3300026037: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNE_TuleC_D2 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026037
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116086 | Ga0208655
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNE_TuleC_D2 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 53755599
• Sequencing Scaffolds: 41
• Novel Protein Genes: 43
• Associated Families: 40

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea	9
Not Available	4
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	8
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Chloroflexi incertae sedis → SAR202 cluster → SAR202 cluster bacterium	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → Nitrososphaera → Candidatus Nitrososphaera evergladensis	1
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	4
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Alcaligenaceae → Candidimonas → Candidimonas bauzanensis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium 70-9	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): 38.052509
  • Long. (^o): -121.76873
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000289	Metagenome / Metatranscriptome	1365	Y
F001667	Metagenome / Metatranscriptome	654	Y
F002543	Metagenome	550	Y
F002896	Metagenome / Metatranscriptome	522	N
F005922	Metagenome / Metatranscriptome	386	Y
F006898	Metagenome / Metatranscriptome	362	Y
F007623	Metagenome / Metatranscriptome	348	Y
F007651	Metagenome / Metatranscriptome	347	N
F010005	Metagenome / Metatranscriptome	310	Y
F010272	Metagenome / Metatranscriptome	306	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208655_1000018	All Organisms → cellular organisms → Archaea	5968
Ga0208655_1000072	Not Available	3659
Ga0208655_1000096	All Organisms → cellular organisms → Archaea	3470
Ga0208655_1000126	All Organisms → cellular organisms → Archaea	3221
Ga0208655_1000162	All Organisms → cellular organisms → Archaea	3078
Ga0208655_1000391	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	2446
Ga0208655_1001707	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	1515
Ga0208655_1001778	All Organisms → cellular organisms → Archaea	1492
Ga0208655_1002157	All Organisms → cellular organisms → Archaea	1391
Ga0208655_1003214	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Chloroflexi incertae sedis → SAR202 cluster → SAR202 cluster bacterium	1205

