3300004150: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqC_D1

Overview

Basic Information

• IMG/M Taxon OID: 3300004150
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101405 | Ga0055520
• Sample Name: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqC_D1
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 883598516
• Sequencing Scaffolds: 38
• Novel Protein Genes: 42
• Associated Families: 36

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota	1
Not Available	11
All Organisms → cellular organisms → Archaea	2
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae → Phycisphaerales → unclassified Phycisphaerales → Phycisphaerales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → unclassified Flavobacteriales → Flavobacteriales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → unclassified Desulfobulbaceae → Desulfobulbaceae bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Alteromonadales → Alteromonadaceae → Glaciecola → unclassified Glaciecola → Glaciecola sp.	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	3
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Eisenbacteria → Candidatus Eisenbacteria bacterium	1
All Organisms → cellular organisms → Bacteria	5
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Bacillales → Bacillaceae → Bacillus → Bacillus cereus group → Bacillus gaemokensis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Sorangiineae → Sandaracinaceae → Sandaracinus → Sandaracinus amylolyticus	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → unclassified Nitrosopumilus → Nitrosopumilus sp.	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → unclassified Acidimicrobiia → Acidimicrobiia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → unclassified Proteobacteria → Proteobacteria 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): 38.131752
  • Long. (^o): -122.266335
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000701	Metagenome / Metatranscriptome	930	Y
F005564	Metagenome / Metatranscriptome	396	Y
F010932	Metagenome / Metatranscriptome	297	Y
F017617	Metagenome / Metatranscriptome	239	Y
F019000	Metagenome / Metatranscriptome	232	Y
F020728	Metagenome	222	Y
F021303	Metagenome / Metatranscriptome	219	Y
F025141	Metagenome / Metatranscriptome	203	Y
F026568	Metagenome / Metatranscriptome	197	Y
F026597	Metagenome	197	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0055520_10005494	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota	1603
Ga0055520_10019303	Not Available	1100
Ga0055520_10025628	All Organisms → cellular organisms → Archaea	1009
