3300025557: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - China_Galinas_CordB_D2 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025557
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101331 | Ga0210141
• Sample Name: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - China_Galinas_CordB_D2 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 184313335
• Sequencing Scaffolds: 42
• Novel Protein Genes: 44
• Associated Families: 31

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	10
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	6
All Organisms → cellular organisms → Bacteria → Acidobacteria → Holophagae → unclassified Holophagae → Holophagae bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria	3
All Organisms → cellular organisms → Bacteria → FCB group	2
Not Available	10
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	1
All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	1
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Halanaerobiales → Halanaerobiaceae → Halanaerobium	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): 38.015896
  • Long. (^o): -122.501663
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F024682	Metagenome / Metatranscriptome	205	Y
F026597	Metagenome	197	Y
F034003	Metagenome	176	Y
F035820	Metagenome / Metatranscriptome	171	Y
F037736	Metagenome / Metatranscriptome	167	Y
F038247	Metagenome / Metatranscriptome	166	Y
F040632	Metagenome / Metatranscriptome	161	Y
F040940	Metagenome	161	Y
F042909	Metagenome	157	Y
F044506	Metagenome / Metatranscriptome	154	Y
F045765	Metagenome / Metatranscriptome	152	N
F047065	Metagenome / Metatranscriptome	150	Y
F048675	Metagenome	148	Y
F048676	Metagenome / Metatranscriptome	148	Y
F050382	Metagenome / Metatranscriptome	145	Y
F052687	Metagenome	142	Y
F057480	Metagenome	136	Y
F058158	Metagenome / Metatranscriptome	135	Y
F058721	Metagenome / Metatranscriptome	134	Y
F059980	Metagenome / Metatranscriptome	133	Y
F070131	Metagenome / Metatranscriptome	123	Y
F076109	Metagenome	118	Y
F076231	Metagenome	118	Y
F077317	Metagenome / Metatranscriptome	117	Y
F078289	Metagenome / Metatranscriptome	116	N
F078881	Metagenome	116	Y
F084253	Metagenome	112	Y
F084254	Metagenome / Metatranscriptome	112	Y
F093888	Metagenome / Metatranscriptome	106	Y
F099323	Metagenome / Metatranscriptome	103	N
F099975	Metagenome / Metatranscriptome	103	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210141_1000134	All Organisms → cellular organisms → Bacteria	10233
Ga0210141_1000159	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae	9816
Ga0210141_1000552	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	6673
Ga0210141_1000671	All Organisms → cellular organisms → Bacteria	6196
Ga0210141_1000711	All Organisms → cellular organisms → Bacteria → Acidobacteria → Holophagae → unclassified Holophagae → Holophagae bacterium	6042
