3300026061: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushSE_TuleB_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026061
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116115 | Ga0208541
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushSE_TuleB_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 70587126
• Sequencing Scaffolds: 37
• Novel Protein Genes: 40
• Associated Families: 39

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria	7
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	4
Not Available	12
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Nevskiales → Steroidobacteraceae → Steroidobacter → Steroidobacter denitrificans	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	2

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: Fairfield, San Francisco Bay, California
• Coordinates
  • Lat. (^o): 38.224476
  • Long. (^o): -122.019341
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F002104	Metagenome / Metatranscriptome	593	Y
F007876	Metagenome / Metatranscriptome	343	Y
F007982	Metagenome / Metatranscriptome	341	Y
F009010	Metagenome / Metatranscriptome	324	Y
F010406	Metagenome	304	Y
F010927	Metagenome / Metatranscriptome	297	Y
F018950	Metagenome / Metatranscriptome	232	Y
F020200	Metagenome	225	Y
F021303	Metagenome / Metatranscriptome	219	Y
F021565	Metagenome / Metatranscriptome	218	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208541_1000252	All Organisms → cellular organisms → Bacteria → Proteobacteria	2894
Ga0208541_1000286	All Organisms → cellular organisms → Bacteria	2796
Ga0208541_1001126	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	1907
Ga0208541_1001567	Not Available	1715
Ga0208541_1001686	All Organisms → cellular organisms → Bacteria → Proteobacteria	1680
Ga0208541_1001818	Not Available	1637
Ga0208541_1003252	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	1355
Ga0208541_1003782	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium	1284
Ga0208541_1004342	Not Available	1221
Ga0208541_1004554	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1200

