3300025984: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqA_D2 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025984
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101406 | Ga0210082
• Sample Name: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqA_D2 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 157135182
• Sequencing Scaffolds: 27
• Novel Protein Genes: 28
• Associated Families: 26

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Peregrinibacteria → Candidatus Peribacteria → Candidatus Peribacterales → Candidatus Peribacteraceae → unclassified Candidatus Peribacteraceae → Candidatus Peribacteraceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
Not Available	9
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	2
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Archaea	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → unclassified Desulfobulbaceae → Desulfobulbaceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont	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?
F012874	Metagenome / Metatranscriptome	276	Y
F015265	Metagenome / Metatranscriptome	256	Y
F016024	Metagenome	250	Y
F016664	Metagenome / Metatranscriptome	245	Y
F020359	Metagenome / Metatranscriptome	224	Y
F021446	Metagenome / Metatranscriptome	219	Y
F021741	Metagenome / Metatranscriptome	217	Y
F028664	Metagenome	191	Y
F030371	Metagenome / Metatranscriptome	185	Y
F042645	Metagenome / Metatranscriptome	158	Y
F045765	Metagenome / Metatranscriptome	152	N
F048676	Metagenome / Metatranscriptome	148	Y
F057781	Metagenome / Metatranscriptome	136	Y
F059979	Metagenome / Metatranscriptome	133	Y
F060098	Metagenome / Metatranscriptome	133	Y
F070131	Metagenome / Metatranscriptome	123	Y
F071910	Metagenome	121	Y
F077453	Metagenome	117	Y
F078289	Metagenome / Metatranscriptome	116	N
F082881	Metagenome / Metatranscriptome	113	Y
F091056	Metagenome / Metatranscriptome	108	Y
F092076	Metagenome / Metatranscriptome	107	Y
F099324	Metagenome / Metatranscriptome	103	Y
F104552	Metagenome / Metatranscriptome	100	Y
F105216	Metagenome / Metatranscriptome	100	Y
F105217	Metagenome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210082_1001283	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Peregrinibacteria → Candidatus Peribacteria → Candidatus Peribacterales → Candidatus Peribacteraceae → unclassified Candidatus Peribacteraceae → Candidatus Peribacteraceae bacterium	3572
Ga0210082_1001323	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	3508
Ga0210082_1001662	All Organisms → cellular organisms → Bacteria → Proteobacteria	3097
Ga0210082_1005066	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1893
Ga0210082_1010929	Not Available	1370
Ga0210082_1011758	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales	1328
Ga0210082_1013950	Not Available	1231
Ga0210082_1021772	Not Available	1006
Ga0210082_1022411	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	993
Ga0210082_1023899	Not Available	965