Ga0210141_1000984	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	5335
Ga0210141_1002353	All Organisms → cellular organisms → Bacteria → Proteobacteria	3707
Ga0210141_1002543	All Organisms → cellular organisms → Bacteria	3588
Ga0210141_1002669	All Organisms → cellular organisms → Bacteria → FCB group	3511
Ga0210141_1003042	Not Available	3299
Ga0210141_1003045	All Organisms → cellular organisms → Bacteria	3298
Ga0210141_1006907	All Organisms → cellular organisms → Bacteria	2217
Ga0210141_1008524	All Organisms → cellular organisms → Bacteria → FCB group	2008
Ga0210141_1008699	Not Available	1988
Ga0210141_1011398	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1736
Ga0210141_1011482	All Organisms → cellular organisms → Bacteria → Proteobacteria	1730
Ga0210141_1015960	All Organisms → cellular organisms → Bacteria	1462
Ga0210141_1016181	Not Available	1451
Ga0210141_1017027	Not Available	1412
Ga0210141_1019140	Not Available	1328
Ga0210141_1019501	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	1315
Ga0210141_1020322	All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	1287
Ga0210141_1021930	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales	1234
Ga0210141_1023353	All Organisms → cellular organisms → Bacteria	1192
Ga0210141_1029305	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1055
Ga0210141_1029365	All Organisms → cellular organisms → Bacteria	1054
Ga0210141_1032591	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	998
Ga0210141_1035943	Not Available	948
Ga0210141_1038011	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	920
Ga0210141_1039041	All Organisms → cellular organisms → Bacteria → Proteobacteria	907
Ga0210141_1039988	All Organisms → cellular organisms → Bacteria → Acidobacteria → Holophagae → unclassified Holophagae → Holophagae bacterium	896
Ga0210141_1041435	Not Available	879
Ga0210141_1041785	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	875
Ga0210141_1043123	Not Available	861
Ga0210141_1044079	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae	850
Ga0210141_1061915	All Organisms → cellular organisms → Bacteria	711
Ga0210141_1066691	All Organisms → cellular organisms → Bacteria	683
Ga0210141_1078686	Not Available	626
Ga0210141_1085404	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	600
Ga0210141_1098326	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	556
Ga0210141_1100854	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Halanaerobiales → Halanaerobiaceae → Halanaerobium	548
Ga0210141_1113286	Not Available	514

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210141_1000134	Ga0210141_10001345	F034003	MKKRRKRNPAFKKTNQLSFDFSLNDPIEIHTPKSNISDLRRELAWEHRPIIEIFKS
Ga0210141_1000159	Ga0210141_10001593	F076109	MEVLFKILFVIAFIAFILCLFVFVGGLFMAFQKNELPDLEDV
