3300026068: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushSE_TuleC_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026068
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116116 | Ga0208657
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushSE_TuleC_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 72966976
• Sequencing Scaffolds: 36
• Novel Protein Genes: 37
• Associated Families: 35

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium 21-66-5	1
All Organisms → cellular organisms → Bacteria	5
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	2
All Organisms → cellular organisms → Bacteria → Nitrospirae	1
Not Available	11
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	5
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	2
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	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: 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?
F000676	Metagenome / Metatranscriptome	941	Y
F002140	Metagenome / Metatranscriptome	590	Y
F005060	Metagenome / Metatranscriptome	413	Y
F007886	Metagenome / Metatranscriptome	343	Y
F009970	Metagenome / Metatranscriptome	310	Y
F012266	Metagenome / Metatranscriptome	282	Y
F015847	Metagenome	251	Y
F016087	Metagenome / Metatranscriptome	250	Y
F016687	Metagenome / Metatranscriptome	245	Y
F017154	Metagenome / Metatranscriptome	242	Y
F019578	Metagenome	229	Y
F020200	Metagenome	225	Y
F023288	Metagenome	210	Y
F023894	Metagenome / Metatranscriptome	208	Y
F024435	Metagenome / Metatranscriptome	206	Y
F024580	Metagenome / Metatranscriptome	205	Y
F026912	Metagenome	196	Y
F029799	Metagenome	187	Y
F031021	Metagenome / Metatranscriptome	183	Y
F031537	Metagenome	182	Y
F035813	Metagenome / Metatranscriptome	171	Y
F040161	Metagenome	162	Y
F040163	Metagenome	162	Y
F042500	Metagenome / Metatranscriptome	158	Y
F045132	Metagenome / Metatranscriptome	153	Y
F045445	Metagenome / Metatranscriptome	153	Y
F046145	Metagenome	151	Y
F056185	Metagenome	138	Y
F058256	Metagenome / Metatranscriptome	135	Y
F058543	Metagenome	135	N
F060098	Metagenome / Metatranscriptome	133	Y
F085853	Metagenome / Metatranscriptome	111	Y
F093171	Metagenome	106	Y
F095691	Metagenome	105	Y
F105956	Metagenome / Metatranscriptome	100	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208657_1003293	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium 21-66-5	1343
Ga0208657_1005716	All Organisms → cellular organisms → Bacteria	1086
Ga0208657_1006502	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1034
Ga0208657_1008225	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	940
