3300008251: Methane-oxidizing microbial communities from mesocosms in the Gulf of Mexico - GOM8C Gulf of Mexico

Overview

Basic Information

• IMG/M Taxon OID: 3300008251
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0118071 | Gp0127834 | Ga0105359
• Sample Name: Methane-oxidizing microbial communities from mesocosms in the Gulf of Mexico - GOM8C Gulf of Mexico
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 1019492571
• Sequencing Scaffolds: 29
• Novel Protein Genes: 31
• Associated Families: 28

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas aeruginosa group → Pseudomonas aeruginosa	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
Not Available	20
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Marine Group I → Marine Group I thaumarchaeote	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	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
F001048	Metagenome / Metatranscriptome	793	Y
F002006	Metagenome / Metatranscriptome	605	Y
F002187	Metagenome / Metatranscriptome	585	Y
F003285	Metagenome / Metatranscriptome	496	Y
F005429	Metagenome / Metatranscriptome	401	Y
F005610	Metagenome / Metatranscriptome	395	Y
F006321	Metagenome / Metatranscriptome	376	Y
F006552	Metagenome	370	Y
F010479	Metagenome / Metatranscriptome	303	Y
F011620	Metagenome / Metatranscriptome	289	Y
F013191	Metagenome / Metatranscriptome	273	N
F015654	Metagenome / Metatranscriptome	253	N
F021319	Metagenome	219	N
F033592	Metagenome / Metatranscriptome	177	Y
F041826	Metagenome / Metatranscriptome	159	Y
F042379	Metagenome / Metatranscriptome	158	Y
F047723	Metagenome	149	Y
F049927	Metagenome	146	Y
F054946	Metagenome / Metatranscriptome	139	Y
F059331	Metagenome	134	Y
F061265	Metagenome / Metatranscriptome	132	Y
F063067	Metagenome / Metatranscriptome	130	Y
F066857	Metagenome / Metatranscriptome	126	N
F086145	Metagenome / Metatranscriptome	111	N
F097523	Metagenome	104	Y
F101886	Metagenome / Metatranscriptome	102	N
F105490	Metagenome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0105359_10076316	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas aeruginosa group → Pseudomonas aeruginosa	1993
Ga0105359_10082996	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1885
Ga0105359_10157637	Not Available	1227
Ga0105359_10174128	Not Available	1145
Ga0105359_10179114	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas aeruginosa group → Pseudomonas aeruginosa	1123
Ga0105359_10204976	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota	1021
Ga0105359_10232925	Not Available	934
Ga0105359_10245116	Not Available	901
Ga0105359_10263276	Not Available	856
Ga0105359_10272750	Not Available	834
Ga0105359_10294631	Not Available	790
Ga0105359_10320183	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Marine Group I → Marine Group I thaumarchaeote	745
Ga0105359_10323607	Not Available	739
Ga0105359_10386330	Not Available	653
Ga0105359_10393092	Not Available	645
Ga0105359_10439080	Not Available	597
Ga0105359_10445109	Not Available	592
Ga0105359_10446337	Not Available	590
Ga0105359_10460862	Not Available	577
Ga0105359_10462061	All Organisms → cellular organisms → Bacteria	576
Ga0105359_10464714	Not Available	574
Ga0105359_10493025	Not Available	551
Ga0105359_10507947	Not Available	540
Ga0105359_10511482	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales	537
Ga0105359_10513938	Not Available	535
Ga0105359_10536991	Not Available	518
Ga0105359_10543422	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas aeruginosa group → Pseudomonas aeruginosa	514
Ga0105359_10555016	All Organisms → cellular organisms → Bacteria → Proteobacteria	506
Ga0105359_10556215	Not Available	505