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208541_1000252	Ga0208541_10002521	F010927	KARLVIEQGRDSILVMRVVVAQNETVALAVGGRLESTTGFLRIRERKDERGRNENKAVGSIVFVPAVGDGDERSPANFQINISMSAAKFEALLKVAISGRLPSKFFVNAGERASARETRGMGYVIRAGVRTKFWDNKRYRTLPVTNFSVILPITVPETPESPAFEEDRAIAESIASNDQVAELADEFAVFQGETKNALTAVVSVVAVIGVLLLFINLVLIIK
Ga0208541_1000286	Ga0208541_10002861	F100542	MRVDYAFAKGTLFEGLVATFRYAWTHQDGTLQNGHQLRAYLNYEVRF
Ga0208541_1001126	Ga0208541_10011262	F085771	YAGALELSVARVPVALASAGPGAMQWSTEQEYIYALLIQQLNMGSLSPVEIDWASAQMRAWGRKLEFQAIPRSTEGFYVDLASKRGLVRRTGGEAGPTMHFLDTTPLADQLERAIHALRQADIGEPGAAAALSQQRIGVLEKVRPVVAPNLYGDLRRAPRTPVTMAAKVRIGLARICAELSPKAVVEPANDPDAGNEQIEVYAVADRPRNRPHVADEHDSLSASIAPVADPAWQIKDRSVAGLRISAAGGIGQSLVLGALVAVRQSDAIDWVLGAVRRLNKVSNDEVEAGVSIIADRIVPITVHAKRPTQDDLGMVVNGVDVSVMGTRFDALYLPPPSRPERPLAVKTLIVPTSEYADGRNVILTTGHSVYTIALRHLVEQRAEWSWAAFQIIDKKPTDI
Ga0208541_1001567	Ga0208541_10015674	F058543	KVEFFQTIESLLGIVKSQCNDIEIRVKDDNSLMIEIIFDGKDQMERIFYNNEFTIIKGTVKSLCKDVIIKVNDSIVSHN
Ga0208541_1001686	Ga0208541_10016862	F032671	MPAHAVPLTAEELTKLCAEADDAAHCGRLVEELQLQRLPNLAVRDRSALRVSLYPSGTTTFTDTEAIDGGRSYSLWDFMSEINAVVLYVTEGDDATFTLLQRTTGRKVELPSDPKLSPDRARLVTADFCASRCSNELALWRVTRDGVRKESTWRPRANWSDVVATWKDAETVVVEYSVAGTQARSRISRRLADAEWVRAQAP
Ga0208541_1001818	Ga0208541_10018181	F047968	MGTEKVDRHKAKMDNMIKDEVTRMFEKVLDYAEVAVPNGEQYRKLRSKILRIGNNCIRNIQKDVEKHFDVRYKATSETIVEVIQR
Ga0208541_1003252	Ga0208541_10032521	F067873	SPMALNLSLSPVDLNPASPPETRPAQVAAWLDQALTRHAIEAARVVGDALAATNAVAVGGTRRLELADKYWHTAEILWPRLELYFASATHPLRGEPLEAAKATLFLAQELFVAYKRVLEHEANKRVLFGGNRALGALVHRCMQCLWRILVNSYVAYAPVLPRTWLDAHRIYAFAHERDVHQRAIAGDDPAATPERVYVQALLLALANPYGFLQGQFDTVIRYVQEHSHWVTLTDVAPVHRMAKAVAVVPVGHDFPPFSASKGGTIEGSKFYLLTFDLAFQIQEQVHKLEAGGEFPAGIGRDPASRRRYLTLLKRLLRQWAIPPARQFNRLPSQARVVMCTELLGVWQYSRGRHSGVTVSTKAMPPLMHCQVINHTPAGYALRQMDAQPPPLRIGELLALRSEGRAGPQVAIVRWFRNTMRGTGLEFGCEVLSDHPEAAAAALETAPEGKRV
Ga0208541_1003782	Ga0208541_10037822	F020200	MCWVCERLEHLITSWNEEQEFQEQTSSDDYHRGLSKGFSECVKALSEAVASMRLKGICEKFPEYERALNDKQRLDILEDLLKLRDEDTNQE
Ga0208541_1004342	Ga0208541_10043421	F045255	MLWACLLLPSLPLDVFARAASPADAAKPFAVGSGGRTPR
Ga0208541_1004554	Ga0208541_10045542	F002104	MKSKNVSSIAANQSEAQLLERLRQHPEMMERVQSILDIAYNTEGPLKSADQVEELLIQEMRRLGNTSMHQWATQAEQRVSRELKAQDGTVRSRKKKR
Ga0208541_1004687	Ga0208541_10046872	F081923	MYRRSSIFLLIIAAALAAACTMANIGSVRTSPEVTRQFESLQIHPNYRYWYLNQENNPFGVIGLDREYEFDGGPVWRAVEPDSPTFKKVVGLVASFPMPSSMTTGYTIFEHQGRPIGVWYSSIGLGVTIDPATKTVSPATTTPWKSPF