Ga0208657_1009177	All Organisms → cellular organisms → Bacteria → Nitrospirae	900
Ga0208657_1009397	Not Available	891
Ga0208657_1010181	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	863
Ga0208657_1011291	Not Available	826
Ga0208657_1011334	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium	825
Ga0208657_1011939	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	806
Ga0208657_1012741	All Organisms → cellular organisms → Bacteria	784
Ga0208657_1014477	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	742
Ga0208657_1014941	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	732
Ga0208657_1015297	All Organisms → cellular organisms → Bacteria	724
Ga0208657_1016127	Not Available	708
Ga0208657_1016270	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	705
Ga0208657_1016625	Not Available	699
Ga0208657_1017473	Not Available	684
Ga0208657_1018134	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	674
Ga0208657_1018679	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium	665
Ga0208657_1019425	All Organisms → cellular organisms → Bacteria	654
Ga0208657_1020288	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	642
Ga0208657_1021494	Not Available	626
Ga0208657_1022477	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	614
Ga0208657_1022972	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	608
Ga0208657_1023599	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	601
Ga0208657_1024509	Not Available	592
Ga0208657_1024538	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium	592
Ga0208657_1026480	All Organisms → cellular organisms → Bacteria	572
Ga0208657_1027353	Not Available	564
Ga0208657_1030316	Not Available	540
Ga0208657_1031197	Not Available	534
Ga0208657_1031834	Not Available	529
Ga0208657_1032199	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	526
Ga0208657_1032582	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	523
Ga0208657_1033631	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	516

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208657_1002315	Ga0208657_10023151	F085853	ILANEIAAPLEKLNIKEFDQWKAELQAGMKKYAERFRSEMTTNPSFWRNFNQKAPIYQSMIEGVHRFWSDHQFEEIGRRMEQAAAASQAEVEQLNQKKEQIQKGKEGLNNALKNIKTRFGKLGLEAEDAILLAPIAFAALFLFASLNLCQNIQLRKSFHRLFQARDPQKVAITDSEIALAMPLWVDPLAPPIQRRLKLAVMMIPAIASVLALAVVFYCWTIPDAFPGLTGMDYVKYILYYLLSAGLFFFGFQRIRDAVKNYGV
Ga0208657_1003293	Ga0208657_10032931	F016087	RRAMKKLWNPLGRLLDFVDIMVVVLLFTALAFSVGYQIGFTAGLDTKVTLVGEKYTMLLKGNSKR
Ga0208657_1005716	Ga0208657_10057161	F046145	MLQVCLNFYWKLFEWITDRYEKTIPDLLECDHMALKPKPFSEAKTGFFIMSCYLR