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0105359_10076316	Ga0105359_100763162	F101886	MLKKILIIGFCLFNVAFFIQIGIEVAAVTPEQAMLEGMTQRIYASISTLDYIMAALWGAILYTILTAKKEHFLRASYLYLGFYLCDIHFSHYMSIEMNDPYFTPGALA
Ga0105359_10082996	Ga0105359_100829962	F101886	MLKKSAIIGFCLFNVVLFILIGIEVAAVTPEQAMLEGMTQRIYASISTIDYIMATLWGAILYTILTANKEHFLRASWLYLGFYLCDIHFGHYMSMEMSDPYFTPGALALVVIQAWFLYWAKNKISAANAAVPS*
Ga0105359_10157637	Ga0105359_101576372	F066857	MCRLSCRRLDYLHDWQEKAKRVIDIFLITKGNVQFLDVFCIFQCQQNKGFSHFLDTDSKLTVYRDGVVRPSRKDNIPLPAVFDEFSAMP*
Ga0105359_10174128	Ga0105359_101741282	F086145	MRRIVCKGYAGCWEGIFYTQEASRGYLKLLAFFLIWQKKTTVSLKIPIIVRV*
Ga0105359_10179114	Ga0105359_101791142	F101886	LLANCATKYPLPYEIIYQVKKEEKTMLKKIAIIGFCLFNVVLFILIGIEVAAVTPERAMLEGVTQRIYASISTLDYIMAILWGVILYTILTVKKEHFLRASYLYLGFYLCDIHFSHYMSVEMNDPYFTPGALALVAIQIGFLFWAKNRINTANLALSN*
Ga0105359_10204976	Ga0105359_102049761	F006552	VEIPLLISPVLKIKSSRINPVANIPKPIPIAKKAIDNLNNVGLAVFLNPIYEIVPITRPTKSPTRLRIISKKNSNYADSVTVLNKV*
Ga0105359_10232925	Ga0105359_102329251	F006321	GIEETKDILDFMFSFVEAVGKAQKDGEMTWSDARYFIDPVKKLFEAVDDIEEVLPEIEDLSGEEYDELVEYVRGKWDYDEENLDWIVDTAIDAGKSILMLINMKK*
Ga0105359_10245116	Ga0105359_102451161	F005610	VRSFKEYLTEADSEEVRDAKKVFTALQGMYPKIPKFPLVFKNLKGRGSGYLETSKLKGGKVIFVDKMVIDDSGMSSFEPDYAVVHEFAHAILAVTKGDLGHNKRHADLTYKL
Ga0105359_10263276	Ga0105359_102632762	F011620	MIDKIIQVVLRFFGKEKPEPPTEENNESLEALERIEALDKIGESS*
Ga0105359_10272750	Ga0105359_102727502	F041826	TPPNAECAKASPNRENLLKTRNSPTALQSREMAIPDISACGIDSYVTDSKVILNQW*
Ga0105359_10294631	Ga0105359_102946312	F013191	FDLIPSMHYDTLKQTTDKKYKIGENQPKTDHFIQFAHEGVMYFIWIDPSDPTENIAWWSDTTFEEWVTDTVALRLAAQQNPSETFFYCVGFDYYHDQTKDGIFLGTSITDFHDEKQNSWVGQHKHIEEEFPNSKFIFVGKDMDYGEFENLLNK*
Ga0105359_10320183	Ga0105359_103201831	F005429	MELRKETVEEFLQRGGTVTKVPQVLDTVGSWWGYQERYQAESIKDGTQQVVSWKSVQPVERFDTEDDDRKYWKKLDKRCNQLLKKMKV*
Ga0105359_10323607	Ga0105359_103236071	F049927	KAVGNVDKDFIEVICDPIIPLKKTVIILAVNPKT*
Ga0105359_10345627	Ga0105359_103456273	F000245	MKTFKEYSLDRKLDKYVSDEIKKRKLARHPVNATDDYKMKKGKPDFKFPSPTGEMMIHVWLRPMAKPASKDTKAFNYQLEDK*
Ga0105359_10386330	Ga0105359_103863301	F063067	EKSLIIKDYIDGMEKIMKKHSKILGTLLTDYTKKRIQEPDPDSGDKPMWDELVVNNFKIKKVHISPEFGPDFEDDDDIDGFPFELYQDVGDMVDYITRTVSKIKL*