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208655_1000018	Ga0208655_100001810	F012471	MTVFNVSEKWSNGHNRCFRKFDPDDDRLEVRANGNTLCLIDGNGNCTITGDKRRIYCYYNNYNAILTIVLIPHFKSMKDNCSLKMRSRHNEQGQSCEGGAPLDPNKFGGYGFAINTKGWDAKREPTHNCHDQHKSGLIPTNLENDKAVRLRQTVKDESGKVHQIGEIDYMDGNGFHKVMDIFDSSPNPWMVDKNLYETKSYFWIRNNGSGYITVRDVSLEILS
Ga0208655_1000072	Ga0208655_10000727	F091749	MIKSDIKSNAQNWELEVTCKNKKYLEAVVKAILKYGMIDFEVENVECISNSDVWDGRYLVLMSCSWFSNLKAISNDLAKIENKLNN
Ga0208655_1000096	Ga0208655_10000961	F006898	VITTTTALLLFSIFFLPGAYSAEKFKGLTFTIEVPDTWAYTETPEPPIERILGVSSYTSVVLVPVQFAELLIEEKGDIEMGNGSAAIVFAKASDYSVKNAPLDLYVKYRMNEDDSLNVISQKATTIGNDKAVRIEGHENNNASNIRILEYLLLHNDEPYVIRYIASMDDFERNLPAFELMVKSFAFGTNATDSKQT
Ga0208655_1000126	Ga0208655_10001265	F002896	MDKMNEDTILHFYRILENSLLESDISKINEEDIDAWSQSFKKVVRESREKSGKGVFVPFLMWKLGEISPVEASKYLGNRKQDECRVSYDHNNVEYILWVMALMFMSWSVTNLKRKTQNGHCQNIDHPHGDTNPRLCKEGTIF
Ga0208655_1000162	Ga0208655_10001621	F017423	VTFFLSFTLFIPNVNSSFALQYSNYLSEKYQIGFQYPSDWTIKEKLNNLEEGTEIDVSNKKIGDGKIGIHYYDDLLEGFGSTNFEFAFSDFYKHRINDDLKFEYKTIQPPSLLEIDSHKTGSFHIMFTQKDEIDPISGKVQYWITFVGENGYMIEFLSIPENFDTPDNTEVRDHFISSINFLGVSNTTDTNGKISSVAMSN
Ga0208655_1000391	Ga0208655_10003914	F001667	MNSKYLVVVAAMAVMLIGATAFATDSVFAGGKKHYEKNQATSQTNACGNGFNPIDVFCQNAASQIQGDENIVTLLPTQSSTESEPVE
Ga0208655_1000818	Ga0208655_10008182	F091559	MNKTRTKPFIPIFKIVGGSILIFISLLNYVNIEGAILQTNPFWMPLEFDIGKGYFKANVFINGLKEDTGLIKVCVIPESTNHKLCHYMNATEEEGQIISPYVSVHAGIYIFRSSLVPADKNVNVCVSILEDQRTVCKTVTNTQKGTEEMIDINLDK
Ga0208655_1001707	Ga0208655_10017072	F057184	VANKYLKTLILIMIPSYPIMLLPPRVKTAMTRTITKLIVLSCLVSPLILNNEALAQNQSRSDVLDLDIRGVSAFVPENRNIYTITGEVFNNNTFPFNSVQVSATLYDDIGQVVGVGSGFTSPSGIQSGLKAPFKIDIFGTEIMGGIEAINNFTLQVAGDLQVQLFQ
Ga0208655_1001778	Ga0208655_10017781	F021640	LSPKFGFFKRKTFDYFQDKKSHSDSVQSVTDRRLLEIIEKQRKVFEEDLSKDVEPIRISVLDCLNRLRNGADELEEQDIKIENPKFESLINTSKKILITSIRKDSFIESSELKNYEDALKFKNNLELLINRFGQVGDSHNRILNEFMRKQINKLKNEFDNLSSLLKEANKVFSIKETEINKCDSCQKDLMLLKEKISERQYKQSRLLELSQEGQTIDKNIDASKREYEGFQKSKEFLEASNALKKINDKKNEIAIFEKSMINKVSNLSRPITKFS
Ga0208655_1002157	Ga0208655_10021572	F013352	MKYTLPGKLLMNSIEKYFPEYLAKNWHSASQFSGLVCLSIAIAGFLFSLMASTTYAQIEVTVDENVSTPISNNTLSEDAEPRPDILYSALNKDTIVGEVLNNFSYPIELVRITATVYDKNGIIVATGDKYVNDYLIKPGSRSGFDIFLDETLPSKSKYALTTSFEKSEDDKPEALQLSVGKNSKSSNTFRVLGEVMNQGKNDANAVKVSAIFYDEKHKVTDTDYVFTNPDIISPNKKAPFEFSLYVDNPEKIKSMAFNVQSDEYSLITDNGQNNTISQQ
Ga0208655_1003214	Ga0208655_10032142	F093463	MSQVEPRGAVHWIDHYVVGTNDMVAWADWAVNATGITRRPLIGLTTAARKRNIKITCFLWWEG
