3300025799: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - Muzzi_CordB_D2 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025799
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101360 | Ga0210122
• Sample Name: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - Muzzi_CordB_D2 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 237114107
• Sequencing Scaffolds: 40
• Novel Protein Genes: 42
• Associated Families: 34

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae	2
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	2
Not Available	12
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Methyloceanibacter → Methyloceanibacter caenitepidi	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria	8
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium 70-9	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Betaproteobacteria incertae sedis → Candidatus Accumulibacter → Candidatus Accumulibacter phosphatis	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	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): 37.928627
  • Long. (^o): -122.504829
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F003627	Metagenome / Metatranscriptome	476	Y
F004052	Metagenome / Metatranscriptome	455	Y
F004928	Metagenome / Metatranscriptome	418	Y
F005564	Metagenome / Metatranscriptome	396	Y
F008223	Metagenome / Metatranscriptome	337	Y
F016971	Metagenome / Metatranscriptome	243	Y
F018371	Metagenome / Metatranscriptome	235	Y
F019205	Metagenome / Metatranscriptome	231	Y
F020359	Metagenome / Metatranscriptome	224	Y
F025809	Metagenome	200	Y
F027211	Metagenome / Metatranscriptome	195	Y
F029006	Metagenome	189	Y
F033045	Metagenome / Metatranscriptome	178	Y
F035820	Metagenome / Metatranscriptome	171	Y
F042887	Metagenome / Metatranscriptome	157	Y
F042909	Metagenome	157	Y
F048676	Metagenome / Metatranscriptome	148	Y
F048812	Metagenome / Metatranscriptome	147	Y
F056282	Metagenome	137	Y
F064729	Metagenome	128	Y
F069741	Metagenome / Metatranscriptome	123	Y
F071270	Metagenome / Metatranscriptome	122	Y
F072365	Metagenome	121	Y
F074893	Metagenome / Metatranscriptome	119	Y
F078289	Metagenome / Metatranscriptome	116	N
F082775	Metagenome / Metatranscriptome	113	Y
F084253	Metagenome	112	Y
F085266	Metagenome / Metatranscriptome	111	Y
F090405	Metagenome / Metatranscriptome	108	Y
F098856	Metagenome	103	Y
F099325	Metagenome / Metatranscriptome	103	Y
F104552	Metagenome / Metatranscriptome	100	Y
F105195	Metagenome	100	Y
F105216	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210122_1004319	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	4330
Ga0210122_1004375	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae	4299
Ga0210122_1005352	All Organisms → cellular organisms → Bacteria → Proteobacteria	3790
Ga0210122_1006078	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	3503
Ga0210122_1006289	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	3421