Ga0208541_1004927	Ga0208541_10049272	F021303	MKERPVSTDVLSLRANVLNHSSEFVELVYRDAPAEYRRLMTLERFRRELGQQTRFNHGKLYAYAEYVVFRNEFRERFPDASPAACINAFSSLFLKNDISITNLVEFVEGPDHRGQLLLKRRPEPG
Ga0208541_1007810	Ga0208541_10078101	F087857	VPLLVIAFVAIQIVPPAHAEPITLTIMAIAGITTVMTAACTDMAVHGEHIVQANSPNEKPAEVFASERSADSSNNHDVQVTTAR
Ga0208541_1009404	Ga0208541_10094043	F051241	PRQQYWDRLYQMLEEEAEKRGRTPPPAPLVYALDHEPTENDKIERLQEQVAWADRNQLLHRVQMFFDAMPASAWNHLER
Ga0208541_1011503	Ga0208541_10115032	F021565	MAIKYYAHFLVEEPDPRGLQEYRGVVELDGQPRRTGRELREAAHIIARNMGRQLRDVKVLQWARLH
Ga0208541_1011731	Ga0208541_10117312	F056991	MKTRLVIGIAMVCLTAGMWALPACGDESSADHQKNYYLKCIKAEIDNYSCKVAFTTSRSKNLQAYGESAARRAAFLSQNRDALVQEMFAQKVSMRPHAVQQYLGQRFTQENQVQLALERP
Ga0208541_1012228	Ga0208541_10122281	F007876	MATGVNLSNLASALDGADFVLFDGVVFAKEYTRVPDERTVADDVVLEATHGDTEITFTRQEMEGAEHLGEGVYRLRSGAELRFLSTATIH
Ga0208541_1013728	Ga0208541_10137281	F085853	MECRLRQYMEARAAQYQKILANEIAAPLEKLNIKEFDQWKAELQAGMKKYAERFRSEMTTNPSFWRNFNQKAPIYQSMIEGVHRFWSDHQFEEIGRRMEQAAAASQAEVEQLNQKKEQIQKGKEGLNNALKNIKTRFGKLGLEAEDAILLAPIAFAALFLFASLNLCQNIQLRKSFHRLFQARDPQKVAITDSEIALAMPLWVDPLAPPIQRRLKLAVMMIPAIASVLALAVVFYCWTIPDA
Ga0208541_1014622	Ga0208541_10146222	F105751	PPGELEAGCLRRAWTRFQTRVSTLKEAFGLLIASVTSGAADLWKQMRLAKETLAGILGFLAQTRKVSLLGDYRCLRLPT
Ga0208541_1016388	Ga0208541_10163881	F073723	LERLLLPLVRRFVALWVRPSILPDDLGGSFESGRPVVYVLEKRSVVDVA
Ga0208541_1016388	Ga0208541_10163882	F007982	MRPVASWMLSAVVMALLVACTERAPQDKEEARAKGRDTDETVFDDMIQTQDRARAVEDLTLGRKAEMDAAIEQSEGDAATDEP
Ga0208541_1019009	Ga0208541_10190091	F068280	MNNGSFASWIVDRPGPAVLVTGLLGLLPLLGLGFAFFRP
Ga0208541_1019364	Ga0208541_10193641	F046145	VCLNFYWKLFEWITARYEKTISDELECDHMALIPKSFLKAKTDFFIMSRYLRVLSEK
Ga0208541_1019803	Ga0208541_10198031	F009010	MPEVPKFLYLLVDNPLLIALPIVGFAALALWSRSNTAAVAAVAWNLYLIYELGMKAEEFCSGLDCMKRTPLYGVYPLLALVSLLALVQAYVHIRDDRRSERFR
Ga0208541_1020029	Ga0208541_10200291	F086748	AGQDTDAARQIGNWFRDTGFPGFFRVGVPDAKILREAPGQIAGQPAWIAVAYLPNSSPLGLNVRNSYEVIRNDSWRGLAVVARGKRYYVLQTELRIEKLAPPDFRFDHEAADWNAFVPELDALYHRIEFLKP
