Sample 3300025790

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 Open in IMG/M
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
Location on Map

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

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

Bioinformatics & Integrated Biology Lab
Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

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

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences