3300025817: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - Muzzi_PWA_D2 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025817
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101362 | Ga0210144
• Sample Name: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - Muzzi_PWA_D2 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 362305846
• Sequencing Scaffolds: 45
• Novel Protein Genes: 50
• Associated Families: 40

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales	3
All Organisms → cellular organisms → Bacteria	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	5
Not Available	14
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → unclassified Myxococcales → Myxococcales bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium PC51MH44	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Marine → Wetlands → Unclassified → Natural And Restored Wetlands → Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: San Francisco Bay, California
• Coordinates
  • Lat. (^o): 37.926434
  • Long. (^o): -122.509186
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F003627	Metagenome / Metatranscriptome	476	Y
F004928	Metagenome / Metatranscriptome	418	Y
F008223	Metagenome / Metatranscriptome	337	Y
F016304	Metagenome / Metatranscriptome	248	Y
F016664	Metagenome / Metatranscriptome	245	Y
F016971	Metagenome / Metatranscriptome	243	Y
F017250	Metagenome / Metatranscriptome	242	Y
F018371	Metagenome / Metatranscriptome	235	Y
F019205	Metagenome / Metatranscriptome	231	Y
F020359	Metagenome / Metatranscriptome	224	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210144_1000148	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia	40255
Ga0210144_1000250	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales	31527
Ga0210144_1000261	All Organisms → cellular organisms → Bacteria	30585
Ga0210144_1000280	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales	29393
Ga0210144_1000389	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	24230
Ga0210144_1000467	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	21482
Ga0210144_1000492	Not Available	20880
Ga0210144_1000833	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales	14135
Ga0210144_1000931	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	13183
Ga0210144_1001672	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	8967

