3300026054: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Sandmound_TuleC_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026054
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116120 | Ga0208659
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Sandmound_TuleC_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 51819384
• Sequencing Scaffolds: 32
• Novel Protein Genes: 33
• Associated Families: 33

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1
All Organisms → cellular organisms → Bacteria	6
All Organisms → cellular organisms → Bacteria → Terrabacteria group	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1
Not Available	8
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Nitrospirae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Hyphomicrobiales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Methyloceanibacter → Methyloceanibacter caenitepidi	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 → Terrestrial → Soil → 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): terrestrial biome → wetland area → soil
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: Antioch, San Francisco Bay, California
• Coordinates
  • Lat. (^o): 38.000706
  • Long. (^o): -121.624306
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001314	Metagenome / Metatranscriptome	725	Y
F001965	Metagenome / Metatranscriptome	610	Y
F004253	Metagenome	446	Y
F006533	Metagenome / Metatranscriptome	371	Y
F007548	Metagenome	349	Y
F007886	Metagenome / Metatranscriptome	343	Y
F010202	Metagenome / Metatranscriptome	307	Y
F013243	Metagenome / Metatranscriptome	273	Y
F019097	Metagenome / Metatranscriptome	231	Y
F021340	Metagenome	219	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208659_1000039	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	2861
Ga0208659_1000129	All Organisms → cellular organisms → Bacteria	2263
Ga0208659_1003307	All Organisms → cellular organisms → Bacteria → Terrabacteria group	1001
Ga0208659_1003474	All Organisms → cellular organisms → Bacteria → Proteobacteria	987
Ga0208659_1003594	All Organisms → cellular organisms → Bacteria → Proteobacteria	976
Ga0208659_1004096	All Organisms → cellular organisms → Bacteria → Proteobacteria	940
Ga0208659_1004203	All Organisms → cellular organisms → Bacteria → Proteobacteria	931
Ga0208659_1004743	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	895
Ga0208659_1004761	All Organisms → cellular organisms → Bacteria	894
Ga0208659_1005219	Not Available	864