Ga0208655_1003308	Ga0208655_10033081	F022369	MHKHKLIELQKIIEEKIGSLKEEVEIGTNVKLNPLYIADRRDEIEFLQWTIRIIQSILNRDNDERQQPGANKKRLEMMQTIEFENALQQRVQELNLKLKESNNLRESDILINEIDTLESILGRLSDLKYGDKTRAIEIAEADNNFQHANRLRKQLIKIQDMESEINAQCSYTNSRLTS
Ga0208655_1003593	Ga0208655_10035933	F090038	TAFLSKKLSQELLNLDIDEGIRIESNKNIKCKMYINKRTSGYFVLEIEDTNSTNIKEFRFYRDIKPIHRLIDKIFGKQYSITIY
Ga0208655_1004022	Ga0208655_10040222	F033343	MDLVEASMKEEGGQHVHGWENITLVEEKPVAVLENKLVSV
Ga0208655_1005031	Ga0208655_10050312	F002543	MTQLEKAQKVQLTSLLGKFKQLQKQLENIHKKTGYEDLAHGVLALQIAEHAVEETLEHTGLGGEIQHKRNPRAHRQAKQWHKIVKGLRVQGGKFLKTHPSEDLETALKALEIAEGSLEEVAERYE
Ga0208655_1006026	Ga0208655_10060261	F081902	MKFLPALCSFPFLLILQIVPIRPSFATTIVVLKTQSEIVAGADSMGLYLTGNRRMSNSFCKIHQVHDFFIANAGFYDTRAGQRLNIQELVTRVARKSDPLTVAVNRSSGAIAGALSQAISDAREDDGLYNVLVGGNVVTFFFGFEDGKPAAYANRFSVMTQPEHSKVPLIDGTYESCGPQCVPANGNPYLMHTRSEAMDEFRSKNLGLLRDDPVAFVRSMIFSDMAANKDRSGPPVDILQIDRNGPKWIEKKPNCP
Ga0208655_1006460	Ga0208655_10064602	F007651	MSNDLNELIARKDKLEGELHHELSSDYNELMKNLSESFRDMHENSVQYYKQKANEELDKMEKNIQSGNKLSAINGKLLADTYISFATTI
Ga0208655_1007016	Ga0208655_10070162	F014366	MQKKFKHSSRQRPVLYLICILLLVITGCQRKDEVVAGVDIPIPEKMTRNPDKVFDPIPGFQDGQVSYQGKVTPKEIFTFYQEVMAAKGWQPTARFADQKDRIAYTKGNRLVLVWYNENPDGTTVL
Ga0208655_1007213	Ga0208655_10072132	F024052	MGQTDWAKLYAAMDKRIDLKYRQLPEGEQVGKRPEKEEKASESSRS
Ga0208655_1007232	Ga0208655_10072321	F022369	MRKHKLIGLRKIIEERIGSLTEEVEIATNVKLNPLYIADRRDEIEFLRWTETVIDSIMNRDNEHKQIQLGTTKMRLELADTVEFENILHSRIQELNLRLKESNNLRESDVLINEIDTLESILGRLADLKYGDKARVIEIAEANNNYQQTNRLRKQL
Ga0208655_1007413	Ga0208655_10074131	F001667	MAVILIGATAFATDSAFADGKKKYEKNQAISQANACGNGELPLNVGCQNVDSQIQGDENVVALAADQAFPEEET
Ga0208655_1008760	Ga0208655_10087602	F016471	MFKAGLLKRVKASTVAIGLLNKDTKDVIGTFGTGFFIGGKYIVSSAHVFSQCLNYNSLYKEKNNSTEGIYSAFRVIRRGQKLDLDTYRINESIRLPPVKEAAGFNGSIDLDIGLGKLDRNSDSFLPIKEPGGLELYQDIAMCGYPSGRLSL
Ga0208655_1009094	Ga0208655_10090941	F016054	LLVTALMVQSLLENEKKPDLSELSVAEGIKEMLALRGFTKEKILNSTVSNLADTPQIDYYVA
Ga0208655_1011848	Ga0208655_10118482	F005922	MSTNREFQRTDDEIVSLLSQWLMGSLGNDELRKRIEEIGTEELAPGQRTAVEELLVKLGNAFPGERGDLEMVVRETIESLAYGE
Ga0208655_1013052	Ga0208655_10130521	F012381	AGKSKVLMRLDKVTARWISQIQYVSEEGIRRQDDDIRKVMKGLFAAIRYMTEQTAEAAGIISKKIGWSPEAVLAAHKISGGLMSHDGTVSVEALRSMQDTLLEHGVIKKRLPLEEHVARGFTPVKLG
Ga0208655_1013757	Ga0208655_10137571	F007623	LSRHRFETYLDKVFDFSRRVGALPEGRQSPRHPWQKVFDAVFLGA
Ga0208655_1014328	Ga0208655_10143281	F022219	EKGLPNGSRGRMNESKSWKILQIIPAQGGWKAVHCQELENKQIAISNRCVICWALVESIGESAVVGTQVRGIEQESNNLTVVEDLINMDEVGEDGMDRNQYFLGYNDPETHKESEYWIKLANQRLRTEREKRLARKMGQAAFRAAS
