3300004075: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqB_D1

Overview

Basic Information

• IMG/M Taxon OID: 3300004075
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101404 | Ga0055519
• Sample Name: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqB_D1
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 826492866
• Sequencing Scaffolds: 34
• Novel Protein Genes: 37
• Associated Families: 36

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon	1
All Organisms → cellular organisms → Bacteria	5
Not Available	10
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Halieaceae → Pseudohalioglobus → Pseudohalioglobus sediminis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	2
All Organisms → cellular organisms → Archaea	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Marine Group I → Marine Group I thaumarchaeote SCGC AAA799-D11	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium ADurb.Bin063	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Streptomycetales → Streptomycetaceae → Streptomyces → unclassified Streptomyces → Streptomyces sp. AA0539	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?
F002989	Metagenome / Metatranscriptome	515	Y
F008179	Metagenome	337	Y
F011939	Metagenome / Metatranscriptome	285	Y
F013096	Metagenome / Metatranscriptome	274	Y
F021303	Metagenome / Metatranscriptome	219	Y
F029294	Metagenome	189	Y
F031139	Metagenome / Metatranscriptome	183	Y
F035771	Metagenome / Metatranscriptome	171	Y
F038247	Metagenome / Metatranscriptome	166	Y
F042645	Metagenome / Metatranscriptome	158	Y
F043410	Metagenome	156	Y
F043507	Metagenome / Metatranscriptome	156	Y
F048676	Metagenome / Metatranscriptome	148	Y
F053306	Metagenome / Metatranscriptome	141	Y
F054044	Metagenome / Metatranscriptome	140	Y
F058158	Metagenome / Metatranscriptome	135	Y
F070125	Metagenome / Metatranscriptome	123	N
F074893	Metagenome / Metatranscriptome	119	Y
F075466	Metagenome	119	Y
F076890	Metagenome / Metatranscriptome	117	N
F077207	Metagenome	117	Y
F077315	Metagenome / Metatranscriptome	117	Y
F077325	Metagenome	117	Y
F078881	Metagenome	116	Y
F081352	Metagenome / Metatranscriptome	114	Y
F082716	Metagenome	113	Y
F084125	Metagenome	112	Y
F084254	Metagenome / Metatranscriptome	112	Y
F087210	Metagenome / Metatranscriptome	110	Y
F090406	Metagenome	108	N
F092076	Metagenome / Metatranscriptome	107	Y
F093897	Metagenome	106	Y
F095491	Metagenome	105	Y
F102138	Metagenome	102	Y
F105198	Metagenome / Metatranscriptome	100	Y
F105215	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0055519_10008506	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus	1361