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208659_1000039	Ga0208659_10000391	F040709	MIELIIFIVVAFIAWVVWTEQKSKQALERDALDQAWREVLDDPHYMERRHYEERMRVEDQARAAAANR
Ga0208659_1000129	Ga0208659_10001292	F007548	MAEASITADSKINDVLAKHPGTAPVFTQGRRLYVDQPGELYARFPGLSVGDFARQNGMDPGPLLAQLNAFAESGASARASGAHAADESRAGQFSLTLGYTCSHRPRDDAAPDSVSVVAVQSAHGPE
Ga0208659_1003307	Ga0208659_10033073	F001314	PTPTRGETARDLYDKRLTWITDAMRDSARSHGCLFHRCWYAADGSAFYALACWATREGASAFFNEWDIYDEEGEEAIYLEGDWGLVPVP
Ga0208659_1003474	Ga0208659_10034742	F025674	MTYFVEGLSGHTEPETKVRRIGEYDSLADAVAAAKRLVDGYLRREYRPGMEPRSLVSRYQEQGEHPYIFRDDDTTFNVPGFNHLHYATARSADVCAGKK
Ga0208659_1003594	Ga0208659_10035943	F027082	MGNKTESRRTTSCELPRDMRAESILEFVFNDEEEALCNEEFVLSHQRDMPAIQEFLQEMNELDARPATARRH
Ga0208659_1004096	Ga0208659_10040962	F013243	VSALRSSSRLGPLLVGAALVTALAAVGVDAARAGERRAGTVLAVDPQARTVILDEFGANAERRALRVQVPREALVLLSQRNQAGRDVKDVFRSSSITLADVREGDFVVVEMSDDPDVARLVMITLRRGAGS
Ga0208659_1004203	Ga0208659_10042031	F034498	VARSSLPQFFDLALRIRTLTPMLYDPGVWLFALAVGLFVAGILGVVLSTRRVPPSGTLGVPGLTGDPGAERLLLELEAEVERLRAERDELRGVLGRLASLLERRYPHLSAHRTAHLVTAGDDEEHRADGS
Ga0208659_1004743	Ga0208659_10047431	F027922	RNFHRRHLTTSQRALIAAEMCKLRPRGNAGTSPYLTAAQASTLMGVGQDLVKDAKHLLRTGDAELLRSVRDGVQSVSAAVQEKKKKKAPFTFLEQFAQRLDRALQGHNDRDAQVIYAAKPLLQYITLRLHDYLDPRTAEPLSGEDGALLWDPAELKVPDWLYTERGETIAAERRARLAAVLPKAREAAVGFPGERCSECGLPLLSTIRTGDPSYCAVCKGNVLWEWSWMREQVEVAFSSALRSVGPHP
Ga0208659_1004761	Ga0208659_10047612	F080668	ERVLTLNELFANPKLNLEITRRLEAGQKSVSISGEDAAKTGEF
Ga0208659_1005219	Ga0208659_10052191	F103981	FPQLERRILPKNDALKASQLTRGVLNCPNQVEGLAMSDVAGLNVQVLQDCDLVVTEPGTGEKVVYRKDGDSPVLVMMDSLRADPDAARVRFLVSAWKAAHAKAQQLGWLKS
Ga0208659_1005606	Ga0208659_10056062	F019097	IVQLAFMLGPLLGAAAGYLLDGVTGATSGFVIPMGPFVLVWLFGGR
Ga0208659_1005767	Ga0208659_10057672	F021340	VAIVTPFFVIVFGASLFLGTVMVIGTFHGTDPSNELTANGRAGRIARGLRDGTLCHYMVFDNKTGLPVEDRIDRCDENKPKPKQEKPATFTSEK
Ga0208659_1006172	Ga0208659_10061722	F083816	YLTLAISKTDDVIAFFALAACGLIAAAFGRRRERLSDVADRADQELTTLARFAERSRSGRPLDGLLQDLRAEFDLGGLVLRDADGRVLAAVPADAGARPAPRMALDGATLFAAGDESPRMGDNGLRLPEGGGRLTLQTPRGPVSLDLWEGNDRGFGRDESRTLAIAAAILGLGMR
Ga0208659_1006333	Ga0208659_10063331	F038873	VFVGTPDERRRVEILRGSLVSALIRALPGIDIRIVANRAERRALAP
Ga0208659_1007420	Ga0208659_10074201	F079856	FIGDYDLMARREPDPLTQAAGMREGYVYNETLMARYLTGVQFAQRYPAWKLCRQPQIVQSGVLRRETETVNAEVARFARGMGSATVATVGEAIFRCTQGGDGFVMATTLLLRPASGPGPSMWFVYQLAGFVTRDPAQGYFAKYVLSHMLASLQTNREWEIRSAQVAGQYANAMMQISNAVTQSTIQHARQQAAQGSAGGWNHPNTGGVPKITRDPGVEQRRDDANRGTRRVCDDVGTCKTVDNSWSNVWRDHNG