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210144_1000148	Ga0210144_100014827	F003627	MDRETARRELTAGLVTGGIAAGVFALCFVAAMLYIAS
Ga0210144_1000250	Ga0210144_10002503	F019205	MFDTRKTFSRRLADAVDLTIDFATLGEYGLEPVESRPAACQARRRSRSIRSTGAWNAAVNRFATHP
Ga0210144_1000261	Ga0210144_100026126	F081707	MYVRIAQFEGGDRDWDEFAAGIRDSIRSGAEGTPLETTLDAVKRVMLLVDRESNRGANLIICETEDDLRRVDAALNKMTPAGGRGNRTSVEMFEVVLDEEPRA
Ga0210144_1000280	Ga0210144_100028028	F003627	VDRETARRDLTAGLVAGGIAAGVFALCFVTAMLYIAS
Ga0210144_1000389	Ga0210144_100038916	F016304	VLVGFLLIADAFTVGALLVVRPDGWLPPFVAFGLLLVGLVVFELWAIRHRHDD
Ga0210144_1000467	Ga0210144_100046710	F016304	VLVGFLLVADAFTVGALLVVRPHDWLPPFVAFGALLVGLIAFEAWAIRHRHDD
Ga0210144_1000492	Ga0210144_100049218	F091541	MASKSILGRQSSVFGDRRERSKRIPFGLGKPAPHPNSDGGVGVGEAQHCLKCGFGNVPVIEEVVWTIPLPLTATEALATLGDTVNLLSGSSSVPGVASIDSTFLINGILQTDILTRGVGVHIFCEPMSFSTIGNAFLAPAVATQTLPASPDVFTLNDLAAGALGDDVNTDPNDPNFFPAVFEFGAPVWRAGWNFINAYQFQWRTSQRELVLNELAADVSYFGSFADAAASGTSEIPIIEYVALVNAVYRSKNSATVFLPVSFRRVGSVGQNGNPVGPPAGVNVGVFHPTRDFDLAPVTWGGLRWQGYGCRGQMYRPIESPCFLERGIPIGMLFVVQDAVHQAQMLESISIDNEPFGSNVQVDENLGCLTNVSANAEPGANPPTTGTGNVMLEQTLDANPVLVEQRVNVCRQVFKGGILKIGIKLKGWEMPGGWKAYCSKNMPQIMKGATPAS
Ga0210144_1000492	Ga0210144_10004928	F061612	MPKLIHQETMCCGYKKCPTVKVFEDGSMELTDNDAEKGSMGTIKLAPEQVERLTALAKK
Ga0210144_1000833	Ga0210144_10008334	F022258	MAIHSPPGGRYWYYWLVVVGGTIFVIAYYLTDGFGLKP
Ga0210144_1000931	Ga0210144_100093116	F018371	MDYTNIIRPKRLTNMQEMEIHVGGPDGANRLFMYSGMAEVELCGGLPHPRWSLEVVCFDIGRTYDKSKGEEVIKILTSASLAGSRTDGVASFAGWEIFGAAGELDHEDRRVRMNIAAGARDTQAFLEQICFTVNVLAKV
Ga0210144_1000931	Ga0210144_10009316	F069741	LENITFDVDELSRLDKMEQARRLEEAARQIDDVQRAAAGDPDSLDWVSQQRQYLVDMQHLIFEC
Ga0210144_1001566	Ga0210144_100156611	F028568	MNRPSVPRSLGVEAVWAAVERADVRLLDLRSEAERRRHGAPPGAEPVSLAEHLANPGGPGVVYLCQHAIRSKLTLRRGAAEVAGGFVAWKRAGLPVERIG
Ga0210144_1001672	Ga0210144_10016726	F059476	MAEQGNRQQSTRMVVTVLLLVLLALGFFTASFFVLT
Ga0210144_1002201	Ga0210144_10022013	F008223	MGLFGKLFSGNRRADDEIDTINGILQRFTTATLMGVDAEDIGRYPPKQYKVMAFHYGAIEYLASLYGLDENRTLGVFVSFINRNFNLPVTETGSITERLAGFHGDPEQRRYLEAGRAVFRRWHEENDRRAPLELGVMLKSA
Ga0210144_1002230	Ga0210144_10022304	F039145	MMNRLLMQLLVPLILLTACSQEGAQAPPELAAFIEKLQESGVDGTLSIRGPLNEDMEYVAEYAIAKYSRTRIISLFKCKDAEKAAANLEQALKNPKLSGQAGNGTFIMAATFYPPDEAAVNRIRAIFLAHRFE
Ga0210144_1003392	Ga0210144_10033924	F048676	MLFRYSRLCGKASDAVDGVKLEIPQGFKLLKFKMAEYLKDIVKLTISKI
