3300008254: Methane-oxidizing microbial communities from mesocosms in the Hudson Canyon - EN4B Hudson Canyon

Overview

Basic Information

• IMG/M Taxon OID: 3300008254
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0118071 | Gp0127826 | Ga0105351
• Sample Name: Methane-oxidizing microbial communities from mesocosms in the Hudson Canyon - EN4B Hudson Canyon
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 534822864
• Sequencing Scaffolds: 46
• Novel Protein Genes: 52
• Associated Families: 45

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
All Organisms → Viruses → Predicted Viral	3
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Porticoccaceae → unclassified Porticoccaceae → SAR92 clade → SAR92 clade bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Gammaproteobacteria incertae sedis → sulfur-oxidizing symbionts → Candidatus Ruthia	1
Not Available	22
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Gammaproteobacteria incertae sedis → sulfur-oxidizing symbionts → Candidatus Ruthia → Candidatus Ruthia magnifica	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → unclassified Flavobacteriales → Flavobacteriales bacterium	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Spongiibacteraceae → Oceanicoccus → unclassified Oceanicoccus → Oceanicoccus sp. KOV_DT_Chl	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Methylococcales → Methylococcaceae → unclassified Methylococcaceae → Methylococcaceae bacterium	2
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → Caudovirales → Myoviridae	1
All Organisms → cellular organisms → Archaea	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Pelagibacterales → Pelagibacteraceae → Candidatus Pelagibacter	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: Hudson Canyon
• Coordinates
  • Lat. (^o): 39.54
  • Long. (^o): -72.41
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F002715	Metagenome / Metatranscriptome	535	Y
F007241	Metagenome	355	Y
F012354	Metagenome	281	Y
F015151	Metagenome / Metatranscriptome	257	Y
F016531	Metagenome / Metatranscriptome	246	Y
F022907	Metagenome / Metatranscriptome	212	Y
F024813	Metagenome	204	Y
F025396	Metagenome / Metatranscriptome	202	N
F026708	Metagenome / Metatranscriptome	197	Y
F029446	Metagenome / Metatranscriptome	188	Y
F030553	Metagenome	185	Y
F030561	Metagenome / Metatranscriptome	185	N
F031645	Metagenome	182	Y
F037935	Metagenome	167	Y
F038690	Metagenome / Metatranscriptome	165	N
F039346	Metagenome / Metatranscriptome	164	Y
F041826	Metagenome / Metatranscriptome	159	Y
F042383	Metagenome / Metatranscriptome	158	Y
F042578	Metagenome / Metatranscriptome	158	Y
F047906	Metagenome / Metatranscriptome	149	N
F049927	Metagenome	146	Y
F052648	Metagenome / Metatranscriptome	142	Y
F054946	Metagenome / Metatranscriptome	139	Y
F055198	Metagenome / Metatranscriptome	139	Y
F055413	Metagenome	138	Y
F057395	Metagenome / Metatranscriptome	136	N
F058538	Metagenome / Metatranscriptome	135	N
F063198	Metagenome / Metatranscriptome	130	N
F066454	Metagenome / Metatranscriptome	126	N
F066857	Metagenome / Metatranscriptome	126	N
F071644	Metagenome / Metatranscriptome	122	N
F071971	Metagenome	121	N
F075324	Metagenome	119	Y
F083669	Metagenome / Metatranscriptome	112	Y
F084730	Metagenome / Metatranscriptome	112	Y
F087322	Metagenome	110	Y
F092216	Metagenome	107	Y
F094427	Metagenome / Metatranscriptome	106	Y
F094922	Metagenome / Metatranscriptome	105	Y
F096688	Metagenome / Metatranscriptome	104	N
F097521	Metagenome	104	N
F099328	Metagenome / Metatranscriptome	103	Y
F103884	Metagenome	101	Y
F105373	Metagenome	100	Y
F105864	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0105351_1000842	All Organisms → cellular organisms → Bacteria	14265
Ga0105351_1005797	All Organisms → cellular organisms → Bacteria → Proteobacteria	5201
Ga0105351_1011207	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	3613
Ga0105351_1037319	All Organisms → Viruses → Predicted Viral	1801
Ga0105351_1038832	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota	1759
Ga0105351_1039864	All Organisms → cellular organisms → Bacteria → Proteobacteria	1731
Ga0105351_1042002	All Organisms → Viruses → Predicted Viral	1676
Ga0105351_1046412	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Porticoccaceae → unclassified Porticoccaceae → SAR92 clade → SAR92 clade bacterium	1578
Ga0105351_1048703	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Gammaproteobacteria incertae sedis → sulfur-oxidizing symbionts → Candidatus Ruthia	1533
Ga0105351_1054428	Not Available	1433
Ga0105351_1054456	All Organisms → Viruses → Predicted Viral	1433
Ga0105351_1056314	Not Available	1404
Ga0105351_1063659	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Gammaproteobacteria incertae sedis → sulfur-oxidizing symbionts → Candidatus Ruthia → Candidatus Ruthia magnifica	1304
Ga0105351_1074368	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota	1186
Ga0105351_1077871	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → unclassified Flavobacteriales → Flavobacteriales bacterium	1153
Ga0105351_1079933	All Organisms → cellular organisms → Bacteria	1135
Ga0105351_1087304	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Spongiibacteraceae → Oceanicoccus → unclassified Oceanicoccus → Oceanicoccus sp. KOV_DT_Chl	1073
Ga0105351_1100628	Not Available	985
Ga0105351_1101294	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Methylococcales → Methylococcaceae → unclassified Methylococcaceae → Methylococcaceae bacterium	981
Ga0105351_1106703	All Organisms → cellular organisms → Bacteria	950