Ga0210122_1007959	Not Available	2951
Ga0210122_1009057	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Methyloceanibacter → Methyloceanibacter caenitepidi	2730
Ga0210122_1010120	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae	2549
Ga0210122_1011032	All Organisms → cellular organisms → Bacteria → Proteobacteria	2410
Ga0210122_1012631	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	2215
Ga0210122_1020052	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1671
Ga0210122_1023688	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1511
Ga0210122_1027618	All Organisms → cellular organisms → Bacteria	1376
Ga0210122_1031502	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1269
Ga0210122_1032839	Not Available	1238
Ga0210122_1033678	All Organisms → cellular organisms → Bacteria	1221
Ga0210122_1035755	Not Available	1176
Ga0210122_1035916	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1173
Ga0210122_1038091	Not Available	1132
Ga0210122_1038116	Not Available	1132
Ga0210122_1038273	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1129
Ga0210122_1047470	All Organisms → cellular organisms → Bacteria	992
Ga0210122_1054420	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium 70-9	917
Ga0210122_1058111	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	883
Ga0210122_1059587	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Betaproteobacteria incertae sedis → Candidatus Accumulibacter → Candidatus Accumulibacter phosphatis	869
Ga0210122_1060669	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Betaproteobacteria incertae sedis → Candidatus Accumulibacter → Candidatus Accumulibacter phosphatis	860
Ga0210122_1074030	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	765
Ga0210122_1074319	All Organisms → cellular organisms → Bacteria	763
Ga0210122_1080540	Not Available	728
Ga0210122_1082387	All Organisms → cellular organisms → Bacteria	718
Ga0210122_1089304	All Organisms → cellular organisms → Bacteria	684
Ga0210122_1093910	All Organisms → cellular organisms → Bacteria	664
Ga0210122_1100569	Not Available	637
Ga0210122_1112294	Not Available	595
Ga0210122_1113192	Not Available	592
Ga0210122_1114631	Not Available	587
Ga0210122_1116534	Not Available	581
Ga0210122_1116691	All Organisms → cellular organisms → Bacteria	581
Ga0210122_1121961	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	565
Ga0210122_1129927	Not Available	543

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210122_1004319	Ga0210122_10043193	F004928	MEQAIHNTENESAHTVEIVVHISDDLVEQQRRDLVAALNSNAGIVAAEFCPLRYHLMLVRYDRGTYSSQDVLNRVNSHNVSARLIGPI
Ga0210122_1004375	Ga0210122_10043751	F084253	VLIKAAQGFSVRRTSVRRSRKPAENAEQDKNGHIWMDTK
Ga0210122_1005352	Ga0210122_10053524	F008223	MNLFKRLFGKRPTPPAPGGQAAAVLHRFTTATIVGVDREDLGRYPAKQRKVMAFHYGAIRCLAREFDLDETETLAVFVRFVNTYFNMPVSETGSISERLQGFQENPEERRYLEAGEAVFRRWHEQGERRAPLELGEMLQV
