Studies
|
56,336 |
|
Biosamples
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196,965 |
|
Sequencing Projects
|
525,338 |
|
Analysis Projects
|
385,100 |
| Organisms | 484,220 |
| PROJECT INFORMATION | |
|---|---|
|
GOLD Project ID
|
Gp0013281
|
|
Project Name
|
Simiduia agarivorans DSM 21679
|
|
Other Names
|
|
|
Legacy ER Project ID
|
21051
|
|
Legacy GOLD ID
|
Gi11903
|
| NCBI BioProject Name | Simiduia agarivorans SA1 = DSM 21679 |
|
NCBI BioProject Accession
|
PRJNA185368 |
|
NCBI Locus Tag
|
G409
|
|
NCBI BioSample Accession
|
SAMN02440904 |
|
Source Sample ID
|
|
| PI | Nikos Kyrpides |
| Added By | JGI automated process on 2012-01-11 |
| Last Modified By | JGI automated process on 2022-09-05 |
| Project Comments |
|
|
Project Status
|
Permanent Draft
|
|
Project Relevance
|
Tree of Life GEBA-KMG |
|
Sequencing Center
|
DOE Joint Genome Institute (JGI)
(USA)
|
|
Collaborating Institute
|
Leibniz Institute
(Germany)
|
|
Funding Agency
|
U.S. Department of Energy (DOE)
(USA)
Leibniz Institute (Germany) |
|
Project Description
|
Genomic Encyclopedia of Type Strains, Phase I: one thousand microbial genomes (KMG) project. The goal of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative is to sequence genomes to fill phylogenetic gaps, generating reference genomes for every major and minor group of bacteria and archaea. Currently sequenced genomes have provided highly uneven coverage of the type strain material present in public culture collections. The Microbial Earth Project is an initiative of the Microbial Genomics Program of the DOE Joint Genome Institute that focuses on 1000 Type strains from the DSMZ and ATCC repositories.
|
| Is JGI Project |
Yes
|
|
Project Information Visibility
|
Public |
| PROJECT TYPE | |
|
Specimen
|
Organism |
|
Nucleic Acid
|
DNA |
|
Sequencing Strategy
|
Whole Genome Sequencing
|
| EXTERNAL PROJECT LINKS | |
|
JGI Data Utilization Status
|
Unrestricted
|
|
JGI Award DOI
|
10.46936/10.25585/60000886 |
| JGI Portal Download | Raw Sequence Data |
|
Genome Publications
|
Nature biotechnology: 35(7):676-683 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. PubMed: 28604660 DOI: 10.1038/nbt.3886 |
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Other Publications
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|
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Ignored Publications
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|
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Unassigned Publications
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| SRA Experiment |
|
| PROJECT COMPOSITION | |
| Study |
Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project |
| Organism |
Simiduia agarivorans SA1 |
| Analysis Projects |
Simiduia agarivorans DSM 21679 |
| Number of Analysis Projects (AP) |
1 |
| Number of Derived Analyis Projects (DAP) |
0
|
| SEQUENCING INFORMATION | |
|---|---|
|
Sequencing Status
|
Complete |
| Sequencing Quality (MIGS-31) |
Level 1: Standard Draft |
|
Finishing Goal
|
Level 1: Standard Draft |
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Contamination Screening Input
|
|
|
DNA Amplification Method
|
|
|
Single Cell Lysis Protocol
|
|
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Single Cell Lysis Approach
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|
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Sequencing Comments
|
|
|
DNA Amplification Kit
|
|
|
Sequencing Technology
(MIGS-29)
|
Illumina HiSeq 2500 |
|
Library Method
(MIGS-28)
|
|
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Library Layout
|
|
|
Library Screening Method
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|
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Number Of Reads
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|
|
Read Size
|
|
|
Vector
|
|
| GC Percent |
56
|
| Chromosome Count |
|
| Plasmid Count |
|
| ORGANISM NAME | |
|---|---|
| GOLD Organism ID |
Go0013281 |
| Organism Name |
Simiduia agarivorans SA1
|
| Other names (alias, synonyms, short names, common names) |
|
| Organism Domain |
BACTERIAL
|
| Phylogeny |
PROTEOBACTERIA-GAMMA
|
| Genus |
Simiduia
|
| Genus Synonyms |
|
| Species |
Simiduia agarivorans
|
| Subspecies |
|
| Species Synonyms |
|
| Strain |
SA1
|
| Strain Synonyms |
|
| Serovar/Cultivar |
|
| Culture Collection ID |
DSM 21679
|
| Type Strain |
Yes
|
| Exemplar DOI |
10.1601/ex.13777
|
| Exemplar Name |
Simiduia agarivorans
|
| Taxon DOI |
10.1601/tx.13777
|
| Biosafety Level |
|
| Organism Comments |
|
| Cultured |
Yes
|
| Culture Type |
Isolate
|
| Organism Type |
Natural
|
| Uncultured Type |
|
| Commercial Strain |
|
| Commercial Strain Comments |
|
|
ORGANISM TAXONOMY
|
|
| NCBI Taxonomy ID |
1117647 |
| NCBI Superkingdom |
Bacteria
|
| NCBI Kingdom |
|
| NCBI Phylum |
Pseudomonadota
|
| NCBI Class |
Gammaproteobacteria
|
| NCBI Order |
Cellvibrionales
|
| NCBI Family |
Cellvibrionaceae
|
| NCBI Genus |
Simiduia
|
| NCBI Species |
Simiduia agarivorans
|
| ISOLATION CLASSIFICATION | |
| Ecosystem |
Environmental
|
| Ecosystem Category |
Aquatic
|
| Ecosystem Type |
Marine
|
| Ecosystem Subtype |
Coastal
|
| Specific Ecosystem |
Unclassified
|
| ORGANISM EXTERNAL REFERENCES | |
| Strain Info ID |
802432 |
| Genbank 16S ID |
EF617350 |
| GENERAL PROPERTIES | |
|---|---|
| Oxygen Requirement |
Facultative
|
| Cell Shape |
Rod-shaped
|
| Motility |
|
| Sporulation |
|
| Temperature Range |
Mesophile
|
| Salinity |
Halophile
|
| pH |
7
|
| Cell Diameter |
0.4-0.6 um
|
| Cell Length |
2.0-5.0 um
|
| Color |
|
| Gram Staining |
Gram-
|
| Biotic Relationships |
|
| Symbiotic Physical Interaction |
|
| Symbiotic Relationship |
|
| Symbiont Name |
|
| Symbiont Taxon ID |
|
| Cell Arrangements |
|
| Diseases |
|
| Known Habitats |
Marine Aquatic Sea water |
| Metabolisms |
Nitrate reducer |
| Phenotypes |
Vancomycin resistant Non-Haemolytic Catalase positive Streptomycin resistant |
| Energy Sources |
Heterotroph |
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