3300008226: Methane-oxidizing microbial communities from mesocosms in the Gulf of Mexico - GOM9C Gulf of Mexico

Overview

Basic Information

• IMG/M Taxon OID: 3300008226
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0118071 | Gp0127830 | Ga0105355
• Sample Name: Methane-oxidizing microbial communities from mesocosms in the Gulf of Mexico - GOM9C Gulf of Mexico
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 1058818894
• Sequencing Scaffolds: 17
• Novel Protein Genes: 18
• Associated Families: 14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Cellvibrionaceae → Pseudomaricurvus → Pseudomaricurvus alkylphenolicus	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas aeruginosa group → Pseudomonas aeruginosa	2
Not Available	8
All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium TMED264	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Pelagibacterales → unclassified Pelagibacterales → Pelagibacterales bacterium MED-G40	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Marine Group I → Marine Group I thaumarchaeote	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?
F003092	Metagenome / Metatranscriptome	508	Y
F005336	Metagenome / Metatranscriptome	404	Y
F005429	Metagenome / Metatranscriptome	401	Y
F005516	Metagenome	398	Y
F013570	Metagenome / Metatranscriptome	270	N
F018382	Metagenome	235	Y
F027865	Metagenome	193	Y
F031898	Metagenome	181	Y
F042560	Metagenome	158	Y
F052648	Metagenome / Metatranscriptome	142	Y
F061265	Metagenome / Metatranscriptome	132	Y
F066857	Metagenome / Metatranscriptome	126	N
F066858	Metagenome / Metatranscriptome	126	N
F101886	Metagenome / Metatranscriptome	102	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0105355_10008817	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	8219
Ga0105355_10030844	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Cellvibrionaceae → Pseudomaricurvus → Pseudomaricurvus alkylphenolicus	3854
Ga0105355_10058026	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas aeruginosa group → Pseudomonas aeruginosa	2566
Ga0105355_10068627	Not Available	2293
Ga0105355_10077170	Not Available	2118
Ga0105355_10170328	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas aeruginosa group → Pseudomonas aeruginosa	1220
Ga0105355_10180613	Not Available	1170
Ga0105355_10183560	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1156
Ga0105355_10352272	All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium TMED264	719
Ga0105355_10390637	Not Available	667
Ga0105355_10428000	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	624
Ga0105355_10470077	Not Available	584
Ga0105355_10483067	Not Available	573
Ga0105355_10483205	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Pelagibacterales → unclassified Pelagibacterales → Pelagibacterales bacterium MED-G40	572
Ga0105355_10513089	Not Available	549
Ga0105355_10563928	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Marine Group I → Marine Group I thaumarchaeote	513
Ga0105355_10567280	Not Available	510