Ga0208657_1006502	Ga0208657_10065022	F019578	VGVIAANSSVVAVLPRKKAGEDTRLKEAYLLAAAPLLFDACSKINSILESSLIVTPEGIKINCTDIKKSLSDALLRAMGYRKSPEEP
Ga0208657_1008225	Ga0208657_10082252	F040163	MNPADPALLAEVLHHALDGVAIVEAGGDSSTRLVYGNATLAGLLRRPEEWLPGRALEEIEIEAPADPNATSTGAGQRVRLRRADGSTVECERWAHMLPDARLAMFYRPLPRSAPGALAAAVDRASGLSTPEHLMEVLRRDWTVAQRDGRSITLMRFSVDGYGDYLEVF
Ga0208657_1009177	Ga0208657_10091771	F105956	MKPEEPTLVEKLPIYMVAWSLPPCFVILAVIVLALDSFNDAGVAILKGKYMFLLLVGGTLLNLWFYAVRQFKLKRKFSPLHIIASLLFPAAYMSFYYGADTTLVVAICLVGIPVSILSARQSMNMV
Ga0208657_1009397	Ga0208657_10093972	F058256	TGLDPPPGLVEAGCLQRAWNRLLTRVPILKHAFGQLLPSKLHTAQQLWKALRRGMGSAEEMLRFLARSCKRSLLGDYTCLRPAP
Ga0208657_1010181	Ga0208657_10101811	F045445	LYLLEQARKGDIAKMIEVIDDLGGIGAGKPVPGAGNKRPQEFADYCKVGPTRVPFVTFPEAELDKAHKRAAHWMELNKKYRPLVETLRSRSAA
Ga0208657_1011291	Ga0208657_10112912	F035813	LAESRYPDTETAAEAKRLMRDVLDHYLDSRRIESRRILADLQALNGDH
Ga0208657_1011334	Ga0208657_10113342	F020200	MCWVCERLENLITSWNEEQEFQEQTSSDDYHRGLSKGFSECVKDLSEAVASMRLKGICEKFPEYERVLNDKQRLDILEDLLKLRDEDSNQE
Ga0208657_1011939	Ga0208657_10119392	F031537	MSGTNSKKALHVATFSGWYRFEQNGKEFIQTKRDLSYWTITCMTVDPEDPKTLYAGTEHSGLFYTKDAG
Ga0208657_1012741	Ga0208657_10127412	F046145	VSLNFYWKLFEWITARYENTFPDWLECDHTALKPKPFSEAKISFFITSRYLRVLSEKI
Ga0208657_1014477	Ga0208657_10144772	F031021	MNARKDRWESYTDKAGRRHWRWPATNAAAERGGRDAEADSRPRAGLPSPQQTSFALLPLRGK
Ga0208657_1014941	Ga0208657_10149412	F026912	MDRNEHKPHFSIIDPMIDDSEPLRSEYLRGFHRGIEVQVFGVSDEWIEEHRMLIDYSNGGSGDSYIDTYARGYRHGFDGRTPESPSLSSESLPIASIV
Ga0208657_1015297	Ga0208657_10152971	F095691	MLQQDGSIRIAWQTDGYEAIFVRARFRPAPERDDFARGVADVALLERTLPDLRRALRARYPGAFDLLTDEPLDQPGRVIVNFHPPRGEPNPDPW
Ga0208657_1016127	Ga0208657_10161272	F005060	MPTALDWLAIAEECFADEYGSLRQGLLTSVFSLVIGMERIFHLDEMEDAGFARLCGGRRCPSRHTVGGWRRNLS
Ga0208657_1016270	Ga0208657_10162702	F060098	MDASSLRGATAAAAMSVGGLLWLSAILFMARTAQHSEPFSRLHPW
Ga0208657_1016625	Ga0208657_10166251	F023894	LVIAGALMLLACDQPSGQSDLSKKAPPSLGAIANVDGSDDEKKDGKKAQAGSEQAPAQSPAGGQPAQAAPKQ
Ga0208657_1017473	Ga0208657_10174731	F029799	GRPGPPASGLMLALTLSTVGCVLLCYTLGRYNRTVTLQRWQFVLNAPGRQAVDTLRAQMQLDSVLAQQALDAASRARAAGRAPDAVTVLRVALSVLEEAGTDRLTRLKAMGIYSRMVRALQPLPAPTAEPFRGAQLRTVVASAGLVHHFLVGAEERFRLWLLMLGLGVRIVLRGGRRSAEAATRHPHAPRPWDQFAEGLTDFRTLDDAHLAAFEALAASLAAVDRGG
Ga0208657_1018134	Ga0208657_10181341	F024435	MFGFLTPHTKDDADPLVSARTISAWLRHLPTQDVIARQHNVMRVFDGMRQSSRQVDLARVTAIQFLDTALGADRRQLVKQYVENIDRMARVADRAWQAAQEMSQGFVYAYQTSLEQALSEGGNPRWKPVIPQLFARLLHYH
Ga0208657_1018679	Ga0208657_10186791	F058543	METVTILASINEKKKAEFFQTMESLTGLVESQCNDLDIRVKDDNSLIIKITFDGKEQMERNFYNNEFTIIKGTVKSLCKDVIIKVNDSIVSHN