Ga0210122_1006078	Ga0210122_10060783	F099325	MKRRPRRLRWGTDMRKRMRDALFRFWRWSQKSPAERRAAKARARFWVEMREGQLEAEAHSRP
Ga0210122_1006289	Ga0210122_10062892	F016971	MNQVAQHLLNEEKRTVEVVVHISKDLGDEQRNLVVSALEKTDGIIGAEFCPSRNHLVLAKYDKDIFSSQDVLEHFNSMNLEARLIGPI
Ga0210122_1007959	Ga0210122_10079591	F004052	MRIFTATFQLALVTLLFSCDQQHSASEIDPVLGLECYDSHRATLPPGTQYEGIEKLADNRLTIKIMNGVDVVTLDCKLKTDGTLQRIEN
Ga0210122_1009057	Ga0210122_10090575	F003627	VDRESSRQDIRAGLVAGGFAAAVFGLCFVAAMLYIAS
Ga0210122_1010120	Ga0210122_10101204	F048676	MLFRYSRLCGTASNTVDAVKLEIPQGFKLLKFKMSEYLKNIVKLTISK
Ga0210122_1011032	Ga0210122_10110322	F004928	MVQALHSKETEPEHTIEIVVHIAENLEEQQRGNLVASLGNNDGIVAAEFCPLRYHLMLVRYDRDLYSSQDVLAKVNSQNVNARLIGPV
Ga0210122_1012631	Ga0210122_10126314	F074893	MVSSGLQAIANNGALIIRIKGPMDLLLTSALRDFCHGTGDVYRRYIIDLRDVSVVRDSGLALLLMLKRLASRTGATLHVTNGNTDLMQRCLRLGIKPA
Ga0210122_1020052	Ga0210122_10200522	F069741	MENIFFDVDQFSRLGKIEQARRLEEAERRIDEVQRAAADDPDSMNWVDQQRQYLVDMQHLIFEC
Ga0210122_1023688	Ga0210122_10236882	F072365	MGEYQKECQECGWRGPAAELDETDNDSSGQTQIFCPDCGGSDIQDLNPAES
Ga0210122_1027618	Ga0210122_10276181	F084253	VLIKAAQGFSVRRTSVRRSRKPAENAEQDKNGHLWMDTN
Ga0210122_1031502	Ga0210122_10315022	F078289	MKKTVIILVTLFIVVPLYGFNSLVRHEDIPKMRELGISQEVIQYFISNQTSSVSSEDVINMKQSGLNNDAILSAIKSDLYRPEHTSTSMKEAELIAKLKESGMSDEAVLQFIQTVKSTRRVDSYGNVTKQYTNESHRTQYPTTGATFPKLDNYGYDPSNGRFLFFITPQNQQ
Ga0210122_1032839	Ga0210122_10328391	F005564	MNKIFIALMVIFLLGDPGMDTIAWLGDMKNYVIAAAITLLSMPFIVSQLDG
Ga0210122_1033678	Ga0210122_10336782	F020359	MSARKKAETKTPEEFWSKVLAAPKVKRILEKRGFDAEAFRRDYEADTSRGPRAPKRPSKQEMDAVEAFQRTGDFDALKESLGTRSTAVANTALRRVLQFKALGGVKTVRRRSGAVE
Ga0210122_1035755	Ga0210122_10357551	F033045	MKTSELELPQHLYTDETSSHCGAMTRLIAPDKLISWAEEGRGDAIARFCHTVYERKLASIDAWESDRILQLEDEWMVAGNDEDMSGCKYVNVKHYHTTREDVAREAELKRASVKERMAEHQTAIEDLVKEAREFISAYVAQQDEGDMLAYLLAIIVIVAAGYAIFN
Ga0210122_1035916	Ga0210122_10359162	F033045	VTINHPGHYMKTSELELPQHLYTEETSPCGAMTKLIVPDKLVSWAEEGRGDAIASLCYTVYERKLASISVWESDRILQLEDEWMVAGNDEDISGRKYVNVKHYHTTREDVVREAELKRARVKEQMTEHQTAIEELVQEARVIISNYVAQQDEGDMLPYLFGIVVIAAAGYALFS
Ga0210122_1038091	Ga0210122_10380911	F105216	DKAPEPWKAAEMNRLSEQFGHIAEAYAVVDTCIPMIDADKDAKRRVISKIGVRHYSKLSQLNTEAELAKFIAYNRESGGTDEQAATLERIYRESHRAATQLLTSVDNCADTVSDYANTILNTKVQPAP
Ga0210122_1038116	Ga0210122_10381162	F042887	MSEGVDSIPNPWRIQVRGHPARRDSSEWRNAIGAAVEAAYPQAPFTSPHLKAARFTVEVTFWMTPLDLARPAVDLDNFVKPVLDTLFTSQNVRRLTGVLLPDVNDTRVFRLLIEKAEVDSPEDQGADITISWDPVTTPGLSAP
Ga0210122_1038273	Ga0210122_10382732	F090405	MKSALAFVFAIGLLVPGIAASDPSDCGRLMYQITHFEDMVGRAEALGRDDWAEKTQRHVDLLETRLADRCPSFSARDEQQEAARQMALLLKMAATAAAKFFTMGMY
Ga0210122_1047470	Ga0210122_10474702	F019205	MFDSRKSFSHKVADAADLVIDFATLGEYGLEPVEQPTRACEGRSRIGTPRSTGAWSAAIARFATQA
Ga0210122_1054420	Ga0210122_10544202	F027211	MVRTYWLVPVFYEASGNLDLRPFARTDQIEACRPRAMCNRL
Ga0210122_1058111	Ga0210122_10581111	F105195	MAALLVWSLMDLQPPRIITSDMHVIDLLETDPSTWVNQISEENKRRVIAEVQRWQTAVESGADATEAYEYAVGGIGVDFQAWLVKEKESCSG