Ga0055520_10026412	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae → Phycisphaerales → unclassified Phycisphaerales → Phycisphaerales bacterium	1000
Ga0055520_10031647	Not Available	945
Ga0055520_10035009	All Organisms → cellular organisms → Bacteria → Proteobacteria	916
Ga0055520_10035157	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	914
Ga0055520_10036529	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → unclassified Flavobacteriales → Flavobacteriales bacterium	903
Ga0055520_10039950	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → unclassified Desulfobulbaceae → Desulfobulbaceae bacterium	878
Ga0055520_10048834	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Alteromonadales → Alteromonadaceae → Glaciecola → unclassified Glaciecola → Glaciecola sp.	824

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0055520_10005494	Ga0055520_100054945	F093897	VNKIMKPGFYISMGIAIAGLIVGFVLLNDIQQEKESKNIWIQKIPIQCNDVWEREHQEFYDLNPELLNSNKEKSKEILETIIKNHYEKAGISILDLNLELDVIDEIRCESCDCLGSDRVSIKIPKNQFELISQSEGWKPLE*
Ga0055520_10017695	Ga0055520_100176951	F020728	MFYLLWGVGILNFTDAAQTIYLLNVKLMVEANRFMAFLLDHSPYVFWMYKTLVPTVGCVLLWRFRKKVRWLPGAVITVFAVYLTVVLRSFLYMVLPSAPAV*
Ga0055520_10019303	Ga0055520_100193032	F005564	MENDMNKIFIALMVIFFLGDPNMETLTWLGDIRNYVVAAAVALCSMLFIVSQLDG*
Ga0055520_10025628	Ga0055520_100256282	F103291	MFGLSPVFATILIVSMGVILQNFLGWLKSKEDYDIKNALASTIIAFIVGITIIGPQIEAIQDQMLSELSELTIFASLIASIAGFDVLTKNVFKIANSKIHLQNKPI*
Ga0055520_10026412	Ga0055520_100264121	F091343	MDDKPFQHAALWLIGPDMPGLLRQGAQYVFERGGNIDKDIADKFGEKAVVFMSITADPEDIGRMDKDKEKLKAQTGCGVVFQPMHSPTVPDGFQNDLHGFDVVTDDHPGLIAALTELLAEYKILIVGHTGERYLERGPQAHPKAGQKYIVMLPHTFDHLAFTRALDSL
Ga0055520_10031647	Ga0055520_100316471	F066277	MDRKKFFALISTSLLGAALLGAIPLNFFKSKSNSIKVKINPNAVNR
Ga0055520_10035009	Ga0055520_100350091	F019000	MLKNFIRDERGEDLIEYGLLAAFVAAIAVAVIIADPLGLSSAVEGAYQSAVDALTDVTP*
Ga0055520_10035157	Ga0055520_100351572	F026568	MHKPSPHKELYDPYYHYTRGVLYFDEDHFTFTAYRVPYMELDSKSWETEQEFKADYRRVLERKYSV*
Ga0055520_10036529	Ga0055520_100365291	F103291	MEMFGLSPVVATLTIVSSGVILQNILGWLKSKEGYNVRSALASTIIAFVVGITIIGPQIEAIQNQMLSDLSELTIAASLIASIAGFDVLTKNAFRIANQKINLQNKPV*
Ga0055520_10039950	Ga0055520_100399502	F099324	MFKQIIFVIMLGWVLVLSGCAAIDKGEDYRTGYPPRAGYTSTTPHKALVSEACNIEANNLVGDKDFMADDRARRVYFSQCMLRNGYNAAGNYVGIPSK*
Ga0055520_10048834	Ga0055520_100488342	F084255	RQNAAPNWAKDMESSRRYLLQAEIEYWHEMLKLNKNRVSRNRQEEMRHCLKKAVRALNTSMRSEFRVAA*
Ga0055520_10054780	Ga0055520_100547801	F073723	MSGFTALERLLLPLVRRFVSLWVRPSVLPDDVHERLAASPPVVYALEKRSLVD
