3300025790: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_CattailNLC_D2 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025790
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101344 | Ga0210075
• Sample Name: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_CattailNLC_D2 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 153508804
• Sequencing Scaffolds: 37
• Novel Protein Genes: 37
• Associated Families: 36

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	10
All Organisms → cellular organisms → Bacteria	9
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	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	2
All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium HR30	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Oxalobacteraceae → Collimonas	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): 38.197102
  • Long. (^o): -122.010033
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001012	Metagenome / Metatranscriptome	806	Y
F003217	Metagenome / Metatranscriptome	500	Y
F024397	Metagenome	206	Y
F025805	Metagenome / Metatranscriptome	200	Y
F026037	Metagenome / Metatranscriptome	199	Y
F026597	Metagenome	197	Y
F028404	Metagenome	191	Y
F030799	Metagenome	184	Y
F034962	Metagenome / Metatranscriptome	173	Y
F036137	Metagenome / Metatranscriptome	170	Y
F037146	Metagenome	168	Y
F038633	Metagenome / Metatranscriptome	165	Y
F042227	Metagenome	158	Y
F043262	Metagenome / Metatranscriptome	156	Y
F046398	Metagenome	151	Y
F054696	Metagenome	139	Y
F054977	Metagenome	139	Y
F055469	Metagenome / Metatranscriptome	138	Y
F058543	Metagenome	135	N
F060885	Metagenome / Metatranscriptome	132	Y
F063813	Metagenome / Metatranscriptome	129	N
F065228	Metagenome / Metatranscriptome	128	Y
F067249	Metagenome	126	Y
F072876	Metagenome	121	Y
F073771	Metagenome / Metatranscriptome	120	Y
F075847	Metagenome / Metatranscriptome	118	Y
F077207	Metagenome	117	Y
F080275	Metagenome	115	Y
F094066	Metagenome	106	Y
F097058	Metagenome	104	Y
F097616	Metagenome / Metatranscriptome	104	Y
F097856	Metagenome / Metatranscriptome	104	Y
F100441	Metagenome	102	Y
F101428	Metagenome	102	Y
F105195	Metagenome	100	Y
F105751	Metagenome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210075_1000600	Not Available	7032
Ga0210075_1007758	All Organisms → cellular organisms → Bacteria	1734
Ga0210075_1009297	All Organisms → cellular organisms → Bacteria	1584
Ga0210075_1010287	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1508
Ga0210075_1014277	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1285
Ga0210075_1018744	All Organisms → cellular organisms → Bacteria → Proteobacteria	1126
Ga0210075_1019144	Not Available	1115
Ga0210075_1025278	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	976
Ga0210075_1028603	Not Available	919
Ga0210075_1030916	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	884
Ga0210075_1031872	All Organisms → cellular organisms → Bacteria	872
Ga0210075_1032155	Not Available	868
Ga0210075_1037003	All Organisms → cellular organisms → Bacteria	813
Ga0210075_1038127	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	802
Ga0210075_1049810	Not Available	708
Ga0210075_1050928	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	700
Ga0210075_1055814	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	671
Ga0210075_1057180	All Organisms → cellular organisms → Bacteria → Proteobacteria	663
