Study Human Microbiome Project (HMP) Reference Genomes
Organism Porphyromonas sp. 31_2
Analysis Projects Porphyromonas sp. 31_2
Porphyromonas sp. 31_2
Number of Analysis Projects 2
Number of DAPs
0  
SEQUENCING INFORMATION
Sequencing Status Complete
Sequencing Quality (MIGS-31) Level 2: High-Quality Draft
Finishing Goal Level 2: High-Quality Draft
Sequencing Comments
  
Sequencing Technology (MIGS-29)
  
Library Method (MIGS-28)
  
Number Of Reads
  
Read Size
  
Vector
  
GC Percent
45  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0005629
Organism Name
Porphyromonas sp. 31_2  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
BACTERIAL  
Phylogeny
BACTEROIDETES  
Genus
Porphyromonas  
Genus Synonyms
  
Species
Porphyromonas sp. 31_2  
Subspecies
  
Species Synonyms
  
Strain
31_2  
Strain Synonyms
  
Serovar/Cultivar
  
Culture Collection ID
BEI HM-169  
Type Strain
Unknown  
Exemplar DOI
  
Exemplar Name
  
Taxon DOI
  
Biosafety Level
  
Organism Comments
  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 658663
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Bacteroidetes  
NCBI Class
Bacteroidia  
NCBI Order
Bacteroidales  
NCBI Family
Porphyromonadaceae  
NCBI Genus
Porphyromonas  
NCBI Species
Porphyromonas sp. 31_2  
ISOLATION CLASSIFICATION
Ecosystem
Host-associated  
Ecosystem Category
Human  
Ecosystem Type
Digestive system  
Ecosystem Subtype
Large intestine  
Specific Ecosystem
Fecal  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID
GENERAL PROPERTIES
Oxygen Requirement
  
Cell Shape
Rod-shaped  
Motility
  
Sporulation
  
Temperature Range
Mesophile  
Temperature Optimum
  
Salinity
  
pH
  
Cell Diameter
  
Cell Length
  
Color
  
Gram Staining
Gram-  
Biotic Relationships Free living
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements
  
Diseases
  
Known Habitats Host
Human fecal
Metabolisms
  
Phenotypes
  
Energy Sources
  
HMP METADATA
HMP ID
1002  
Show in DACC?
Yes  
HMP Project Status
Complete  
BEI Status
  
NCBI Submission Status
5. annotation (and sequence) submitted to NCBI  
Isolate Suggestion Source
  
HMP Isolation Body Sample Site
Gastrointestinal tract  
HMP Isolation Body Sample Subsite
Rectal  
HMP Finishing Goal
  
Source, Sample & Medical Relevance Comments
  
Isolate Availability Comments
  
Project Comments
  
DNA Received
Yes  
Date DNA Received
2009-07-13  
Date Sequencing Begins
2009-08-22  
Date Draft Sequencing Completed
2009-12-29  
Cross Reference ID
  

 

 

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