Ga0105351_1116808	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → Caudovirales → Myoviridae	899
Ga0105351_1120023	All Organisms → cellular organisms → Archaea	884
Ga0105351_1130776	Not Available	837
Ga0105351_1130935	Not Available	837
Ga0105351_1140537	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Pelagibacterales → Pelagibacteraceae → Candidatus Pelagibacter	802
Ga0105351_1149173	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Methylococcales → Methylococcaceae → unclassified Methylococcaceae → Methylococcaceae bacterium	773
Ga0105351_1162307	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → unclassified Flavobacteriales → Flavobacteriales bacterium	733
Ga0105351_1174288	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota	702
Ga0105351_1174681	Not Available	701
Ga0105351_1176238	Not Available	698
Ga0105351_1178693	Not Available	692
Ga0105351_1181157	Not Available	686
Ga0105351_1198636	Not Available	649
Ga0105351_1198900	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → unclassified Flavobacteriales → Flavobacteriales bacterium	648
Ga0105351_1215988	Not Available	617
Ga0105351_1216210	Not Available	617
Ga0105351_1229646	Not Available	595
Ga0105351_1233036	Not Available	590
Ga0105351_1234792	Not Available	587
Ga0105351_1241782	Not Available	577
Ga0105351_1246983	Not Available	570
Ga0105351_1257780	Not Available	556
Ga0105351_1265021	Not Available	547
Ga0105351_1277480	Not Available	532
Ga0105351_1294037	Not Available	514
Ga0105351_1299150	Not Available	509

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0105351_1000842	Ga0105351_100084210	F103884	LIVKETTDLDDIKALLCDPDIYDTITDDNSGLAQDFEPPVNDEYLYIGGYVNGKIVALMVYHKYLDGNKCHVQVLPKYRKEYALKFGEQSLLFKGTLPLYAEIPDLYKNVLDFALLNNFKVIDTKENDYIKNGKAYDVNVLEFQHGFC*
Ga0105351_1005797	Ga0105351_10057972	F094427	MDLHLLQHPNTANHISSAEYLQVELLMLYGESCDIGEGKHYTSLTKRGYKRLLKDMHHVQQHLKTLKSTYLIDADGDKLVTVGQRYNDHHCAGGALRASH*
Ga0105351_1011207	Ga0105351_10112075	F096688	MRIIKGLAVVGYALVMLLVLTGGRSANEAEFNAGHQACDAQYNMDAMQAFEMDPSEPFVQCHVAVNEAYPAAWNNWRRQNARSRGLELAGNRFRGGGGS*
Ga0105351_1037319	Ga0105351_10373191	F083669	MCEWENRTKTFMIKSTPQIIEILDNAFDLGGCEDRSVLIHKILLLYVKDVIASDATEIANPEGVYEEIDAVFTQYIDSA*
Ga0105351_1038832	Ga0105351_10388324	F071971	MIIIVFYNAESTINAINKTAKYGLENLNNVHAAVSMGFIVTQTDSPNINAPDAIAVHKYTSPTMFSPLSVVMKNGAIENNTITTVDSAIALADVFSDC
Ga0105351_1039864	Ga0105351_10398643	F016531	MLLMLSGISGVSRLSQAAIISGFDGSVVSNVNAPDRLLVLGFIGSRVASELIHRGESTVIIKDEDRSLANDKINDRTPGDVVN*
Ga0105351_1042002	Ga0105351_10420024	F094922	MNEAKCSEMDTILKVHKQRIDELEKLLDSIHTQLTQIKACAYGAVGYAVATQMGIIEAIKLGS*
Ga0105351_1046412	Ga0105351_10464121	F071644	MEKTRNPRFTGVLIFAGLWNLCIATWALFFTDMFIQVLALEGRGVSKVFQTIVGISGIMFILSGLNNARFRFIIAIAVPGKILAFLGSANALLAGQAGVGIMFIGLGDLLFTIPFIMYLRATRQFGWI*