Ga0208657_1019425	Ga0208657_10194252	F042500	MDPVGELVAAAVVDERVWEAYGAQANDGVYLVGQPGPALPFVIFRAWKVPVGVVSEEIRLIGPSGRTIFRWGPQPRRMAGAMDLTT
Ga0208657_1020288	Ga0208657_10202881	F015847	EGQQLIMQGGLWSPRDDIGTVDQRFKKSYLDERYSLEELEIKYDQWEQLIRRLFGQRK
Ga0208657_1021494	Ga0208657_10214942	F009970	MAANDGVKLHGKNGAIYVNGPKGTGTKVATKSQWDLNLARDYVEVTTFGDTNKEYVAGLKDITGTFNGVLDVSGDLMVNNTSIDDVPLYLYADDGASPVLVASGPALIDSSITLSN
Ga0208657_1022477	Ga0208657_10224772	F002140	MDDVKGQMEGVTRVYTELDNKISDKGGVQNLFGMNRKIRQALETITLGELDSMLAEIHRAKEGLTRLQEDIVEIRVLKEVLSAPMSGKVNGAT
Ga0208657_1022972	Ga0208657_10229721	F046145	VCLNFYWKLFEWITNRYEKTIQNLLECDHMALKPKPFSEAKTGFFIMSRYLRVLSEKN
Ga0208657_1023599	Ga0208657_10235991	F000676	AELSPKAVVEPANDPDAGNEQIEVYAVADRPRNRPHVADEHDSLSASIAPVADPAWQIKDRSVAGLRISAAGGIGQSLVLGALVAVRQSDAIDWVLGAVRRLNKVSNDEVEAGVSIIADRIVPITVHAKRPTQDDLGMVVNGVDVSVMGTRFDALYLPPPSRPERPLAVKTLIVPTSEYADGRNVILTTGHSVYTIALRH
Ga0208657_1024509	Ga0208657_10245091	F045132	GRQSRPSVLMHSSNRYPLGNCDSSGSETNPDYLTQFGAASHRSWLPSSFFAFTGRARTPPEELVNSASAAKYVSTPLLRGRVNQPDPTFPRSPGRILETVSGKLSSTDPPFQFFQ
Ga0208657_1024538	Ga0208657_10245381	F016687	RPRAYHLIEIEEKSRLISEEVPMKTLKFFAGLMTISMIALGAGSASAWDTRWQFKQDAPSNNYGSGTRDIEMQKKFDYNSMNKFKGTIETSSGYTIMRNLNGDTMRGYIDKDGSGLLRDQNGNFHNVNTRW
Ga0208657_1026480	Ga0208657_10264801	F056185	RMQSSPTHWTLGGLQIMRPRMLLLFRLLMVLVSLFIVVGCSGPQAKIRKVDLPKEKELRANWKNYNTYCLGSRGGNVDFADAMLFQLRSDKTIQRDDDWREVTSDQMASGCASLLSDSSPVMELLGENDEIFGYVIYNFNDQIWASIIDPKTIRLFYHVHPKGP
Ga0208657_1027353	Ga0208657_10273531	F007886	VEGGGAVVAVFEGLEVVLAGVLAGGDTAAEAGVEGAVDVVCSDALGADSFFSPVAGAGASLPGD
Ga0208657_1030316	Ga0208657_10303161	F024580	MTTFNRNYRTAAAFAAVVIVGLTGLTLDRGHAGALPQGVIEIGELETVMVGDMNIASLPAVEVIGSREVQLADVVANDADTQG
Ga0208657_1031197	Ga0208657_10311972	F023288	LALLVVGAATSWWAMTLGWAALAIAFFAWVAEADGLLALPRLGRVAIRRGGFDIPLAFKVRRGERVLFFVREEDPERGGWSDVYTVLDRPNGTDGFEPCYYLQTAIPSGWSLRGHVPVDDLRFEHHERVVYVTRGSLERSLSAAGM
Ga0208657_1031834	Ga0208657_10318342	F017154	RIRRGSLALLVAGAGLTLVLGHSLFELLGDEEHRRSFTSSSMIFGLVLLALCGICWQAGYRLAFQRPDRTGTLFSRPAWLAIGTGLVVITASMVVAISQVRQMTLLDLQVLLFLGGIGVWCLVLSFRGGGGTR
Ga0208657_1032199	Ga0208657_10321991	F040161	PSTAWTAAEGLGRGSGLVVRVTPPRRLSALVVGVDLRDSPLAVPWVAQVGGAVVAQGPARSGLAWVNGAPRAGKQALLVAPLGGRSTGEVRLVFQGPGPQLRVSEVFAYGPEEAEQPRAGEENARAAFEASRAGRWDEAERLYAEALRREPGRASLHAAWARVRWRAAGRRWLDV
Ga0208657_1032582	Ga0208657_10325821	F012266	SLLALQLPFCFEVRALSGRLVSSSPARPCDDMRGLNSLLSESDGDAADFLD
Ga0208657_1033631	Ga0208657_10336311	F093171	MIVVAVGVVAALGALWLDPARAAVGPMSAQGLVLPADARYLMGFDVKRFAASPFYARYGSQKGMRPEALAQLEEKTGLNPERDIDQILVAGTGTVRGGVPGIALVTGRFDLYKLGRAIETQGKARGYGHDGVTVYAYGEEGPRATAVAFLDESTLLFGQKDRVEAAVASRTR