Ga0210122_1059587	Ga0210122_10595871	F104552	MVICKASTHFLSRIACSQVWALLLLGLLIPAQAAEALIPDTLPQAQAALERLEQQLASARTATAQELKSLKKEIATVRSSAQDCVQQAEPEIASLDSQLAILQPAPPKGTQAKTAEETQPAEQPQAPLSPAIARQLQDLQSRKASLEGRIVTCKLVLLGSNNLDSKVDDYLRSLQTRQLLARGPDLVSVVQANLDERARWLDFTRQLAVTSTGWDAIRPIHLAGAAAIGLLGFILGRIVPRRLRARAARMKVGEEEVSAGLVQA
Ga0210122_1060669	Ga0210122_10606691	F104552	AEAVKPDALPQAQATLERLEKQFATARTATAQELKTLRKEIATVRSSAQDCVQQAEPKIEILDSELAIFQPAKPRDTQAKTAKETQPAEQPEAPVSPAIARQLQDLQSRKASLEGRIAICKLLLLKSNYLESNVDDYLRSTQTRQLLVRGPTLASVLQANLDERKRWLDFTSQLTVTSTGWDAVRPIHLAGAAAVGLLGFILGSIVPRRLRVRAARMKVGEEEVSAGLVQAVMACGACYAPILLALGGIVAYLALIPRAGGDLPFVLTLMYGLLAYFAIAAGIRTL
Ga0210122_1074030	Ga0210122_10740302	F048676	CGTASDAIDAVKLESPQGFKLLKFKITEYLKNIIIVTISKI
Ga0210122_1074319	Ga0210122_10743191	F020359	TSRKTSVRPSSDLPAGSETGSETGSDMAVSKRTVGGKTSEEFWSKVLAAPKVKRVLEKRGFSPEAFQRDYEADTSRGPRVPKRPSRTQIDAVEAFQQSGDFEALKRALSTESSAVANSTLRRVVQFKALGGVKTVRRRSGT
Ga0210122_1080540	Ga0210122_10805402	F056282	VIDKPVQGVKTDARPHPAGKKGAKLSLKEVAERAWKARMSPRLRAWVSQELHKAGVSRGGRREKAQCILDAYRKKVPYLADPLMGEFMATPDQLLCLDEGGLCIIGGDCDEATITLVAAVMCIGIPGMVIGSSHRDPAEVPTHVFGAFKDDLGDWVMMDGTTSLPIGQTAPHAREWWVEPGEKAKELGEGDFVGMSGDGTL
Ga0210122_1082387	Ga0210122_10823871	F042909	MIELLNFIGRLNLGTFILIWTSAIFFVIFFSLLLIFVSQINKETIILSNKVKILIEALSEKTSTLGDNDS
Ga0210122_1089304	Ga0210122_10893042	F035820	MPDVTQPPLHTLPLDELLAKLRELTNVQVVRDEASPTGYKVEIGPFPGWQDTPTWFAPAAEASTE
Ga0210122_1089842	Ga0210122_10898421	F048812	LRRHRFESYLDKIFDWTPSVAAMAEGRQNPSHPWPKVFDAVFLGSACQFGPVHRIEAECKAGVLEKRIGRLSEDTIGYALQRQAPE
Ga0210122_1093910	Ga0210122_10939101	F085266	RARVDEEDFHGTVGLGLRASLVRTWGNPIGTEPGLTYLGPEVDLSVKKVDVGIGVLWRVGGQRGPSALFSWGVGFRL
Ga0210122_1100569	Ga0210122_11005691	F048676	SDAVDAVKLEIPQGFKLLQFKMSECLKNIVKLTISKI
Ga0210122_1112294	Ga0210122_11122942	F082775	MSEPDILYPAIFVFSMLLIGLLLTMWEFSRLHKRQQQKVENDKRFTGLDSRVYRENVRNVSHF
Ga0210122_1113192	Ga0210122_11131921	F008223	ELGKILDRFTTATIMGIDREDLGRYPAKQYKVMAFHFGAIQYLADQYELDETRTLGVFVAFIDKYFNMPISETGSISERLQGFLENEEERAYLDAGLDVFRRWHEHNERRAPLELGEMLKSK
Ga0210122_1114631	Ga0210122_11146312	F018371	MDYSNIIQPKRLTNMQEMEVHVNGPDGANRLFMYSGMAEVELCGGLPHPRWSLEVVCFDIGRLYDVENEAVINILANAALAGNRTDGVASFAGWQIFGAAGELDHEDCRVRMNIAAGARDTQAFLEQIAFHVNV
Ga0210122_1116534	Ga0210122_11165341	F029006	ATMNKIIITLMAIYFVGDPHLQYLAWLGDLKLYIVAAAIALVSMPWIAEQLDG
Ga0210122_1116691	Ga0210122_11166911	F071270	MADAYSIAKKHLDAGIAEAADNNISINAYGQALVWKLLELYKENGRSVSDIVSEVQYTLD
Ga0210122_1121961	Ga0210122_11219611	F025809	SCDSLVEPTNDAISSESGTPSSTWVEPAFVEPAAEIVQPIETEPEHVVEKFVTAGPDWELGNALPLVEVQSQGGLVMRRADERWALADVTTTPDFVTEVEVDFRSGPGLGVLFRSSIDDEGRMSGYSFDIDPIYDGGGYLVRQWHSDRELWNPIARVGGDDPTSMYGTLLVRLEVVGEHLSAQVNGVE
Ga0210122_1129927	Ga0210122_11299271	F064729	MGDLKEWLKYWRKVIAKCSKIHKDSRAHKRAYSELSDYLNSVEESANDGALDATVLWAVRFMQRMHELEKEIGLHVLEKKVHSTHKE
Ga0210122_1142654	Ga0210122_11426541	F098856	LDPSPHVPNRQDHAEARRLLAYLTEQGPEILVPCHPFYSVLAGGRGHLHIMGLNDVYFWPRTITSDPARDAAIKDRFRRSVRSSFRSRRWKMVIRDDCATPRLFGLNRNYRLVEDLAQSGKAPRSLTGYLCAPRYVWVPRGEGAVP