Ga0105351_1048703	Ga0105351_10487031	F030561	NLVLFIFIAARPVDFNIGSITIKANRFRKKTTSRICKFSDAFLTKITIIEKKTIAKIFKIIALV*
Ga0105351_1054428	Ga0105351_10544282	F055413	MLKVTDLAINKELDSKTLTSVRGGFDPFAILIDGSTSLTNKVADVDQVFAFGFEQNNAAAVTNNQAINGGNGLAYAPVTQNLDQYSDMNVSGIGNVSVS*
Ga0105351_1054456	Ga0105351_10544564	F015151	MITLKNGLILSEDNNGFESWNHLTNKIDPKSFTKFTELPDIFYKEINEDDRVLLTKLAHPELATILDRTKV*
Ga0105351_1056314	Ga0105351_10563142	F055413	MLNITDLAESKELDSKAMAGVRGGFNPFAILDGSTSLTSKVADVNQLFAFDLAQNNAGAVTNNQAINGGNGITYAPVDQTLTQASSMSVYDIGNVSVS*
Ga0105351_1056314	Ga0105351_10563143	F055413	MLKVTDLATNKELDSKTMTSVRGGFDPFAILIDGSTSLNNKVADVDQVFAFGFAQNNAAAVTNNQAINGGNGLTYAPVNQHLDQYSDMNISGIGNVSVS*
Ga0105351_1063659	Ga0105351_10636594	F084730	MRTVAILDTVEFVFTVGYFSYLNCITSGVYLYDLGNRIYGYGTPKRALIFFNSFYK*
Ga0105351_1074368	Ga0105351_10743683	F087322	LLQALRLGLVLTDLWVLRIIHAGTGDVCFIFFNKRIFLPERLRAAIKSQA*
Ga0105351_1077871	Ga0105351_10778713	F058538	MYSQYETTIMNRRRLHHLLSWVNRELHLDYEVIQENRDVFYVIFHDLDIKKTVAIQKHLKSNPHTAN*
Ga0105351_1079933	Ga0105351_10799331	F094922	MNEAKCSEMDTILKVHKQRIDELEKLLDSIHTQLTQIKACAYGACGYA
Ga0105351_1087304	Ga0105351_10873042	F029446	PNLIKVDKKFSITNIVVGFVGALAGAFLGFGDAPLFLKYPFLNEITLMVTVSFLFVFIKIFLTRKRIVS*
Ga0105351_1100628	Ga0105351_11006282	F041826	MKRPNATPPNAECARASPNRENFLRTRNSPTALQRMEMIIPDTSACGIDSYVTASKVILDQW*
Ga0105351_1101294	Ga0105351_11012942	F058538	MYSQYETTVINRRKLHDLLAWVNQKYYLEYEVVQENRDVFYIIFHDLNIKQTVAIQKQIQGSSQPEHFHLH*
Ga0105351_1106703	Ga0105351_11067031	F042383	MKGIKMETTYNNFPNSDDFYKGPSDEELKRIEEDLERYSD*
Ga0105351_1116808	Ga0105351_11168082	F022907	MDDDNTLDIQQNVGDVGGDFTKTIVIGDEVDFTEDGAGSEMGDVEAVIELTYNIFQYIPELLFVSVYGLLMYAGVLLIAKTIKNNE*
Ga0105351_1120023	Ga0105351_11200231	F066857	MCRLSCRWLDYLHDWQKKMEGVIDIFLITKGNVQFLDVFCIFQCQQNKWFSHFLDTDSKLTVYRDGVVRPSRKDNILLPVVFDEFLVMP*
Ga0105351_1122171	Ga0105351_11221711	F105864	KIIPDPGIVVSKLNIASGRYFCGTRLLTRLLISSMKNLITMTLKIRGIQKRRPEIK*
Ga0105351_1130776	Ga0105351_11307761	F063198	VEITKLYIVRMRLEENSLISEDRLILNAPSKIRINRVKVVNTGATEARSSGDVYPNPLGPIRNPSIIRNNTSGILVRRNNASDKKPKIAIK
Ga0105351_1130935	Ga0105351_11309351	F047906	VQEERRLFRLRGIAIVALAAKFTQKRTVTKERTPDAIRVPVAHRPVVGLEVIAVRWHHAVTKVRAALRLNMLAVAKRVSRVEIKFAVTAKAGLVQTQRLGVANAVVIRIVVAERVA*
Ga0105351_1140537	Ga0105351_11405373	F049927	KIAVPTTYKAVGNVDKDFIEVICDPIIPLKKTVIVAAVNPKT*
Ga0105351_1149173	Ga0105351_11491732	F058538	HDLLTWVNQKYYLEYEVVQENRDVFYVIFHDLNIKQTVAIQKQIKGSSQPEHFDMH*
Ga0105351_1162307	Ga0105351_11623071	F066454	MSIRLDILILINSGVTDRSEIMERLGINIRSVSNCVRFLVKEGWVDYSRESISAVGSVGYRITQVGIDKIKASTVDEYRQSPKRKIPDYEVMRSHLGVGGDVTRSELINLWNELTDYYLPYEGDKEFTGSSGLSSL*
Ga0105351_1174288	Ga0105351_11742883	F012354	VIPLLTLPVCVIASSMIYPSAKTPKPIPIAKKAIVSLNSVGLPVFLNPIYEIIPIIIPTEKPIRFRIISNKNSNVANLLAVLNKV*
Ga0105351_1174681	Ga0105351_11746811	F026708	KTNGATARKPTKNRTELKVNGPILSIPVSWAMNVVPQIKVQATKQTNDIVFFIS*