Ga0055519_10015292	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon	1151
Ga0055519_10015875	All Organisms → cellular organisms → Bacteria	1137
Ga0055519_10016113	Not Available	1133
Ga0055519_10019177	Not Available	1075
Ga0055519_10020134	All Organisms → cellular organisms → Bacteria	1059
Ga0055519_10026740	Not Available	972
Ga0055519_10028202	Not Available	957
Ga0055519_10038421	Not Available	871
Ga0055519_10038891	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Halieaceae → Pseudohalioglobus → Pseudohalioglobus sediminis	868
Ga0055519_10042373	Not Available	845
Ga0055519_10044752	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	831
Ga0055519_10048734	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	810
Ga0055519_10056189	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	775
Ga0055519_10057713	Not Available	769
Ga0055519_10065166	All Organisms → cellular organisms → Archaea	739
Ga0055519_10072540	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae	714
Ga0055519_10075040	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Marine Group I → Marine Group I thaumarchaeote SCGC AAA799-D11	706
Ga0055519_10093509	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	657
Ga0055519_10105123	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina	632
Ga0055519_10105135	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	632
Ga0055519_10122770	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	600
Ga0055519_10141907	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	571
Ga0055519_10144303	All Organisms → cellular organisms → Bacteria	568
Ga0055519_10151448	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	558
Ga0055519_10166051	Not Available	540
Ga0055519_10172363	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	533
Ga0055519_10173361	Not Available	531
Ga0055519_10176188	Not Available	528
Ga0055519_10178707	All Organisms → cellular organisms → Bacteria	526
Ga0055519_10185445	All Organisms → cellular organisms → Bacteria	518
Ga0055519_10189558	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	514
Ga0055519_10194364	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium ADurb.Bin063	509
Ga0055519_10202396	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Streptomycetales → Streptomycetaceae → Streptomyces → unclassified Streptomyces → Streptomyces sp. AA0539	502

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0055519_10008506	Ga0055519_100085062	F077325	MTSRGNWTEKDEATITAIIVNMINQKQMFQDLGKKNELNNSFGIQNPREYTLGLYTGIVINLFANYWIGEHEAGLQPEDLDYLYQKISSYGDVILQGLFE*
Ga0055519_10015292	Ga0055519_100152922	F093897	MGVAIAGLIAGFVLLNDIQQEKESKNIWIQKIPTQCNDVWEREYQEFYDLNPELLNPNKEKSKEILETIIKNHYEKEGISILDLNLELNVIEDIRCESCDCLGSDRISIKIPRNQLDLISQSEGWKPLQ*