Ga0210144_1006178	Ga0210144_10061785	F019205	MFETKKTFTGRLADAVDLTIDFATLGEYGLEPVDPRPRACEARQSTPRRSTGAWSAAIDRFAAHS
Ga0210144_1006763	Ga0210144_10067631	F046383	MRLAALRLCRWAFIGGLLITADALACEPELDGCLGCADDELPMCLQIFVEEVCASSGPVDNCDSRRVYDDAERNVTISTGSHMSHIRSMVRSARKYQLHHH
Ga0210144_1009328	Ga0210144_10093284	F017250	VKHSALSTIPTPEKPALSDEQRAERLRLLAERLRSPDGLDRDTLKHVEQLTDAER
Ga0210144_1016968	Ga0210144_10169682	F055037	MDDGRYGLDATFQGASGYERVERHAEGLKRDRVRHSLRQELDGGWTLRFGPLSAAEVGGALGAFVF
Ga0210144_1018863	Ga0210144_10188632	F080582	LNFNVNWMGTALPAENKQGMMDSQATNLELLKDVCENNPA
Ga0210144_1021532	Ga0210144_10215322	F027211	MVRTYWLVPVFNEASGNLDLHPFARIGHVEACRPRAMYIDCSLCG
Ga0210144_1025974	Ga0210144_10259742	F045770	MADLTADAYLRIWGEATTQRWVLDNSAAQTIYKGQPMIMDLSEDTVYPRGFVDATVVAAIDIFIGIAAEGATVATTDTETDNELNIYVEPTIVGFPGSVFTDADVGDTMYMSDSATLSATAADNPMIGKLVRVEGGFQYVRLSSPTVTTGA
Ga0210144_1027640	Ga0210144_10276403	F086605	MVDPWTHGTVNPVYSDADNYVCLIAAVFAGGECGAAKSVVSVSEIRTKA
Ga0210144_1032568	Ga0210144_10325682	F056029	MDLFMSWARSTVANAERALGRSDEWFDRILVGILVLLAVAVVFLFAQ
Ga0210144_1036449	Ga0210144_10364492	F022258	MAIHRQRGGRYWYYWLVIIGGTAFVIAYLATDGFGLQP
Ga0210144_1038061	Ga0210144_10380612	F004928	MDQAIHEKEAEPAHTVEIVVHIAEDLEEQQRRDLIAALNSNAGIVAAEFCPLRYHLLLVRYDRDTYSSQDVLNRVNSHNVSARLIGPV
Ga0210144_1042050	Ga0210144_10420501	F087939	PVPTAKGHVARLDRPGLGIEVDEERVQRHRVPIAAREVA
Ga0210144_1045305	Ga0210144_10453051	F044746	PALKKAKVKTGSTAILTITGTDTSAAQAQLDSFIEKWKSEGVNTVFLAGNNVSAKQFAETIKGAMPKVQLVTDTDTTIQQARDEATAGTKPNPYEGLLSGTGLTASERWANKSPLLKQCVNIYEKASGTKVPGPDEEKVDSSGKKVQTDVAVVDFCGELFMFRDIAKKVGPKLTVKNWQKTVDKLGPIALVPDKYASLCKGKYAAEDSFRLVAYDSSIGASGDWKTLTPIKDASGGKCAKATG
Ga0210144_1079030	Ga0210144_10790302	F008223	PVAAATRVLERFATATSMGIDREDLGRYPAKQRKVMAFHFGAIECLAEAFALDETEMLAVFVVFLDRYFSLPVTETGSISEHLQGFRDNPDECRYLEAGRDVFHRWHEHDERRAPLVLGEMLQAD
Ga0210144_1079233	Ga0210144_10792331	F020359	MAVEKRAKQKTPEEFWSKVLAAPKVKRILEKRGFDPEAFRRDYEADSSRGPRTPRRPSKQQMDAVEAFQRTGDFEALKTSLGTESAAVANSALRRVVQFKALGGVKTVRRRAGSD
Ga0210144_1085372	Ga0210144_10853722	F105203	MHQAKHAEAMVNRFRELVEDAGDSLPLNHYNELKLIVEAGLDTALLESMKKVAGQLNSLAEDIQHNADFFD
Ga0210144_1110031	Ga0210144_11100312	F022258	MAIHNPRGGRYWYYWLVVVGGTVFVIAYYLTDGFGLKP
Ga0210144_1122714	Ga0210144_11227142	F008223	ARPALALTGMGLFDRLFAGKPRKPTPTEEINRIIGRFTTATIMGVDREDLGRYPAKQYQVMAFHYGAIEYLAQQYGLDETQTLGLFVAFIDRYFNMPVNETGSISERLQGFRDNPDEQRFLEAGVDVFRRWYEHNERRAPLQLGEMLKDA