Ga0055520_10062743	Ga0055520_100627431	F071971	MIIVFYNAESTINAINNTAKYGLENLNKVHAAFSIGLIITHIDNAIINAPDAIAVHRYTAPIISSPLSVTKKNGAIENNTITTVEPAIALADVFSDCTAVNIGTFTLL*
Ga0055520_10064540	Ga0055520_100645401	F021303	YHGAGYQRRISWCIFCGMTERTISTEVSGLRASVLDHSSEFVELVYRDAPAEYRRLMALERFRQELGRQNRFNHGKLYAYAEFVVFRREFRERFPDASPAACINAFSSLLLKNDISVTNLVEFVEGPDHRGQLLLNQPPAPG*
Ga0055520_10068887	Ga0055520_100688872	F021303	YHGAGYQRRISWCIFCGMTERSISTEVSGLRASVLDHSSEFVELVYRDAPAEYRRLMALERFRRELARQSRFNHGQLYVYAEFVVFRREFRERFPDASPAACVNAFSSLLLKNDISVTNLVEFVEGPDHFGQRLLDQPPGSG*
Ga0055520_10073164	Ga0055520_100731641	F021303	MTERPISTDVSGLRATVLNHSSEFVELVYRDAPSEYRRLMTQQRFRRELALQNRFNHGKLFAYAEYVVFRKEFQDRFPDASPAACINAFSSLFLKNDISITNLVEFVEGPDHRGQLLLNQPPGPG*
Ga0055520_10075963	Ga0055520_100759631	F044663	PSLGLTYAVTQYLARSLSALRNPETERALGQSLEVIRQGIERLGSDARHHAEVMALAPETVRLLQAGDMAALERLLREEARERALDYVCLYDIGGEQEIRLFGARLGPRITLPTPERAALLAARDAGGLVSGSDVPRQVSGVAALGDAHVIFAGYQLDPEVSSEIEALQKNLTMYRRLGIYTSLSQRGVWLFAALWTIILGLVSFTLAVAISRGVARPVLELRSGMERVTQGDLAHR
Ga0055520_10079430	Ga0055520_100794301	F026597	MFERHRLIVSFSLALLIIAVVGVTVSSFSPSKKSEYFKELKQIYNTVNNYDNKEINSWEAAKNTLVDLNYWFDFIPRYDAISDEDNDVLVLQEKVRDLTIRQQLRTLPEIRKYFGEYLSDKLYGLDYKVTILNDERNKIIVFTHDSFTGRSALEKFHNTVANDLRALGFKQIRYKWYELEKLKEEKYIHYNFKDLPDNEPRRFN
Ga0055520_10080694	Ga0055520_100806942	F105200	SCNDGWKTMIITFPKTMADPVAGRHRRRNVPDSFDRKLEQLLQYKEAPQPEAFTMDVMRGVRRGQRTRKIILWAFGLVGALFGLSGASMLAGPVSELFSFSLAMPAMQTMQATLFIVGAAAFYLWFMNDDFSLGD*
Ga0055520_10089603	Ga0055520_100896032	F069503	MDPTPLTLELRPLHNGVYTQITLKGPVATVPQVWQVRRLLSLLSFWHGGPVDVVLCADGTNPGACWLEVWADVLGRVHRRHLDVRYLISRDTLAASAGHER*
Ga0055520_10094991	Ga0055520_100949911	F099324	VFRKVIFVIMLGWVLVLSGCAATDKGGNIEGEDYRSGSPPRGGYTRTNSHKVLVTEACNIEANNLAGASDFMADDRARRVYFNQCMLRNGYDADGNYIGIPPK*
Ga0055520_10096003	Ga0055520_100960031	F044016	MKSRNTLSVAVAVLSLVAPVATGLAQDARGQDKWDSVARTDSQEAFVNTSSITVAGAQLEAKVKQNFAEAQPSAKKNKSYLSSRTTFRFDCTGRRMAMKEVRTYAGSDLQGDPVQKATSGDKNL
Ga0055520_10096968	Ga0055520_100969682	F032624	MKKFTTRKYNGDDDYSWAVFKAADIKGTRGVIFLGDARPVVSGCSRSEARYHANTLNSKSS*
Ga0055520_10107648	Ga0055520_101076481	F077987	MRIEYKCSGGFGGLRLAYRGETDDLPSEQAKELSDLVEAAGIFELTPKQLSKKSPTIPDDFSCLLTVLKAGKRKTLSFNELGAPANLRRLSVHLRKLAIQ
Ga0055520_10116718	Ga0055520_101167181	F075466	MSDERVLCSHVLTIRFDQLEENRINWYVQPDEQVRATLPLSLIDLAECDAPLAAMGIHALWKLCVDGLVFNALEQANGIQAAVGKRLSAIET
Ga0055520_10120904	Ga0055520_101209041	F105216	MPTSRSAALFCGLAIAAAACSDEAPKPWKAAEMRKLSEQFGHIAEAYAVVDICLPMIDADQDAKRSVIAKIEIRRYSQLSRINTEAEFANFLAYHRQTGGTDEQAAALDQIYRESYETAARHLTSVDNCAETVSDYANTILQTRVEPVP*
Ga0055520_10121054	Ga0055520_101210541	F105202	ADVYVPSISALKPEEYSGEIDKYNKIIQSDLHLDIQQRAHLYLASLYFSPMNPKRDYGLALEHLETYALFDPDFANAVDPRLLLAAIIEIERFSALAEAQTKEIQALSQELDILKRQSAAFRGSRQDIQSANLKLQKRIGQLQKKVRNLETSNAKLNKTIEMLSTLDSRLKEKRINFIKTDSIEEK*