Ga0208541_1023132	Ga0208541_10231321	F073721	GEPGVALGFASDMLRIGGSTTPLADYTVGALISVRHAAGVNHWAFGIASEAWARPGARSLLVGVEAAVINEEPDNLYPKIASNAVIKNRSDGAPQVDVPMNANSIAYWVSAQPGTGFERGLAFDRHSLLAVGKRSAAIDLSDLPDEAIAQVDLIRIRKDVALRYDPSTRQLVLHVDPPAAAAP
Ga0208541_1024182	Ga0208541_10241821	F104669	TLARKGGLWIVVGTATGTAVGVVFGVASVGLALGFAVGILGGCLARR
Ga0208541_1026611	Ga0208541_10266112	F036723	WRPDRVHDQVRTIDFDDLPTHFDPYIKGMVRGRTVVRIAPDSHP
Ga0208541_1026749	Ga0208541_10267491	F028592	QWCQPLRLTLEPSSASSFYIDLGGREGLKRRAAAPLEGKVLFLDTRPLHAVLMQNIVVLEQNLRMQPLSERAPKLTEQLALLTKVAAQADPEFRPFARRGERVAAAGIVDAIVGFNSIAGYLRDAERAPLRHAESDHGYGDTMELAVFGRLRNEEDRLAEQARRRLAAFSARGGPWQVKDVSQTGFRLIAST
Ga0208541_1028111	Ga0208541_10281111	F045785	MLEPALTWIRSLKDPFRNANAAAQWIAALPASDALALQKEALELVAKFPGSRHVAGYAQAEALLRIDARFEPVLAQLAQQYATNYQKSTDVETRLWHAVFDLVKAFVAAYGAVLRAGYPRADQKRWHALLPWILVRLVHYKGIDGKFRLFRYGTWVPAQW
Ga0208541_1028115	Ga0208541_10281152	F021565	MAIKYYAHFLVDEPDPRGLQEYRGVVELDAQPRRGGRELREAAHIIARNMGRQLRDVKVLQWARLH
Ga0208541_1028255	Ga0208541_10282552	F102756	LTPPASPAPPLHRLHDEEVERLLASGEHRRELIALFGEAGYRELSGLARRAAAVRRRGVAVYVLPGLMGSRIGARGRLVDDV
Ga0208541_1029029	Ga0208541_10290291	F061020	FAAQASAGAVTDLYRSGAYGLPWNATKDAIQAKYPGGKWAQNDKGQEQYCAASKQTLLKLPAPHQSRELCFVMGSDGTLASATAVMDASLPSLLAIVNRCRTTFGDFDAVVRDQQAIQSRSTAMLWTKDKQFVVRIVSENDTDGRPLMVSYTVADEPGMYTDGAAKVSNIPGSR
Ga0208541_1029225	Ga0208541_10292251	F056368	MNSFRNRLLVLIIGLIAVTQTVTLVAVLESTRRSVEARAAEQLTA
Ga0208541_1029717	Ga0208541_10297171	F018950	AALLGTPWTAVAAVSGSFLQLRVEYTATSLIGADARAMPGRLWRTRSALRHEGKRQGRSLTVIARLDRNLCWLVMADSRFTIETDLSAFDLPLDVLNGGGDMRQIREGRERANGLDTMRIRVERNAGSGSRFTGHVWATDQGVIARLSGEGESRGRRGRTLMNFRDVRIGPLEPGLFEAPRGVQ
Ga0208541_1031306	Ga0208541_10313061	F042409	VAKLPFPIPPRPKLILMLCALIPLLFFSCGGGKAAQRNSSNEWLSSNIGIATLDDLIPTMGPPQQSIDTPEGIWHTWRKVNFGTVSGGVSMGFLGMGMTTPAETGEELNCLFDRNTGRLRNYNYREW
Ga0208541_1031400	Ga0208541_10314001	F048318	MATVENVRLDITASTTKPGYSKIAYSYELHPSEMDCAWQREYTVCVDFWGEDLIDDDLLAWGKDEHTVKFDDSGPCEPKKVERVFEVETKILDEDLFGDDEVYLIVEASSGLGSDEAGEDPVVGRSNTVIGDF
Ga0208541_1031663	Ga0208541_10316631	F010406	MTPLRTIVFLLLLANLTFLGYTRLDSAGGGEAARLAQQVQPDKIKLLTPQQVAALGPGKVAALA
Ga0208541_1032488	Ga0208541_10324881	F027335	LEENMIVACEINHYPVKLEHLLRVTKDGPEILSEYPVDPELVPA
Ga0208541_1033764	Ga0208541_10337641	F103344	TTPAIMPFRQRGSILGSILGILVCGVGGGFAAWASVTALGVGGVLGAILAAVIGMVVATALWTGGTTLLRALGWVR