3300008227: Methane-oxidizing microbial communities from mesocosms in the Gulf of Mexico - GOM15C Gulf of Mexico

Overview

Basic Information

• IMG/M Taxon OID: 3300008227
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0118071 | Gp0127833 | Ga0105358
• Sample Name: Methane-oxidizing microbial communities from mesocosms in the Gulf of Mexico - GOM15C Gulf of Mexico
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: Y
• Use Policy: Open

Dataset Contents

• Total Genome Size: 845437039
• Sequencing Scaffolds: 13
• Novel Protein Genes: 14
• Associated Families: 14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Candidatus Nitrosopumilus koreensis	1
Not Available	6
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas aeruginosa group → Pseudomonas aeruginosa	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Marine Group I → Marine Group I thaumarchaeote	2
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales	1
All Organisms → cellular organisms → Archaea	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Methane-Oxidizing Microbial Communities From Mesocosms In The Gulf Of Mexico And Hudson Canyon, Usa
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Marine → Unclassified → Unclassified → Methane Seep Mesocosm → Methane-Oxidizing Microbial Communities From Mesocosms In The Gulf Of Mexico And Hudson Canyon, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): marine cold seep biome → mesocosm → sediment
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: Gulf of Mexico
• Coordinates
  • Lat. (^o): 27.37
  • Long. (^o): -90.57
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000245	Metagenome / Metatranscriptome	1468	Y
F008561	Metagenome / Metatranscriptome	331	Y
F010197	Metagenome	307	Y
F012354	Metagenome	281	Y
F013095	Metagenome	274	Y
F021319	Metagenome	219	N
F034217	Metagenome	175	N
F035075	Metagenome / Metatranscriptome	173	Y
F043988	Metagenome	155	Y
F059074	Metagenome	134	N
F063198	Metagenome / Metatranscriptome	130	N
F063768	Metagenome / Metatranscriptome	129	N
F075076	Metagenome	119	Y
F101886	Metagenome / Metatranscriptome	102	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0105358_10084391	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1458
Ga0105358_10146769	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Candidatus Nitrosopumilus koreensis	1032
Ga0105358_10216825	Not Available	809
Ga0105358_10265499	Not Available	713
Ga0105358_10303617	Not Available	657
Ga0105358_10309116	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas aeruginosa group → Pseudomonas aeruginosa	650
Ga0105358_10316320	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Marine Group I → Marine Group I thaumarchaeote	641
Ga0105358_10349712	Not Available	603
Ga0105358_10369730	Not Available	584
Ga0105358_10398182	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Marine Group I → Marine Group I thaumarchaeote	558
Ga0105358_10403154	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales	554
Ga0105358_10416451	All Organisms → cellular organisms → Archaea	544
Ga0105358_10425831	Not Available	537

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0105358_10084391	Ga0105358_100843912	F063768	MGDGRVSDPVTTAEGAGEFIVLAELSMALSGRLAGWSTDGADPYTSATMASLAARLGEHAGWWMDRTPESVLLEGERAAASGAGRLTDILALLDVPPSDRRSAVAPVLDRLVAYLGVLSERLSPVGDAPALRTIRLVLADLEDRPR*
Ga0105358_10146769	Ga0105358_101467692	F034217	MYTIPVITITTAVMADHAPNATKSNSAMFYLLNGNKINTLEMVELHA*
Ga0105358_10216825	Ga0105358_102168252	F059074	MEIDLSLNRSLEELISSYFEAYEAGFGCDSFLDVNVDSTTADVSDYYVLENYLSDYGAI*
Ga0105358_10265499	Ga0105358_102654991	F075076	MATASRGKGFVKPMEWWDHLKWCKRPQNKRVRQDGKKQIKEEIKN*
Ga0105358_10303617	Ga0105358_103036171	F010197	LFLLPNTTHELKAFTIKHDFAQHKKKILSRQDGIFF
Ga0105358_10309116	Ga0105358_103091161	F101886	MNMFINLFVIGFCLFNVALFVWFGIEVATVTPEQAIAEGMTQRIYASISHLDYVMATLWGGILVTILLAKRELFLCVMWLYVGIYLCDIHFGYYMSVEEGSP
Ga0105358_10316320	Ga0105358_103163202	F013095	MPIKLPINSTVSLTSPTSGAQKIAIKKPVTIIGTPIPMVICFDAMLSVAPKIVYEVYDEM
Ga0105358_10349712	Ga0105358_103497121	F008561	MKFDELIEHYENAIGYESTVKGVPMSEENLELCRKFVTDVHDCPRKDVRVMFRGPRTSTANATMKKDARSFDVY
Ga0105358_10358256	Ga0105358_103582562	F000245	MKTFKQFDETKLDDKLDKLVSDEIKKRKLAKFPVNATDDIKMRMKPNKPAFKFPSPTGEMMIHVFLRPMKGKKGMMAFNYQLEDK*
Ga0105358_10369730	Ga0105358_103697302	F063198	VEITKLYIVRMRLEENSLISEDRLILNAPSKIRINRVKVVNIGATEARSSGDVYPNPLGPIRNPSIIRNNTSGILVRRNNASDKKPKIAIKLNASNAVLTFIALR*
Ga0105358_10398182	Ga0105358_103981822	F012354	MSSRMYPSARIPKPIPIAKKAIVNLNNVGLPVFLKPIYEMHPIVIPIANPTKFRMLSCKNSNYAN*
Ga0105358_10403154	Ga0105358_104031541	F021319	SMECIINPEKDANIKMNCEVGAARFIEIPSATTINGTKIKPPPIPNRLDIIPAKKLAPAEKTSNKRETSIGFSSIFLLRNMYDAEEIRTSANKILKMSGDISEDTNAPSMVPGTAIKPSFQPSESSIRFCLAYIAVEATELLNTANRLLLTASVGENPMNVNTGTIIIPPPKPIIDPNIPATNP
Ga0105358_10416451	Ga0105358_104164511	F043988	GFKAPFGLITLFNLSDMPGVCGFVHLLDSEAMEHGLEINY*
Ga0105358_10425831	Ga0105358_104258312	F035075	LVIKKLICGYDNAISIKYVNKKNQRKSWDTQKNIEVAEKWAQKNEELE