Ga0210075_1058001	Not Available	659
Ga0210075_1061728	All Organisms → cellular organisms → Bacteria → Acidobacteria	640
Ga0210075_1063465	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	632
Ga0210075_1067490	All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium HR30	615
Ga0210075_1074622	Not Available	587
Ga0210075_1077470	Not Available	576
Ga0210075_1078054	All Organisms → cellular organisms → Bacteria → Acidobacteria	575
Ga0210075_1080587	Not Available	567
Ga0210075_1081051	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	565
Ga0210075_1083190	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	558
Ga0210075_1083376	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	558
Ga0210075_1086234	All Organisms → cellular organisms → Bacteria	549
Ga0210075_1086876	All Organisms → cellular organisms → Bacteria	547
Ga0210075_1089786	All Organisms → cellular organisms → Bacteria	539
Ga0210075_1092331	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	532
Ga0210075_1092967	Not Available	530
Ga0210075_1093638	All Organisms → cellular organisms → Bacteria	528
Ga0210075_1099219	All Organisms → cellular organisms → Bacteria	514
Ga0210075_1103128	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Oxalobacteraceae → Collimonas	504

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210075_1000600	Ga0210075_10006002	F072876	MEMSKQSYDHVIKMPVKRFYNYLKWKSDLEEEKKTMLAEQVLSGLGKGYK
Ga0210075_1007758	Ga0210075_10077582	F043262	MKYSREEAIERIRSFLVGSQRPDETTCQAAARLGIFCHGYDQWSVDQLRQRYPWLAKKMPADTPREEFLKLIVAWDGARQLVNRTTTTCDAKAADHEGCLGFDRFSEAKLKRLFPQLFSAEDEITKF
Ga0210075_1009297	Ga0210075_10092971	F100441	PESYVESTAVPVTFFAASLQCDPYYQDWATIGLLHVTASVIAPSSIYQVENVSDICMGSEGTCAAVSPPMTVATRRWGDVEVPYNPPSATAQPDVGDIAALVNKFRSASDAPIKARALLAGSDQFGNINISPDLNFIHIAACVDAFRGEPYPFTISSCQ
Ga0210075_1010287	Ga0210075_10102871	F097616	PLLISLLPPEQTWDSPVAISGHTSFVAILLLIGFLLSLLLRHPGH
Ga0210075_1014277	Ga0210075_10142772	F058543	METVTILASINEKKKAEFFQTMESLTGLVESQCNDLDIRVKDDNSLIIKITFDGKEQMERNFYNNEFTILKGSVKSLCENVIIKVNESLLNNN
Ga0210075_1018744	Ga0210075_10187441	F055469	MLKRTVVILAAAAFFWGTVPTQTAQAGDDMWDLMDPSWWADKMFDDDHDDWLYYRHHRYSPYWGAAYGQRPRVIVVLQQPETKAQNPETRPPE
Ga0210075_1019144	Ga0210075_10191442	F024397	MIGRKILQEQQASANYNLRQVERRRTGEISWEVVEASSGTAVVTGLASRDEALRTIRGWEHLSQKLEGGLPGHVLVH
Ga0210075_1025278	Ga0210075_10252782	F028404	MNLEELKLLRLVQGILVRNYVDTQRLDVQVIGHSVYIAGEFKVYEYHPSQRKEDPLERDLGLRRNLLHIEQQIRGLGEVTYLEIKFTNWERRGMQWAPKHGV
Ga0210075_1028603	Ga0210075_10286031	F105751	LRRAWTRFQTRVTTLREAFGLLITRATDSAAALWKQLRLARATLPGILQYLAQSGQGSLLGDYRCLRLPR
Ga0210075_1030916	Ga0210075_10309161	F075847	MGETRNSVSPARVFARPTADQIWLGPTQQSALSQLSQPARLRLLAGPPSSGKTTLLGHLALQPAADDVVLNCRGSKDDAMSVLANLLLSADLTPWDLSEIEQRNLFTVFV
Ga0210075_1031872	Ga0210075_10318722	F026597	MLNMFERHRLTVSVSLAVIIITVVGVTVSSFSPSKKSEYFKELKQIYNTVNNYDNKEINNWEAAKNTLVDLNYWYEFIPRYDAIGDEDSDVLMLQNKVRDLTIRQQLRTLPEIRKYYGEYLSDKLYGMNYKVTILNDERNKIIVFTHDSFTKRSELEKFHITVTNDLRALGFKQIRYKWYELEKLKEEKYIHYNFKDLPDNEPRRFNLSVLKNK
Ga0210075_1032155	Ga0210075_10321551	F080275	MLKRNGQKRDGVAPPSLKRMSDTEYAAYFEAFDAIKGDYQALCLIGDKLREVEATARGLSTLDSQTQTGHAWSPDSNNDRSPWEVCAPLMRLDRNEVLLCKRVSEYGLEYAVIDQSPAASAYTKAHGSLEVLRTGDNPRQVLRDFLRGERETLQLMVHDITANVRVLIAERFPKQDLRRVVNEITRMCKSVARLGFSETLEAGAQTQMRRHGIRV
Ga0210075_1037003	Ga0210075_10370032	F101428	LILLVSISIFLATAVGTIGLFLWLESRKESLPERFKEIVREEAHAPRGRSVVSSARAWLGKVRNPFAAKAPTDIELVEMLSGKELKGGRLLLNQAGIRGAGAHNAYFVVRWVLPVVLVVLAVAYGKISGIASKS