Ga0055519_10015875	Ga0055519_100158752	F084125	MSESLMSRDKAVARKKGLFALGTWAGAGILIFYRPMFGLLVAAGAAVLTYRWFMFRAKRGMRF*
Ga0055519_10016113	Ga0055519_100161131	F105215	MYIKTDPKNSEGFSRTLLFHQDPDIRLDAALQLGGDTNRIADQRLALEALTAALEDPCSTVQEAVLQSLMRMSVKNG*
Ga0055519_10019177	Ga0055519_100191773	F092076	LDGQISIIKLGAMFSHKIDKLQEIIFTQASGTPTTVTMMDHIQNVMNDPDFDAKYNSIIVLEEHTHIAGVPTEKIETIRRVLDGYAQQRTGRNWAVVAPNERLEAFVKLNLELISPVIFNIRIFRSEEDALNWIKSR*
Ga0055519_10020134	Ga0055519_100201342	F078881	MSKKIINLFLIVVFLLILLLSGCGTGQFSVGVGVYVPGAWGGPYGGGYYPPVRVGYPVY*
Ga0055519_10026740	Ga0055519_100267402	F029294	MTQETGETRDAIIEDDNKKIAEIVEANKHLKEPYWIVVFAKPSKSCVDGLPTLVKHIKAYKTQPSSQVGMIAGKVDNAKGTIDWEVNMPQRPFNFDALPGLGAKACNEVVVETTTIPHAYVTQ*
Ga0055519_10028202	Ga0055519_100282022	F084254	QSKRHPRADQVASALAMRGLPIAEKDVMIVFDQYDIEKKTPDSHYFDT*
Ga0055519_10038421	Ga0055519_100384212	F081352	SLMIRLIRKILAITFACFLVLNLSAGAAVVVEHCQSPLGSSSAMDMDHCDGMLNFAFPMQGCCGDCNDIFCHLMKNPLQDANAVNASPFQGSYYFFILGTVDSIAESGAWIAASAPRYLFCAAPAWSQIPLYIENLALII*
Ga0055519_10038891	Ga0055519_100388912	F090406	MKCERNVLWLIVVLAGLAACSTTLTSVDKEGGNVYALPPTVVDQMLKDAMSTEISTGTLRRGSTPYPSYLGEVTWGSLDKDTITASARPAKGRKLDGTIIDGYVFEVTRKGTAPATGEPTVKRIFAKLQNDAELTGTGVAFVEFTD*
Ga0055519_10042373	Ga0055519_100423732	F043410	VAQYANLQKMVNAPSEGFDLQGMINKALIGILISKGIITEEEVKIILGNINRQQEIFSKKQNRA*
Ga0055519_10044752	Ga0055519_100447522	F053306	MRTKLLSTIASTLILSACGQPEPITYESLVWVNNYYVEHPVASLSATAGGWLFRGAREFGTEIRVGFLLPTPMNPDPAKRQAVLNTICPAKSETIWKALPEDNKLVIMVW
Ga0055519_10046304	Ga0055519_100463042	F087210	SAETALAHTPDSGFLSNFGHQLTSLHHSPAAMLLGVLVLGLLLVAVRSLKTR*
Ga0055519_10048734	Ga0055519_100487341	F021303	ISTDVSGFRTNVLDHSSEFVELVFRDAPAEYRRLMSLERFRRELGQQSRFNHGKLYAYAEFVVFRREFRERFPDASPAACINAFSSLLLKNDISVTNLVEFVEGPDHRGQLLANQPAE*
Ga0055519_10056189	Ga0055519_100561892	F070125	VTSAEDKRRWIEALHAYRDDSERLFGLVASLANLLDRTLVVETMESVLGVTAVHEGDCVIFDDFAIRFGSDDRVKSVFRTIDGTGSGG*
Ga0055519_10057713	Ga0055519_100577131	F058158	FTKTEKDDIDIWELHVKEREYILAQIANDRRTSRIRNWIELIFMLGFIWYMLYDIYKDKDLDTIIKFLKA*
Ga0055519_10065166	Ga0055519_100651661	F082716	MISKKDFKLMPFTFIVAPILLISLTFVVVTAYYDVIAEKEFIASLSCPELMIYTDKQIIESKLYFGNENYLIYAEERLDKLC*
Ga0055519_10072540	Ga0055519_100725402	F048676	MLFRYSRLCGTASDAVDAVKWEIPQGFKLLKFKMSEYLKNIVNLTISKI*
Ga0055519_10075040	Ga0055519_100750402	F013096	MLVSCGGDRAVGLSTLSQTNAVTSNVPEFSGIHDKAGLNDCPGDNEPVI
Ga0055519_10093509	Ga0055519_100935091	F095491	ALKDFSTLLPRLMVKVSPVGRFGMLGSAGMFAEKLIEELEKRIEPEIRSFLAESSDRILQRAAEFTISKIDDPASIEFRSNFIRFVLAKSPAFFLEAADDELIGEIGAVVELSARHVAEMPELVTEVRRWIEGGLAHTAGKTLAEALEIDSMELRPPIDAIAEATWPAFVTVLSSPQAQAWMNGLVDELVDAGFP*