Ga0210141_1000552	Ga0210141_10005528	F076109	MEVLFKILFFVSVIAAILCLCVFLGSLFILFQKNELPDIEDV
Ga0210141_1000671	Ga0210141_10006711	F084253	FVLIKAAQGFAVPAHGTGRRTSVRRSRKPAENAEQDKNGHLWMDTT
Ga0210141_1000711	Ga0210141_10007115	F040632	MGNSTEHTAAFEIEDLRDPASTQDMVHVVVATREEDLLWAVFDGFCELPTVRVTGCSTLPQTRQICAADPPTYLIIDVGLLEHEPMDLITLANLSDSQCHIVALTNHPVFEIGARFGNARLTFLQKPVSAHDLLLLLRLRIGDGMQRAKVC
Ga0210141_1000984	Ga0210141_10009844	F040940	MGTLNNIFSLVFGMNLILVGLVALLAGIVSLAKKDASVKKLTSMIYIIAGAAAVYFGVVLSKSAYSL
Ga0210141_1002353	Ga0210141_10023531	F084253	FVLIKAAQGFAVPAHGTGRRTSVRRSRKPAENAEQDKKGHLWMDTN
Ga0210141_1002543	Ga0210141_10025434	F078289	MKKTVIILMTLFIVVPLYGFNSLVRHEDIPKMRELGVSQEVIQYFISNQTSSVSSEDVIKMKQAGLNNDDIMSAIQSDLYRPEQKSTSMKEVELIAKLKESGMSDEAVLQFIQTVKSTRRVDSDGNVTKQYTNESNRTQYPTEGATFPKPDNYGYDPLNGRFLLLVKPQNQ
Ga0210141_1002669	Ga0210141_10026694	F078881	MSKKITNLFLIVVLLLILLLSGCGTGQVSVGVGVYVPGAWGGPYGGGYYPPVRVGYPVY
Ga0210141_1003042	Ga0210141_10030422	F047065	MTDLLNKFSEAAKAATSSKTNLWECVKRAFADHLNDINTDSLPEEIKIFYDSVKLRVKSAEVFGYIDNDEACYIANDIMYLADVISSGLRKS
Ga0210141_1003045	Ga0210141_10030451	F026597	MLSMFERHRLIVSVSLALLIIAVVGVTVSSFSPSKKSEYFKELKQIYNTVNNYDNKEIYSWEAAKNTLVDLNYWFDFIPRYDAISDEDNDVLVLQEKVRDLTIRQQLRTLPEIRKYFGEYLSDKLYGLDYKVTILNDERNKIIVFTHDSFTGRSALEKFHNTVANDLRALGFKQIRYKWYELEKLKEEKYIHYNFKDLPDNELRRFNLSVIKN
Ga0210141_1006907	Ga0210141_10069072	F077317	MEETLIKPADETVWYENDQIIKEFLESFRKPEILDADHQAEELSWIKIIEKSIQI
Ga0210141_1008524	Ga0210141_10085243	F052687	VTRFLAILLLLVAVGGGLYYLLTMETVEDVKVTGKLQISQQIGNYVKASQTDDEAYFAVVEGKIKNNLGKPIKNVFIKYMIAGKETSATVFDVAPGQEIHFNTRGVNTSASNPEYDFVGIYYD
Ga0210141_1008699	Ga0210141_10086992	F058158	MGVTKKDRENRIDKRIVNQKSYMSDFTKTEKDDIDIWELHVKEREYILAQIANDRRTSRIRNWIELIFMLGFIYYMLYDIYKDGDLDTIIKFLTT
Ga0210141_1011398	Ga0210141_10113982	F076109	MEVLFKILFVIAFIGFILCLCVFAVGLFMAFQKNELPDLEDV
Ga0210141_1011482	Ga0210141_10114822	F044506	MMEQLDSGVMGSGILQYWIYGPATGWIDDKIKVAIILLKTNIPAFHHSIIPISGKIRKPQNATIFSVGCRNSETLITGRPNPAGRFDKT
Ga0210141_1015960	Ga0210141_10159601	F045765	MKNNSSKSDNTTPIKIDDRLYGLLRKFCDKEGRRLKEFVEDALENAIYTEESIKVLTEEIRTLKRKEAKYDYAFRRGFQKGFYISFCALHGQILVEPDDEAFEILKNDPYRISKGAQLDLFR
Ga0210141_1016181	Ga0210141_10161813	F047065	AKAVSSSKTLMWECVKQAYADHLSDISRDDLPEEIQIFYDSVKLRVTSVEPPGYIGNDEAIYIANDIMYLADVINSGLRKS
Ga0210141_1017027	Ga0210141_10170272	F093888	MIVNFFSQLSKTTGLPLIVSTCALVIIFAICTFGILILFRVRSIKKVLNNLDDRLDIIGHQLGWQSGEFENIQVDKDNLGSHENDEIDPGGHSSLQTSHPADIAQQNGSEEQGINPKISAKIHELLKKSGKPTPYHELTEKLSKDYPGYNYDFFLKEVEDLQKEGKVEVQLIAGKLYFQIGKKG
Ga0210141_1017027	Ga0210141_10170273	F042909	MAELMTFIGNLNLGTFIVLWTSTIILVICVSLLLFYIRQINREANTISKKAKILILKLSEEKNKSWK
Ga0210141_1019140	Ga0210141_10191401	F070131	MMKTKLTKIGKIGVLSFCFLLQVGLAGGDAAIYHQNKTKINVPMEIELYFSSAPMLNEPTILNIEIRVLRDAPNTLIDIELPSEGFELISGNLHLNEDLSSGSTTIYQLEVLPVARGQYKIAASATSEQTDFIFGKKEELYVNITDGFSEQSKNNFIPETADPWSEATKIGNVCEAPTQALQDLKPIVSQDVSYFAAPDPGQIMVKGYWYYQDRAGVNQPL