Ga0055520_10125636	Ga0055520_101256361	F075466	KVLCSHELVIRFDQLEDNRVNWYVVPDEKIRQTQSLSLIDLAESGAPLAAMGIRALWKLCRDGLVYNALEQANDTRVEVNRRLATGPVEALMELAPEGVTIN*
Ga0055520_10127631	Ga0055520_101276311	F098862	QREPDQMKRFVYQQQEDAKACSLPHVLNQLPMQPTVMGIDSPHQTGDHICYDMLTRGPLYCMTSHFTRVAPEAPVRGMHRHIGAPTLFCVTGKGWEWNDGETYHFETYDLMIVPPYTIHQHGGDKDIGCTIYVPETGRVGNLMGLTWREQHKLNEKPTFRDGTEPIYGEDGALKGYRIKKGVLGITEDLEVILGGEPN
Ga0055520_10132853	Ga0055520_101328532	F036163	MALIKLSCMYGHLEGIDGKFARDVTGYLSIADGIYAKHGLEISWNHVQGTEERYRRLANGEAQLSFVVGRASLQHFLDTKTTRIIGCAMNSCP
Ga0055520_10136791	Ga0055520_101367911	F000701	GYLWQPSRSKLEALSAICVFMYVGEDDEYRWHEEMKSEVEILTAGGTLARYSEEQGQPHRIETLAGPDAGRLFDGFEEAGNGCRL*
Ga0055520_10146627	Ga0055520_101466271	F059979	MKSFFFVLAQLTLVTIVYAFAYRAGYRDAKSKAMSVVRKFADPVTCLLDQLNESLEEAKEFEDEHPTSNIERSTSNEKNNVEP
Ga0055520_10152555	Ga0055520_101525551	F043464	DVTVILAEFELPSGSGKQANPYRWKIQDIGAPQFQLQVSELDALLERTAEAGYRILSIGAKPIQRPFGRFVFVTDADGVLVEFVEPRTSQ*
Ga0055520_10166088	Ga0055520_101660881	F025141	IPYYMIQCDYCPRGFIETANGLAEKTFHELLHEPEVVNK*
Ga0055520_10170193	Ga0055520_101701931	F058634	QSSPEEFTINTATSQGPEPKNTIGLFEKQGLPAGNCYFSFAAASNTGNTQCTGELTVAVQTNETTEATVVLACIHTPRYGGVRGDGTFNQCAEYRQILVTPTTQAIGNLIDVATQVYDPDGDPVTVGVQAVGACSNVMFTNGNTAASCETVSGCETVLNTVECTDVGLCQIIVAVSDD
Ga0055520_10172506	Ga0055520_101725061	F017617	LVTSDRPDEYIGKKGLVKNQVITCQDVDPSGYRLLMPFDYTMSEDEKGKFAGKLQDKQIVVGVRELMPFGGRLRARGAIITGPDGKN*
Ga0055520_10174027	Ga0055520_101740271	F010932	PDDGTWRSWFFNFRDIPPFDAVEMPYGMKVISRKPGPAAGTEYVDEKSFALPAILQIGDTEFTHFKQPREALAAGSHNAHLMFVTPNDDASFTLYTVNHYTGPDKEFFAKLAPSRRVQAPMEKKPYDPREFSPFRGNVRTEDIACQATQKLLGERNEQLASTDRGVILLRKLILDD
Ga0055520_10176712	Ga0055520_101767121	F098236	AQFVREETGGITYMIARGYELGYETVLRFCAGAGLSVRARIFGELNERVVIRDAQNRPARLSGYAQGAMEISDSNGLVIFRGRYYDSRTIRSLAGDDALTVVGSSLVDHWENGFGEGPYAGHAFSVGGQLTQEGDGPLRGVCRGHID*
Ga0055520_10179608	Ga0055520_101796081	F094059	KYRFLDSFMYPQSFIALCGYFRDLPVGHYTARFLGVFIGAMIGVLFVLFIGVLYKWVLKDWAYSKATRIASLAFILIALMTGFMSDMFNESIGMALHIEEGVPDDLVGKFLVEDYGSFEKGTKITTQNASILSAYGTIKGNNPAGARRWWIASLIFMYAWFGLYFLCAHRLFKR
Ga0055520_10186760	Ga0055520_101867601	F076930	MTQRAYDLGFRRGYEIANRTPIDPSISKDEFVKMVLETARNSLESTVFESISAELESMNTKYPAFDGWTVFAEGVMQGAGENFLDRTGNQE*
Ga0055520_10188705	Ga0055520_101887051	F105200	NGWKTMIITFPRNNMKPVQGRHRRRNVPDSFERKLGQLLEYSDAPHAEAFTMNVMRSVRREQRRRKIILWSFGLVGALFGLSGALMLTGPVSELLTVSLQMPVIKTMQVTLFVVGATAFYLWFMNDDFSLGS*
Ga0055520_10203857	Ga0055520_102038572	F060099	EAMKALRGAEEALEYLIKGVKGLEEPPTLAGRIEEVELYLKRVKMALKFI*