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0105355_10008817	Ga0105355_100088177	F101886	MLKKILIIGFCLFNVAFFIQIGIEVAAVTPEQAMLEGMTQRIYASISTLDYIMAALWGAILYSILTAKKEHFLRASYLYLGFYLCDIHFSHYMSIEMNDPYFT
Ga0105355_10030844	Ga0105355_100308444	F101886	MRRVMLRNIFITGFCIANITLFILIGIEVAAVTPEQAMLEGMTQRIYASISTIDYIMATLWGVILFTTLTANKEWFLRSAWLYLGFYLCDIHFGHYMGIEMGEPLWIVAPLILAAIQSAFLYWSRKHIDKLTMPIPSQKWHETQGTSL*
Ga0105355_10058026	Ga0105355_100580261	F101886	MLKKIVIIGFCLFNVALFIQIGIEVAAVTPEQAMLEGMTQRIYASISTLDYIMAALWGAILYTILTAKKEHFLRASYLYLGFYLCDIHFSHYMSIEMNDPYFT
Ga0105355_10068627	Ga0105355_100686276	F066857	MCRLSCRRLDYLHDWQEKAKRVIDIFLITKGNVQFLDVFCIFQCQQNKGFSHFLDKDSKLTVYRDDVVRPSRKDNILLPVVFDEFSAMP*
Ga0105355_10077170	Ga0105355_100771702	F061265	LVCCGAIQKKEYFMSLDWDLIWKIFQVVALLIIAREIDKRIRKRKK*
Ga0105355_10105337	Ga0105355_101053371	F066858	AKKLAPAEKTSKIRDVSKGFRSIFLFRKMYDADAKRTSANKILKISGDRSEDMNAPSTVPGTAINPSFQPSENSTRFCLAYTAVDATELLNTANKLLLTASVGENPTNVNTGTIIIPPPRPIIEPNRPATNPSGMSQILSINVLG*
Ga0105355_10170328	Ga0105355_101703282	F101886	MLKKSAIIGFCLFNVVLFILIGIEVAAVTPERAMSEGVTQRIYASISTLDYIMAALWGAILYTILTAKTEHFLRASWLYLGFYLCDIHFSHYMSMEMNDPYFTPGALSLVVIQAWFLYWAKNKINAANAAVPS*
Ga0105355_10180613	Ga0105355_101806132	F031898	MEQTVLKEFQEEISEMDRDDIRLKTIREWEKYRERRDLGIRNYPESCMERMLSDEQVHGI
Ga0105355_10183560	Ga0105355_101835602	F101886	MLKKSAIIGFCLFNVVLFILIGIEVAAVTPERAMLEGVTQRIYASISTLDYIMAALWGAILYTILTAKTEHFLRASWLYLGFYLCDIHFSHYMSMEMNDPYFTPGALSLVVIQVWFLYWAKNKINAANAAVSN*
Ga0105355_10352272	Ga0105355_103522721	F013570	KRNNMELEKIKKKREELMTNYNTLIDKKVELEKQLEMTSNDILTMRGAILLSNEFIEEEEKPEPKPLFPEKEVVVNDLDKEKDGGQKNK*
Ga0105355_10390637	Ga0105355_103906372	F052648	LIWTTGGCIPDGSSLTGSFQKTKIPNTIKISDNTQETTGLLMLKSVIYIIS*
Ga0105355_10428000	Ga0105355_104280002	F005516	MIRFKQYLKEFAQQSTSDYVFDTTSGNSSSLKIPISGPMFKRIWPDTIRTTVFHTTDLAGLERLGKLEGRKKSISAFFSMMSRYMETGVATSGDVHVVAEMDADVLVSARDDIWSQVDKTGRRWVELSWFANAQWGGTGPKFAVVERELNDLIRNLVLKHLEPI
Ga0105355_10470077	Ga0105355_104700771	F018382	IDAAKVNLKPIKRKGGKCSIAGLAITKPKPKKIGTNEAKNVSLRLKTYSH*
Ga0105355_10483067	Ga0105355_104830671	F005336	EMTQMLMDLAIKHDPKNKEYLKTLPEIGIGVWWKLQTDFKDDGKKISLIIADYIDGVNAILKKHKKDIQGAVHGYYVRRGTIAVKHASGRMVGGDSEISEWNAWDEQVVDKIKIEKVHTFNTARREADWVKTDIIPRLGKIPHKHWKSATELSTYISQVADAEVRILRRSKG*
Ga0105355_10483205	Ga0105355_104832052	F042560	FAPSVKLRKKGRFPIVSIVTKNNIKEFIKTAVMLLVFRISSWQ*
Ga0105355_10513089	Ga0105355_105130891	F027865	TYDMEFAKLTRMGEKKSVTEYNNIYNDMLTDQFTAHTGMYTSLF*
Ga0105355_10563928	Ga0105355_105639281	F005429	QRGGTVTKIPEVLDTVGSRWGYQERYQAESIKDGTQQVVSWKSIQPDERFDTEDDDRKYWKKLDKRCDQLLKKMKKTSKKT*
Ga0105355_10567280	Ga0105355_105672801	F003092	LNGEEVDVEAEYKRITTFAEEIEYAGYDSSVTFIKKILVIHFQKEDSRVYLNKEHYAVIFTDWEGDTSNGLPIDEGSYQWPSICPVCPRACMHGEPSKWVRMEIIGEDDYGISGTAHIETISESGDTWTISGEGEGVFYNPYAESNMLGRIEFTNLVIETDEENTPYSD