Ga0055519_10105123	Ga0055519_101051232	F035771	RDRNPYGNVEKIRQRRSRPFAVLTYCEYAPRLKMAAVLLDELF*
Ga0055519_10105135	Ga0055519_101051351	F075466	MSDERVLCSHVLTIRFDQLEDNRVNWYVVPDDRIGQTGGLSLIDLAECRAPLAAMGIRALWKICVDGLVYHALEQANDIQVEVGRRLATGPAEAALELVP
Ga0055519_10109358	Ga0055519_101093581	F076890	ELQERLMSMIGTRSVAAMLVAMGALGTSACSTLEVDDYCRYSETRSIRTADPESLALVLGVQAGRARQTPFVVIRSLSESTPGASVTLHTTPAAHPMPMGLDESRCARVDWSTYTLAVDPEEWNAFWQDDRNSPFEIGIAFVEDFHPLPLSAFGAAILDTGSADPLVSCGCFWR*
Ga0055519_10122770	Ga0055519_101227701	F042645	MPRITDLDVLEIRKLFEESLVRAQQADKRRKMRLRRKIRDEVFNLLTWEKPTPTAIMNRWEERLQEAFEVMPYGFKEEIYKLLVDKMQHPLRLRLKKQQ*
Ga0055519_10126001	Ga0055519_101260011	F102138	VNTYDNKEINSWEAAKNTIVDLNYWYDFIPRYDVISDEDNDVLILQNKVRDLTIRQQLRTLPEIRKYFGEYLSDKLVGLGYKVTILNDERNKIIVFTHDSFTSRSALEKFHITVTNDLRALGFKQIRYKWFELEKLKDEKYIHYNFSDLPDNEPRKFNLSVIKAN*
Ga0055519_10141907	Ga0055519_101419071	F077207	ARRNNLLHTQQGRTSVATPWPIPRPSQAMRFPILPIAIAVLATAGCHDRGARTPAEAHARLQAALAAHDSSLLWRSLDQDTHWSWMTIQRAWREAYDITQSVVPEGQERRHLLARFEPGATSENAETLFAKMLTPGDWAASQALVTAAGTRPPEISSTGESAEIATPAGSLVFHKAHNQHWGWGFSGLAS
Ga0055519_10144303	Ga0055519_101443032	F011939	MTEMTINMIEEALRKEVQKIDKSVQVVAVEQGKKKNLYRVTLLKEGKSGSADLQKDLVEQHLSQKGQGRRLRKALAKAVSHL
Ga0055519_10151448	Ga0055519_101514481	F038247	MKSVFFWSEEQARTHRKNNPKPRGIYLSLRHAAFLTKPIQSALFGFEL*
Ga0055519_10166051	Ga0055519_101660511	F054044	MISKYYSNSETFSLPADRLGISSSVGILVLGLAITALIFLFLDSSFRSAADQEECLQLVRALGLNSLSLAPSGRPLRNPDAKDPSIDLRFDPRLGRIHLDGADFVLKV
Ga0055519_10172363	Ga0055519_101723631	F105198	MKRLIFTLFLLLPANQVSAYFAWGIGQQSCIDFVTAKAEYDHARDRRTHLSQLNWIKGFITGINWSRNSDIAKDLSIETVDEWIDAYCRANTDKTIAEASAELVVHLE
Ga0055519_10173361	Ga0055519_101733611	F074893	MGPGQLHAVAGDGALTIRINGPMDLLLTMPLREYCHNSGAAYRSYIVDFQNVSIVRDSGLALLLMLKRWTNRAGATLSVINGNRDLMRRCFSLGIGPA*
Ga0055519_10176188	Ga0055519_101761882	F070125	ARYFELAGRPGNAAPVTSAEDRRGLIEALQAYREDSERMFTLVANLANLLDRPQVVETMESVLGVTAVHDGDCVIFDDLAIRFGSDDRVRSVFRTIDGSAHED*
Ga0055519_10178707	Ga0055519_101787072	F043507	IGLSDPSEWTRDPALARLIGAPENVEFRRLRGILPASTAVQFTEFRGVPRTKFHLRVRDPGAPAMAIRVSDIEGMVARMKVAGVNVLSANNELVDFGNGVRNIFVEDPNGMNLELFERPVGR*
Ga0055519_10185445	Ga0055519_101854451	F002989	MVRFQADRPDGWAVQQLEVLIRTAVFKSANALVGLLLQRAADTIDAAYQPKPGQQYKARVRMQVEGMFGSFPLERDYYYHEGKKQGHYPADAAL
Ga0055519_10189558	Ga0055519_101895581	F008179	MAGLAGKSGPPGNQNAFRHGLASISQRRANGDLRASEKSIREEILAGLLADKGGELQVSTATRVLAEIIASDVSLLVTFNQ
Ga0055519_10194364	Ga0055519_101943642	F031139	MSNLLQLTEHAAAQSDRWLFIASLVVIGMFGVWVMRYFVKQHERLLDDHRQSRECYQESLRGVVAEQSAMNGKLVVCLDNNTKVLEECRDELRCSSRRRNRK*
Ga0055519_10202396	Ga0055519_102023961	F077315	MVICNASTFFLSRFACWQVWAVLLLSGLLIPSQAAEALKPDALPQAQATLERLEEQLATVRTATAQELKTVRKEIATVRSTAQDCLQQAEPKIEILDSELAILQPEKPKDTQKKTAQETQSAEQAEAPVSPAIAGQLQELLSSKASL