Ga0210075_1038127	Ga0210075_10381271	F067249	NPKIVLQGSKIKNALLLLKKDVDPNQENYTFNDVRMIMEIKNNSVGGKILENGKREDPNKVLRFRFNELEAKTKVRNFGVIVLSETLLPPKTPYKYRFKENAIGKENCKVFTLVARELYPRGGLYIKSNLTEMLQKGQMKKTGEFQHLISYLKNV
Ga0210075_1049810	Ga0210075_10498102	F034962	MRSLVVTSRPQLGASEPDSPAAALRELGCEVVAVGYDMDELPDDIEH
Ga0210075_1050928	Ga0210075_10509281	F001012	MSTAADPVEKLVKLLTDDTRVDDRIRATQASLALAKRRVSESLAQHYLASSEPRVQLPEDLMREEQSYERLLQALQDMKSDIARQIRPVEQQIIQANVDHLRQSFNQESRRLSKCLEEIDDNILACRQYLHDYERIRSGLKMLNEKLVQLGADAIAIPDGLATTDLGEIVRQRIEHLRAQGKI
Ga0210075_1055814	Ga0210075_10558142	F036137	MSDSATRLQRKLKMAAWLLIAGLAVEGMTIHWAHPISFMLFIVVGGALILAGVATYLIAIVTG
Ga0210075_1057180	Ga0210075_10571802	F038633	MDTRKLLAASAALLPVGLLAQHATGAEELVRHEAPSVAVVAIDPQLFRSEVDSYVREVNEQMRTNLNEQLRRELAPKIVLASNELRARG
Ga0210075_1058001	Ga0210075_10580012	F026037	MEEKDKVLQLLNAEMKVERQLERLEDVQTLTEIIRYYRQKRARSSEIALA
Ga0210075_1061728	Ga0210075_10617281	F037146	MPMQGESLEVLERAEVPPAQARAIVRAIEIEIAGAK
Ga0210075_1063465	Ga0210075_10634652	F025805	MTKKLATTVALKPASSQPPAGETESQRFERVLSRPEFKPLKAVIDHLRLDGAVMNAALITTNSYQMFLGKLGYRVEMVKQLHEQDCYTRLGPKGGVRAVVPLHDTATYSTMVTLVNFDASLTTTPKSVDYYDAQLAQFKTQLMSKSNNAA
Ga0210075_1067490	Ga0210075_10674902	F094066	MTTDEKLKLAVSVARAAAQSGEYRRLDKLIEVVFRKLNELSPPELGEPHVHDHDREFKL
Ga0210075_1074622	Ga0210075_10746221	F100441	TPHYQDWSTVGLLHVTGSAIVPSSIYDVENVAASCMGAEAGCTAVSEPLEVATTRWGDVEQPYNPPNPTAQPDVGDISALVNKFRSAAGAPIKARALLAGDDAFGNINLSPDLSFNHISACVDAFRGKPYPYTIQSCP
Ga0210075_1077470	Ga0210075_10774702	F054977	LDEDCSRVRNSKAALVLGMFRRLVVSIAQAAIAEVQSKKTRWSVRRYQQQFAHRDGGPERLRALVFAKTPAAWRLKK
Ga0210075_1078054	Ga0210075_10780541	F042227	MAYGSMKAMFQYAEKVFSRFARFRQISDARTNPTVPLAEVLQTWQWGLIRRLPSTEQIGDLLADPRWRALLGLQPEQGGSPDSVARILDGISIPEWNQLLLEDFFTARRAGILSDSGQYGLRCAALDLNELFKSESIHCPHCQVREKT
Ga0210075_1080587	Ga0210075_10805872	F097856	GHVWTAPWQVLSDVFAALVGCGHVSGLLMRQVWPLALMLCADRVPIVHMHLEVR
Ga0210075_1081051	Ga0210075_10810511	F030799	VEVRVLGALPTSGCPDQDYVCVHTDTDPLDDTVVLATIERVTDRTKGPTTTKRVKTLLARQRMSVNEALGLATRYAEWKEVPVVYTDASGLQAG
Ga0210075_1083190	Ga0210075_10831901	F077207	RTPAEAHARLQAALAAHDSSLLWRSLDQDTQWSWMTIQRAWREAYDITQSVVPEGQERRHLLARFEPGATSENAETLFAKMLTPGDWAASQALVTAAGTRPPEISSTGESAEIATPAGSLVFHKAHNQHWGWGFSGLASRADRLKRNASADLERMRRDAADYERAAARGSR
Ga0210075_1083376	Ga0210075_10833761	F065228	RAMLLEETAKIVLYCKQFGGTVSLLPDEWIERLAPLADFI
Ga0210075_1086234	Ga0210075_10862342	F003217	MAYVVQKVEWYQFRDDDGHAFFVMVSSLPNGFFTAVPVDLHMTRIDHSKMGLAASAADALAQLERALEGKKRDELFGPEKA
Ga0210075_1086876	Ga0210075_10868761	F054696	IDCERRYEAPSWKHERRYLRVVTTTPLELLPAGQGWKVGRSRWIIENGTFNRMTSDYALEHNYRHSVSAITGLLAMRSFAFLLTMAYHSHAIARSRGAPVRFVKWFRDIVVEDWVRFLDLALKPRPQLSG
Ga0210075_1089786	Ga0210075_10897862	F063813	INDFLTNEEVLPIIQRDALMSLVQWSQAHGQKLKPTELESNAQPLAKPSPSSKKPAHQFDSRTGSAPIDETKTIERGLS
Ga0210075_1092331	Ga0210075_10923311	F097058	MVTIMRVLLAAATIVLTSHGVSAANPNSLNGVVQTGGTSSSQPLANVNVTLFETTTALPTKLGQATTDAQGRFSIRYTRNSSRTIFFIQADVGE
Ga0210075_1092967	Ga0210075_10929671	F073771	MNKRIAVALLLVLAAGCTSTPRDQVDVPPLDAARKVSEQD
Ga0210075_1093638	Ga0210075_10936382	F060885	VSFGGLVMDQAYLAAAPKGTVEVGELKALDGATVLAQLPEVTVVAKREVATQFAATQLPEIVVVAKRVAQMVAKDDQAALLPTPSINAGF
Ga0210075_1099219	Ga0210075_10992192	F105195	GEMVMTVLLIWSLVDTQPPRIITSDKRVIDLSETDPAIWASYISEENKRRVLAAVRRWETAITAGANAMESHGYAVSGIGVDFQTWLANERESCSS
Ga0210075_1103128	Ga0210075_11031282	F046398	FRTITRTLRNYFLDRKNGSFPTRVSTLVRKPPPADLSGAG