Ga0208659_1008201	Ga0208659_10082011	F066548	MARNSRAWRTPIAIAALVAGCAAPGEAPERPAHSVDGVRKVVDSLGTEIRKRTEDDPYRKLPVVVRTTTAANTGIEPMIAELLRTRLVDAGVTVEAACTPRCMEVSLQEFAIDTPRTTGLTPGQILFVGGGSIPFVGGLIRTFGEQQREQERAANRTTGVFVTFAAREGNRSTA
Ga0208659_1009130	Ga0208659_10091301	F098734	LLATGVTGFGAHLVHLCATARDRLLALQSRKARPGKR
Ga0208659_1010747	Ga0208659_10107471	F007886	VEGGDAVVAVFEGLEVVLAGVLAGGDTAAEAGVEGAVDVVCSDVLGADSFLSPVGGAGASLPGDGFSLSE
Ga0208659_1011282	Ga0208659_10112821	F037023	PEPQVRRIGEYKTVEEAVAVAEKAIEQFLRGEFKRGMDATKLFSLYEERGEHMFIFQDEAKTFNVAGFDHTEYARTRAAEICGGVK
Ga0208659_1012219	Ga0208659_10122191	F006533	QELPGEVQVNIARRVDSYIKIARAAKEETIVAMVASTAMEDQAKAIGQGGDTMDPRWAAPAIAEAWCYATISLSKGYLDRLHAEAIIAAIETFTTSRLNR
Ga0208659_1012948	Ga0208659_10129482	F097964	VTLAHHALRPHLIVPEIGVFRFFVQFGETSGRGVDVKDASSAAARTA
Ga0208659_1013338	Ga0208659_10133381	F028562	RRKPTAARPPAKIKQLEARLAQVEADLARVRSTAARGGLTRVRLAGIEKAMSQHVARAQAGLKDSVNRLSRTLLSARSRKEAAQQLALARQNVKESLDRLARTLGESQKKITHEVGLLTRGLKAGVKAGRAAYRGPRH
Ga0208659_1014046	Ga0208659_10140462	F049465	EQDDLPRIDLRFAKLCMELDCNTVFDSARFRHCPTCGSIEFYPLESWLNRERSEKVTAGLPNLPNLSADRADRDAALPRPLWLERLRAKRAASDARMAPGPLNIPGGGRRRRVG
Ga0208659_1014305	Ga0208659_10143052	F090480	MNKIIACAVLAAEFGFSFTIAKAMPLVPIGMEQAGLAIPVADGCGFNRYRDARGICRKKYVITRHWGRQPFYTGCGGLNSHRVCNLYGQCWMVCD
Ga0208659_1015435	Ga0208659_10154352	F022737	MPPCLATPSVCYSTGHMGVYAELRGFVLTHRECGVLRGATKPIDRGFRLAVICPCGARFARSVYAEDPEAERLQEALAAFQD
Ga0208659_1015841	Ga0208659_10158412	F010202	MRTAKRSGMPRYLRKPMVARAATGPVARIAPVLIRTVAFVPAYQRKRLH
Ga0208659_1019679	Ga0208659_10196791	F048737	CTVVLCSGFTWPPDYAEQSRADVTTCVSYAQRTSPRFEAWVRGVDLVTGRVDIERSPRDDSRGARAFSRCLLAVRHWRLIERNLPKPTEPSMPELATMAGREPDSLTR
Ga0208659_1020113	Ga0208659_10201131	F088683	MIRGSRGFALLAALWLLVALTAIAGVGVGIAQFGTLTTRNRVLLARAGWAREACVEILLARYADDVTVRAVPRVDLGRGTWCEARV
Ga0208659_1020202	Ga0208659_10202021	F061958	MAMKRRIWVFAAAMLAQNYAGLQSRAHAQVFDFGQIEEFESLGSGTQKGSSPQKTIVD
Ga0208659_1021071	Ga0208659_10210711	F025096	PSFTSVFPYESREVGKYQVDNHTKAPLRFVVQAWVNTDAATLYGKAISLEGIADHVTWKREGSPTVDAQHIPGDVRTIPVAWMNLKERLLLTEPVSVHFYTILQDESSAPTPMDHYLGVVTTESIGKGSVITWRVYFDTTGWSPMAGIMSSQIKSGLEKGFQSWIDEYGGM
Ga0208659_1021674	Ga0208659_10216743	F033346	MPTYMMSCTHCAYEVVFRTEPDAKTEGVRHLLQFPAHGVKVTPSEDALIWEEERVTVG
Ga0208659_1022091	Ga0208659_10220911	F001965	SKVCVGLAFMCMAPAVGFAAEKSYLCAINEVYECVAVTGCSRISLDDANLVGIMLIDLEKKQLRTAPLGGEARADDIESVAVTDKAILLHGTGKREADRTWSAVISLETGNVTAGVSTLDSSLSLLGKCTAQP
Ga0208659_1023081	Ga0208659_10230811	F004253	MRMPYNKQLQRTAVRHHAVVASAPFHYALASRITRQRAAAELRR