Ga0208655_1015185	Ga0208655_10151851	F071473	DGQGGLPSYKDLENAVLDGTAAIHCLTHERDHLRSRVELQERELVSLRATNDDLRRQLMTIGESYMKFAASCISQLETISLAMQGVENRMSAPTDRRAAL
Ga0208655_1017042	Ga0208655_10170422	F083861	MHKHKLIELQKIIEERIGSLTEEVEIATNVKLNPLYIADRKDEIEFLRWTAAVISSILSRDINQKQLQLGTTKIRLELADTVEFENILQSRIQELNLKLKESNNLRESDILINEIDTLSYXD
Ga0208655_1017450	Ga0208655_10174501	F010005	RQLEKYTGGFTSPILSLMKRTLRLSDSGVFKPERQPGRYGRRPGCNRAGYFYGDRPSGSNWNFNRLEDFAESVAMYIGWEKDNELSQHAHDRIVRYQLQNGEKDPFHVVDNWMDYAKCFYPENGDYARTRRWQFVENLASGRTNIL
Ga0208655_1018167	Ga0208655_10181671	F039029	MPAWTAGIQVRRDASGDIHVNLGSGHPCRNDDIEEYSP
Ga0208655_1018637	Ga0208655_10186371	F010272	MNPERKLILIAIGAFVTLSLFVFPSTNMIAYSQSENKTQGKEQAQEKLFELAQKFNKILKDSNVNLTLPQNGDLSAKLQELKDSGAFKELSEKFSQAVQELGQGNKTEELKEQAGADLGKLIQKLQDLRNN
Ga0208655_1020727	Ga0208655_10207271	F001667	NSDKQYFRFALRMNVKSMFIVAVMTVMLVSATALATEDAFAGKKKHKEYNQATSQANACGNGFLPENVFCQNIGSQVQGDENAVALDGFQSAD
Ga0208655_1021267	Ga0208655_10212671	F068551	MQLGVILIFIFVILGIVFFIVFGIGYFKTENPQNENLQNRSTAVLPNPDSIPPECKYTPNDLLCQFQLEKQKMKLSQNE
Ga0208655_1023795	Ga0208655_10237951	F022832	YMTGYNSSSIARLAVQRGEAHYHDETLPSFRAAVEPQMVKTGMVTPLYYTDLVSFDGDVIVSADVPELMPFTHYYRQIFGKNPSGIKYEALKAANMSSTNMTRMIVLPPGAPADAIAGLRQGITGLSKDSDFNAEAQKAMRFQPRFEIGEQGERTFQRAAQISPDVFNFLRKYIEDA
Ga0208655_1023855	Ga0208655_10238551	F012443	MYVSRLTFHTLPGKTQEVEEKLRTLLGWVENAGGLGPRVMRTHYGSLGAPDLVFEQEVGDPTTLESQIKEVTGNKDFQAWAREISGLLQQSSKRKLYDITSSDLHTKSARS
Ga0208655_1024038	Ga0208655_10240381	F000289	NLVTSVKMPYPENLSRNRAKTERVWLERDGATTGCIRLEDRRWCYEHIPPIGNRAEMLRIRNEPSRGVAIGEMFYYIVDFDLDGLIDVGSTTRIDAISRKQPRTPIAEVIEFFHRSTKRGDEHVGKFQKMYDEGIQVALKHFGE
Ga0208655_1024555	Ga0208655_10245552	F019205	MFETKKTSITHQVADAVDLAIDFATLGEYGLEPVGSPTRSCEGRSRTRASRSTGSWASAIDRFATQA
Ga0208655_1024610	Ga0208655_10246101	F085871	RLASDPPPTDDHDKVQPTVRDALIGLAIGLLLIYAGTRISYWILRWLVIGVGLVFVGVMSAFVISVIWTKVSPRAHLIMSRARGHVRRDPQLGTLIRNVEAEAWETEFRVRDRTVEILIDGKEEPDPALLARARELVADFDNFERRLNDYLAQTAKDWASETPELAADIGALRL
Ga0208655_1026399	Ga0208655_10263992	F054952	MKIMVVMGEYPPEEQERRRAAVLKCASPGTDIGFSVIKATFFVRANAQINAL
Ga0208655_1026466	Ga0208655_10264661	F101825	SGGKPVPGAGNKRPAEFADYCKVGPTRVPFVTFPEAELAKAKRRAAHWMKLNEKYRPLVEAARSRSAA
Ga0208655_1027250	Ga0208655_10272502	F046618	YDELQTQLQGISTEEVELLQSQIKSTLEQMVGISKSLAVIKTLKMTLNGHDEFADLTKKGHVGKDGRRSLEDR
Ga0208655_1027459	Ga0208655_10274592	F040284	VALFFHSDDVDQLIPFKEAVQITEFALRDLVSPKGVNAPRKRLNLHRQFAEATFDTVLNIYAGGSASYGAIGAQV