Ga0105351_1176238	Ga0105351_11762381	F038690	MALKVTKKELSLFTTNFSLTYFIFFVFLTLLMMFMDSRYDYLKQIRKDFSFITSPLIILTNDSINFFDNFQSLSKSKALLEEEINQLNIQIENLSIENQIRNF
Ga0105351_1178693	Ga0105351_11786932	F031645	LNVINKYSATIIEKKVCLQKRICHKLAPSKDFTIMPPKLKHNAPSRTKTVPGILFNSVNLSL*
Ga0105351_1181157	Ga0105351_11811571	F054946	LAFLYNSDYERGVPHLPQNFASGFSGFPQLLQGEDVSFFFAG
Ga0105351_1186692	Ga0105351_11866922	F099328	QAGTAEACFVFLSRRIFLGEDLRAAIVCQARRALFK*
Ga0105351_1198636	Ga0105351_11986361	F024813	VLIIAKMSNAFESFNAKICVMVIINTRKITSASIENKPEADVIIINQKENPAVTASALNLGEDNSILNWINECYKTALC*
Ga0105351_1198900	Ga0105351_11989001	F066454	MEGLGINIRSVSNCVRFLVKEGWVDYSRESISDLGSVGYRMTQVGIDKIKSLTVDDYRKSPQKKIPDYEVMRSHLGVGGDVTRGELVNLWNELTDYYLPYEGDKEFTEIAVFPPCRL
Ga0105351_1215988	Ga0105351_12159881	F037935	KTVLLLFIFDVADYLKIFEIQHNKTLLYLYFTYEI*
Ga0105351_1216210	Ga0105351_12162101	F052648	TCTTGGCNPDGSSLTGNFQKTKSPNTIKIRDITHETTGLLMLNSVMNI*
Ga0105351_1229646	Ga0105351_12296461	F097521	MINLKNLLTEIVCGQCFRWAYRKVLKGGPLFNLVHGTIHAPFLNKRIDHAWVETKKRVFDWQNHESQDRKHALANIGLWVDVDDKTKVEYYRKGFPKKLYYKMTKAKVDNKYKKMEAAITMMKNKHLGPWD*
Ga0105351_1233036	Ga0105351_12330361	F105373	MARSIPLIFEEVAAANSFGARKKVLLENESNPLKDLLKYAFHPDIKFALPSGEPPYKTIGSPDEYNPTY
Ga0105351_1234792	Ga0105351_12347922	F007241	NITGTVTIKNISRDILSNEISLVIFDPPNNSTDVKTINGIVITHNKLIIAVRDIERATSPFAKEVNKLDVTPPGAAAIIITPIASSGAIGHIFTRINAIIGSKIICEKAPTKKLRGCFITLKKSAPVKPKPNTNIIKAKAKGKITSVTIFIYVSIKIL*
Ga0105351_1241782	Ga0105351_12417821	F002715	MPEEELQSVKLEVGLLKNEVEVRGRQIDTLLSKLDLTTDKLQELTVEIRTLNTRQEDYLRHTSSMRDEFKILHTRIGDLHDKQLASQKEIEIRLDRLDQYKSKLMGMIIVVGGVVGTIVATAISIFLKE*
Ga0105351_1241782	Ga0105351_12417822	F030553	MKTFKQFDETKLDDKLDKLVSNEIKKRKLAKFPVNATDDIKMRMKPN
Ga0105351_1246983	Ga0105351_12469831	F055413	MLKVTDLTVNKELDSKTMTSVRGGFDPFAILIDGSTSLNNKVADVDQIFSFGFAQNNAAAVTNNQAINGGNGITYAPVNQHLDH
Ga0105351_1248794	Ga0105351_12487942	F042578	NVSKSKLESEVKTHSKEIKKVNRNNFHRVLEAFSDCV*
Ga0105351_1257780	Ga0105351_12577801	F039346	MFTSFVITLIECLEIAFITLLISQTKVNKPTVITYGSLGLLGGLLSAFYLHDILENYEWLMYAILSSLFFYLFVKNKEIVAHIQAHVDDISNSSSTVLFLTAFFIYGRESFEIFSNLFLNPNASWLSAGLAAIVAIMIYMFARDSKIKVYIFKFGYWAYLAF
Ga0105351_1265021	Ga0105351_12650212	F092216	MTKHYDRFDLEEEIMNIWQTEDDLDAVVHRMMINPDPLPNKEIANLLMAVSKLHDLRCQKLFDIFEKMVIDKCFINKNISLDYRGVPLEDEDAMQGNFWPSPDNGQVH*
Ga0105351_1277480	Ga0105351_12774801	F055198	KKWKCVINYINIMVVYMSRFEEASCKVLGVILFLIICLLVLQLNGCTTCVNVPPPPSDYIDEVDTSNFV*
Ga0105351_1294037	Ga0105351_12940372	F075324	VNAELSHKKTRIQLGLKQVVSLAVFLLRPQADFKSAHLLKIVNILPNVNSLKVFYLINLRE*
Ga0105351_1299150	Ga0105351_12991502	F025396	MKRDRKKFNTGEIPLKIQNILLKFGEKQKIGISEYLRTFNQSSLKNITHNMDDITVSEIKYHQDCYLIHSENKKVI
Ga0105351_1305541	Ga0105351_13055412	F057395	YQAMHSKLWGSRPTSTTNCKPRGIGLSNSIGEIFVETWHSVSDSKLLKQIFTKYDCVPSKRFISKETWVLIN*