Ga0210141_1019501	Ga0210141_10195012	F045765	MQYNSSKSENTATIKIDDRLYDLLRKFCDKEGRRLKDFVEDALENAIYTEESIKILNEEIKSLKKKEAKYDYAFRRGFQKGFYISFCALHGQILLGPDDEEYEILKNDPFRVSKGAQLDLFR
Ga0210141_1020322	Ga0210141_10203221	F057480	MKKILFIFLSVLFLFLFSAMSPCFAKDEDPCKDQGIIVKNLSFKEIWYKPQGGNCIVLKRHNTFTIKPAEEIGLFSDIVCETPYCPASTYSDYKSYDLNGDCGIRILPHNTLSDM
Ga0210141_1021930	Ga0210141_10219301	F076231	MQLKSSRSGTADISEVSGFISTKQNGIISLTKVVVLISVLLALL
Ga0210141_1023353	Ga0210141_10233533	F038247	MKSVFFWSEGQARTHRKNNPKPRGIYLNLRQAAILTKPIQSVLFGY
Ga0210141_1029305	Ga0210141_10293052	F059980	MEEACSMGFSGGFEQGKPETALPELIRFIPGNVKRVNPQNRFYCG
Ga0210141_1029365	Ga0210141_10293651	F035820	NDPTTNLRAVRDEESSTGWTIEIGPFPGWAEVPEW
Ga0210141_1032591	Ga0210141_10325911	F099975	LLKVKEIKELRGGVLLYAAQAIPQIDAEIGQKGHLWMETS
Ga0210141_1035943	Ga0210141_10359433	F093888	MMILFFNQLSNLTGLPLIVSIFAFVVTSSLALFGILILIKVRSIKKGLNDLNDRLDSISQGLSWQSAEFENIQPYKFKLGSHINDELAADGRTNSEINTTADSANKNGPEEHRINMEISKKIHALLKKSGKPTPYHDLTKHLSKDYPKYNYDFFLKEMEDLQKEGKVEVQLIAGKLYFQIKKT
Ga0210141_1038011	Ga0210141_10380111	F048676	MLFRYSRLCGTASDAVRRSRLRGDAVKSEIPQGFKLLKLKMSEYIKNIVELTILKI
Ga0210141_1039041	Ga0210141_10390412	F048675	MDNSEKHIHSNEVLFSESYAAAQSLKNVWTRLASTYGCIMVVLCRETLTIKPHWFAKWLVSLLGLDLCHEIPITNIRGVTEMGKWFSYGKIELYFMTIDGENQRILLYMKKYREFIDTVKNAIYP
Ga0210141_1039988	Ga0210141_10399881	F040632	MSNRSGHAGSIEREIEELRDPSNTPDMVHVVVSTREEELLWAVFDGFSELPTVRVTGCSTLPQTRQICAADPPSYLIIDMTLLDHEPMDLITLANLSNCRSHIVALTDHPVFEIGARFGKARLTFLQKPVSAHDLLLLLRLRI
Ga0210141_1041435	Ga0210141_10414352	F084254	HIPVFISEPLVIEIMAEVIRQSKRHPRADQVASALAIRGLPIAEKDVMTVFDQYDIEKKIADSH
Ga0210141_1041785	Ga0210141_10417852	F024682	MALDAQDELISKLKQEIGKNLPPMFSGMAENMLENNKDVIINWLKDNKDLVKQVIES
Ga0210141_1043123	Ga0210141_10431232	F076109	MEELFNLFFVISVIATIFCPCVFMGGLLIAFQKSELPDIEDV
Ga0210141_1044079	Ga0210141_10440793	F048676	LFRYSRLCGTASDTVGAVKLEIPQGFKLLKFKMSEYLRNTFN
Ga0210141_1061915	Ga0210141_10619151	F050382	QISNKIKNQLFRILNFGYCDLFVLCVLIFEFLFAET
Ga0210141_1066691	Ga0210141_10666911	F076231	MMHLKPNKTGTADISEFSGFISTKQNSIISLTKLVVLLSVILAVLMVVSR
Ga0210141_1068193	Ga0210141_10681931	F099323	ICGAFFLFNVLFGNYRIGDVTEGHLVVLGIFLIMLLINAFMPDEMIHRRSFRYFLALPGMMLAIHCLSKRTKPDSKNLVLYCSIAVLALTIQFVAYHTVERVVNSGGLESYGLSGNMHHFGSFAGLILPVLFYFSTQIKGWLRLLCVAGVIAAFYLLWESSSRIAWFAFFSSILMAILLFLRNRKLLMGLAGFFTISFIAALVSGLAVIKNRIWDILSNWRSEE
Ga0210141_1078686	Ga0210141_10786861	F058158	MAQIMIDKQKSYKSDFTKTEQDNRDIWELHLKEREHMLAQISKYRRKNRARDWIELILMIGFIYYMLYDMYKAGDLDTIIKFLKYSIV
Ga0210141_1085404	Ga0210141_10854042	F058721	ETLPCADPHCKHQMRLVFQNERFIGYRCLMKPNSHNFRYDIENKRWEKLIIKTKTILKYKEAPFE
Ga0210141_1098326	Ga0210141_10983261	F084253	KAAQGFTARRTSVRRSRKPAENADQDKKGYFWMVTNSFCELQQTC
Ga0210141_1100854	Ga0210141_11008541	F078881	MNKKIKHLLFIIFFFLLLLLSGCGTGQVSVGVGVYAPGAWGGPYGAGYYPPVRVGYPVY
Ga0210141_1113286	Ga0210141_11132861	F037736	VQLDGLQILWLLANPLWTHGIGESRSKTITGWLLMGAADANHIWWLNTNPFTGLLLHLNSYRILHLPCGFLNMLCFLLLCHRQRNDNY