Ga0105359_10386330	Ga0105359_103863302	F010479	MIRFKQFLREFAQRSTSEYVFDTHSANSSSLKIPISTSMFKRIWPDTIRATVFHATDSLEKLGKLEGGKKSISAFFSMMSRYMEIGVATSGDVHVVAEMDADVLISARDDIW
Ga0105359_10393092	Ga0105359_103930922	F097523	CYFTHNSWNLLPADSYDALKHGLDGTEHETYRRFDCEYFVYISGLAANCIETKSYIIWVPKVMENKIKNIGEEVLEWSTGTSALHIACRDFTCNDYEKVYLLGFDHHNNYYDNIYTDTEHYFSKDSKRVDGWKAEYNNWDKQIFKVIEEHPALQFIWVNYRGDDFPKLPNLFSKDETEIWQA*
Ga0105359_10439080	Ga0105359_104390802	F033592	SESTDLSLTGKGKYGLRPGQLKFGNDKIFTLTTDSNVTSYLLVTEFRRN*
Ga0105359_10445109	Ga0105359_104451092	F054946	LAFLYNSDYERGVPHPPQNFAAGFSGFPQLLQDEDVCLVSAGFGLGL*
Ga0105359_10446337	Ga0105359_104463371	F002006	MPEELQSVKLQVGLLKQEVEARGRQIDALLTKLDSTADKIVELTVEIKSLNSRQERHSKVDDEIRSELKLLHSRAGSIHDEIGKSERRVSDSIHKLEERVRAVEQYKSKLMGIAITVSAGVGLAVASIMGLLNIFKN*
Ga0105359_10460862	Ga0105359_104608622	F042379	MEMKKMTFAPGWVQTIDPANEKQDLLTYINDTHKAVYGYRPRWDREWVDTVTLVDLRAEAKSLEDEVGASNKRDRAEEADRQSEMAAHHIAVSMAKKPVARTFKPFANLKEMLV*
Ga0105359_10462061	Ga0105359_104620612	F003285	MPDQESIHNLQTEIQTLKIKDEFRTKELDALMKKLSDTSSKLNALSENIGRLLAGQDLHKTSDNEVRDELKILHTRIGDLHDKCTEMIDKTETRVSSDISLLYKKVDSLERWRWITIGIATAIAWLLTNI
Ga0105359_10464714	Ga0105359_104647141	F001048	MKIVSTKQFWWRLNYLKRNGGEITVTDRTPEMDVKEFNRIESLVNKRVRWELGSEGYSIWSECGYKDIPTL
Ga0105359_10493025	Ga0105359_104930251	F015654	MKRFFKEVYIKGHGKEDKNTFDTFKDTKFYKVNADKFYKELKDCDNLQYITFGDIKR*
Ga0105359_10507947	Ga0105359_105079472	F105490	MKGHTGKRLRQEGAINRIELSIEKYEKILPAERELLKVGRKEKDLPPDNIPTMEKKIKQFEKKLERAKTTLENTKKNLNI*
Ga0105359_10511482	Ga0105359_105114821	F021319	INGTKIRPPPKPYKLYSMAAKKLAPAVKISKRRDTSMGFSSIFLLRNMYDAEEIRTSANKILKISGDISEDMNAPSMVPGTAIKPSFQPSESSIRFCLAYIAVDATELLNTANRLLLTANVGENPMNVNTGTIIIPPPKPIIDPNIPATNPSGINQSCSNILYRYYFQFRIFRYVKLI
Ga0105359_10513938	Ga0105359_105139381	F059331	NVLGILKATKKTSANGPDPRNIAIRTSLIYPSILLIIVKKPNVVVDLIKFINHISLKFAPIVYIIIVNEKI*
Ga0105359_10536991	Ga0105359_105369912	F047723	PSANNLLKVLGSLKATKKASARKLVPKKIAINMSLT*
Ga0105359_10543422	Ga0105359_105434221	F101886	MLKKSAIIGFCLFNVVLFILIGIEVAAVTPERAMSEGVTQRIYASISTLDYIMAALWWAILYTILTAKTEHFLRASWLYLGFYLCDIHFSHYMSMEMNDPYFTPGALSLVVIQAWFLYWAKNKINAANAAVSN*
Ga0105359_10555016	Ga0105359_105550161	F002187	NAVFVDQKFMQTIQKCNEYEDWEPKGAYWFNRLVKKLRSAQEDFNDTRNKMVTKYADEPDKDGNVKVAEVHIPAFSTAMGELMEEEFEIEGIKPIKFPERLKLSPIEMGLMEEVVDMSAFLDDDEDE*
Ga0105359_10556215	Ga0105359_105562151	F061265	KEYSMSLDWNLIWKILQVVALLIIAREIDKRIRKRKK*