Ga0210082_1029256	All Organisms → cellular organisms → Bacteria	880
Ga0210082_1029421	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	878
Ga0210082_1032038	All Organisms → cellular organisms → Archaea	844
Ga0210082_1032358	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	841
Ga0210082_1033244	Not Available	830
Ga0210082_1033573	Not Available	827
Ga0210082_1038094	Not Available	781
Ga0210082_1038749	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	775
Ga0210082_1041622	All Organisms → cellular organisms → Bacteria	751
Ga0210082_1049693	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	692
Ga0210082_1051049	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	684
Ga0210082_1059014	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → unclassified Desulfobulbaceae → Desulfobulbaceae bacterium	640
Ga0210082_1060403	All Organisms → cellular organisms → Bacteria → Proteobacteria	633
Ga0210082_1063861	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	617
Ga0210082_1066032	Not Available	607
Ga0210082_1076683	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont	566
Ga0210082_1087551	Not Available	532

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210082_1001283	Ga0210082_10012831	F030371	MPGDCITPAEISDLAQKDTQRLVGSIAKALAANAPFMNVIGGGVFPSGVSDEIKSTVQMPAAPGDSLAVPTFECDTDVCGTVGLQDLTDAVNFTTRLETKRGFGPRICVKKGYAAFRGSYMAAEDSLKKLIVQYVNSDIRAQLYLRSASKFVAAAGYDFMSIWTGGTENDLGVKFANVLPTGPMTFKALHYIARYMREVMFAEWFANDKGMPHFR
Ga0210082_1001323	Ga0210082_10013232	F048676	MSFRYIRLWETASDAVDVVKLQIPQGFKFLKFRMPEYLKNMIQLTILKI
Ga0210082_1001662	Ga0210082_10016623	F104552	MMICRASTLFLSRLAYYPLWSLLLLGLLIPAQAAVALEPDALPQAQATLERLEQQLATARAPTAQELRALKKEIATVRSIAQDCVQQAEPKIEMLGSEFAILQPGTPKDTPAKTAEETQPAVQPEAPVSPAIARQLQDLQSRKASLEGRIATCKLLLLGSNNLDSKVDDFLRSLQTRQLLARGPDLVSVLQANLDERERWLDFTRQLAVTSTGWDAIRPIHLAGAAAVGLLGFILGRIVPRRLRARAARMKVGEEEVSAGLVQAVMACGASYAPILLALGGI
Ga0210082_1005066	Ga0210082_10050662	F078289	MKKAGSIFILVFIVFPLYGFNSLVRHEDIPKMRELGISQEVIQYIISNQTSSVSSEDVIKMKQSGLNNNDIMSAIKSDLYRPEQKSTSMKEVELIAKLKESGMSDEAVLQFIQTVKSTRRVDSDGNVTKQYTNESQRTQYPTTGATFPKLDNYGYDPSNGRFLFFIKPQNQE
Ga0210082_1008487	Ga0210082_10084871	F091056	LIIEQISLTVNRTCYNSPHILRDEEVTRKMRKIMMALMVAVLLGFAAPAFAGDHMPAIAGGAGSAVDQFSAVKYIRNLSDLACQYRDHGLSLQLDGFNYEWLIFQDSCIRDNIEAELVVLGRSREHIIDPLAWQLHVDMIGATIEQINTITDELATYNFYPNMDKIVAKIAKKANEGTKVLGMVEDELGKGEERNYADLAVYGESLWMVGNDLICLVKDLDFTNWTTMYSGALCAGDCCQNDFPLCVACWDCDNTGCGDGCPMIGSTRVVGKDCDRPVCKAKKKCTSGCKTKCDKGC
Ga0210082_1010929	Ga0210082_10109291	F048676	LCGTASDAVDAVKSEIPQGFKLLKLKMSEYIKNIVELTISKI
Ga0210082_1011758	Ga0210082_10117583	F012874	MPAKAGIQNHLKILDSRLRGNDVKERFKAFYETINVD
Ga0210082_1013950	Ga0210082_10139502	F070131	MMGKMLTKIGIIGVFAFCFLLQVDLAGGDNRAYGQNKQKSNVPMEIELHFSSTPMLNEYTVLNVEIRALKDAPNTLIEIKIPSDGFELISGSTQHHEDLSSGSTTLYQLGVLPVALGQYKIAASAISGETDYIFGKREELYVNIGEEFSELSKSSFIPEIADNRSGATKIGNFSEPPTQVLPDQKPGEGQEDFYLAAPGPGEIVVRGYWLYQDKGGADRPLRDARVEIWDADSSGDTLLDTTHTNNSGY