Ga0210144_1129479	Ga0210144_11294793	F003627	VDRETAKRNVSAGLLAGGIAASIFALTFVAAMLYIAS
Ga0210144_1134354	Ga0210144_11343541	F100914	MQILFQFDVRTIALFIGMTFFVQASVIGAQAFLIRELKQYRGVGAAVLANLCVASGVMLRLYTDRLPGFFTLILSNILLLIAIGIFYVALSQFTGLTYSKALVIGVIVVVLCFLTYFTYWDDDMGKRILSQSLGSIAIV
Ga0210144_1135417	Ga0210144_11354171	F086345	ATITDPTVFVKPVEMRFTLKRVPAEQQILEYSCLEGERSLQHYTEEDGGTKPRAQ
Ga0210144_1136938	Ga0210144_11369382	F032661	YFIRSKNQEERSMIERRMVKRRRYRAFTDFPAINHRGNLIMSNRRQLSTRRAYDIFVDDVDLPTMLLDINKQMY
Ga0210144_1143125	Ga0210144_11431251	F083755	AGDGGLPVWFDALSGGEGDSPNYVPQFEAFCQHAQLASLLPLEEVIVLGDRKMPTQENQLAWLRLGVGYIGPTMMQSHHHQTLQELFSTGQEWTDLPYIAQRDAGQQKAEGTIYQGVGHTVTLTDPETGDEYPVRHLYIRSSALAQRAEKRRQAEMRAIETEIQRIQGLVNKYDYKTAEIIAQRVQKKAFKKRPAQRYFEIKVVEHPDQPEAPFELLYTVEHEQAAQA
Ga0210144_1147614	Ga0210144_11476141	F105195	MTVLLVWPLMDLQSPRIITSDKHVIDLLETDPTIWVNHISEENKQRVVAEVLRWETAVGAGADATEAYGYAVGGIGVD
Ga0210144_1147656	Ga0210144_11476562	F034932	MRRVRIESESNDLIAGFVAGVEWVNDSAVAVVDLDYRSPTAFVVLEDRDVSGEDEVRRLTSDRIAGKE
Ga0210144_1166760	Ga0210144_11667601	F105195	MTVLLIWSLVDTQPPRLITSDKRVIDLSETDPAIWASYISEENKRRVLAAVRRWETAITAGANAIESHGYAVSGIGVDFQTWLANERA
Ga0210144_1177048	Ga0210144_11770481	F072360	MFSRKALYVAFTLLIALSFSAGGVLANSCQGGPDCINCAAAAHPHMPGMDLEMANQSCQFAEQNKSCGFETGHSADKFDRIATVAESGTHTYSGIFSAASDQSDQAPLYRGIITQIQYTDRSKLTP
Ga0210144_1181298	Ga0210144_11812981	F053659	VNINQAKPKRQKRTITLHLGNTLTEYEATYLTEAGLQALIRQVEIADSLNWGCLATEHEADCPRQLRFTHHDSYSRWAKHFNGSQSAVVIHRVRCLECGAVFSVQPSFIIRYKRYETDAVEKLMTLLFITEDSYRMAGISQSLALDDQQAGTWVALESYQEQAIAPMVLWR
Ga0210144_1186894	Ga0210144_11868942	F038581	VSRRGNRRGRPYQPYPDRRVNWGARLLIVAIAFVMVAGIAILAFAR
Ga0210144_1194348	Ga0210144_11943481	F071910	IAALVAALLGAFGLSLGLSAADAVERAVERHSAGVERALSL
Ga0210144_1199159	Ga0210144_11991591	F016971	QDLPVEESCAVEVVVYIKKDLGEDQQGLVISALQQTNGIIGAEFCVMRNHLVLAKYDKDIMTSQDVLKSFNSLHLDAKLVGPI
Ga0210144_1203283	Ga0210144_12032831	F016664	MDQVVQEMPTLKEARNAVEIVVHISESLEEGQRKNLVSALEKEDGIVSAEFCPLRYHLMLVRYDRNQYSSQDVLNAVDAQHLEARLIGPI
Ga0210144_1207113	Ga0210144_12071132	F071259	MKQKQARLIIGTAIGAAAIAVAIDHTRHRLPDPDTQLAGNDAVIIIDEGEAVPAENADCGETTTSGRQPSPCSL
Ga0210144_1237135	Ga0210144_12371351	F018371	MDYSNIIEPKRLTNMQEMEVHVNGPDGANRLFMYSGMAEVELCGGMPHPRWSLEVVCFDIGRRYDVENEGVIKILANAALAGHRTDGVASFAGWQIFGAAGELDHQDHRVRMNIAAGARDTQAFLEQIAFHVNVLARIKE