Ga0210082_1021772	Ga0210082_10217722	F021446	MKTLSIALVATFMLVLAATSTGQAQSAEDGYNDPKPGGRYVYRGCNLAQVIFIRGDKLSEINELTLVIEVQAGKNSHTTRLTFPILAKRQEGNKLILDYQWPNGGDTYEATIIGDTLTNRKTKGYLAGIREEVFTRE
Ga0210082_1022411	Ga0210082_10224111	F042645	MPRITDLDVLEIRQLFEEALVRAQQADKRQKMRLRRKIRDEVFNILTWEKPTPTAIMNRWEERLQEAFELMPYGFKEEIYKLLVDKMQHPLRLRLKKQQ
Ga0210082_1023899	Ga0210082_10238993	F015265	MTKSSIIYPAHMTKKPKLIERNAIVNLNKVGLPVFLNPTNAIIPMVNPTKNPTRFNISSNKNSNDA
Ga0210082_1029256	Ga0210082_10292562	F020359	MAVSKGIVGGKTPEEFWSKVLAAPKVKRVLEKRGFSPEAFQRDYEADTSRGPRVPKRPSRTQIDAVEAFQQSGDFEALKHALSTSSSAVANSTLRRVVQFKALGGVKTVRRRSGA
Ga0210082_1029421	Ga0210082_10294211	F045765	PSSKGENTSTIKIEDTLYALLRKFCDKEGRRLKDFVEDALENAIYTEESIKILNEEIKSLKKKEAKYDYAFRRGFQKGFYISFCALHGQILLGPDDEDFKILKNDPFRIAKGAQLDLFRSRES
Ga0210082_1032038	Ga0210082_10320382	F105217	IFPKDKIASEVAIDGFLFYANSALDLVFVEINKKLELELPPNQINPENIMSNVDSKKSNNSKMMLEEFQKYFQKPTHEEKIISDKEFNDGLNRYGFDVIGFHAEYEARGQEKYQHFWNRASSRLWEIRNQQDLESYDSLLKNAGKRGKDEPRNYLRVKLADDNRPSVYWDSAHYENPKRYFTNVLSLVKQFIDRILEILKPLYPSDSSLAV
Ga0210082_1032358	Ga0210082_10323581	F059979	MKSFFFVLAQLMLVTIVYAFAYRAGYRDAKSKAMSVVRKFADPVTCLLDQLNESLEEAKEFEDEHPTSNIERST
Ga0210082_1033244	Ga0210082_10332442	F071910	MRRIVIAALVVALLGAFALSLGLSAADAVEQAVERHATGVERALSL
Ga0210082_1033573	Ga0210082_10335732	F077453	DGRGVLQDIGRWYEIAEGIVKYDTMCVNYSATICPHPIQHYSAGDAHMPDMRAVAESLPSSVLKHAWNPNCPGFDIRWARNGRGGWNGTSGNLALKIGLAFDYTRIVLAGCPMDNSGNWYSNLVKQDDIKARKDHRHHLWKWCEIATRPIGKFVRSMSGNTRDLFGEPSRAWLNHEPEEGETAWQKMN
Ga0210082_1038094	Ga0210082_10380942	F028664	MKKENQILVGGQALRNLGSDRHTNDTDFLVNDITSKETFITSENVDFLNANGNKFFAEIYKIEAGNSQATPQSLFELKAYAFVQHCQNFNFTKADSCEYDMKFLVRNFGCSPKIVKKYISGGELSEVEKIVNSIKF
Ga0210082_1038749	Ga0210082_10387492	F092076	LDGQISIIKLGAMFSHKIDKLQEIIFTQASGTPTTVTMMDHIQNVMNDPDFDAKYNSIIVLEEHTHIAGVPTEKIETIRRVLDGYAQQRTGRNWAVVAPNERLEAFVKLNLELISPVIFNIRIFRSEEDALNWIKDR
Ga0210082_1041622	Ga0210082_10416223	F021741	MKAAFQGVDRILIDVTERLYRRSQDDDTQREHYSGKKSTTPSKTL
Ga0210082_1049693	Ga0210082_10496931	F078289	GFNSLVRHEDIPKMRELGISQEVIQYFISNQTSSVSSEDVINMKQSGLNNDAILSAIKSDLYRPEHTSTSMKEAELIAKLKESGMSDEAVLQFIQTVKSTRRVDSYGNVTKQYTNESHRTQYPTTGATFPKLDNYGYDPSNGRFLFFITPQNQQ
Ga0210082_1051049	Ga0210082_10510491	F016664	MDQAVHQIPPQSVTTHTVEVVVHLSDQMNDQQRHNLVVALENAQGIVSAEFCILRNHLMLVRYDRDQSSSQDVLKEFENQKVNAKLIGPI
Ga0210082_1059014	Ga0210082_10590141	F099324	MFKQIIFVIMLGWVLVLSGCAAIDKGPNIEGGDYRSGSPPRGGYSRTTPHKALVSEACYIEANNLVSGQDFMADDRARRVYFSQCMLRNGYDAD
Ga0210082_1060403	Ga0210082_10604032	F082881	RALPPGEDPRPRYWEHYADFHRVITQSLTDDELPHSFVEAFSRTYAQTRDELQAKRRERDDDSR
Ga0210082_1063861	Ga0210082_10638611	F060098	MDAPSLSRAASAVVMGIGGLLWLSALLFMAQTAQNSEQFSR
Ga0210082_1066032	Ga0210082_10660321	F105216	MPSADAQKTPTRNRRNCVRTSGIEMPTSRSAALFCGLAIAAAACSDEAAKPWKAAEMRKLSEQFGHIAEAYAVVDICLPMIDADQDAKRSVIAKIEIRRYSQLSRINTEAEFANFLAYHRQTGGTDEQAAALDQIYRESYETAARHLTSVDNCAETVSDYANTILQTRVEPVP
Ga0210082_1076683	Ga0210082_10766832	F057781	MKLPDLQMLAHWLDPALVAAVETRRREKKEWHRCRKLATLQTLWLMLAVSLDTQRSSLHEILRLA
Ga0210082_1087551	Ga0210082_10875512	F016024	MTPIPEEMLAEARQIRKAAKSLRRKAVIDSLIRRGVAPDRIEQTIREAEVAADAIADKAKARIAHRKRAKLRIVKS