Sample 3300026072

Basic Information
IMG/M Taxon OID	3300026072 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116105 \| Ga0208292
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_CattailNLC_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Basic Information

IMG/M Taxon OID

GOLD Reference
(Study | Sequencing Project | Analysis Project)

Gs0111376 | Gp0116105 | Ga0208292

Sample Name

Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_CattailNLC_D1 (SPAdes)

Sequencing Status

Permanent Draft

Sequencing Center

DOE Joint Genome Institute (JGI)

Published?

Use Policy

Open

Dataset Contents
Total Genome Size	104468933
Sequencing Scaffolds	31
Novel Protein Genes	32
Associated Families	31

Dataset Contents

Total Genome Size

104468933

Sequencing Scaffolds

Novel Protein Genes

Associated Families

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	4
All Organisms → cellular organisms → Bacteria	5
All Organisms → cellular organisms → Bacteria → Proteobacteria	5
All Organisms → cellular organisms → Eukaryota	1
Not Available	8
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → unclassified Acidimicrobiia → Acidimicrobiia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	2
All Organisms → cellular organisms → Bacteria → FCB group	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	1

Dataset Phylogeny

Taxonomy Groups

Number of Scaffolds

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria

All Organisms → cellular organisms → Bacteria

All Organisms → cellular organisms → Bacteria → Proteobacteria

All Organisms → cellular organisms → Eukaryota

Not Available

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium

All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes

All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → unclassified Acidimicrobiia → Acidimicrobiia bacterium

All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria

All Organisms → cellular organisms → Bacteria → FCB group

All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium

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

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)

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)	38.209923	Long. (^o)	-122.033409	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Location Information

Location

USA: Fairfield, San Francisco Bay, California

Coordinates

Lat. (^o)

38.209923

Long. (^o)

-122.033409

Alt. (m)

N/A

Depth (m)

Location on Map

Zoom:

Powered by OpenStreetMap^©

Family	Category	Number of Sequences	3D Structure?
F000690	Metagenome / Metatranscriptome	935	Y
F000982	Metagenome / Metatranscriptome	814	Y
F007038	Metagenome / Metatranscriptome	359	Y
F009010	Metagenome / Metatranscriptome	324	Y
F016687	Metagenome / Metatranscriptome	245	Y
F024001	Metagenome / Metatranscriptome	208	Y
F026705	Metagenome / Metatranscriptome	197	Y
F031716	Metagenome	182	Y
F033859	Metagenome / Metatranscriptome	176	Y
F037791	Metagenome / Metatranscriptome	167	Y

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208292_1000185	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	4310	Open in IMG/M
Ga0208292_1000267	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	3905	Open in IMG/M
Ga0208292_1000531	All Organisms → cellular organisms → Bacteria	3207	Open in IMG/M
Ga0208292_1001139	All Organisms → cellular organisms → Bacteria → Proteobacteria	2515	Open in IMG/M
Ga0208292_1001241	All Organisms → cellular organisms → Eukaryota	2441	Open in IMG/M
Ga0208292_1001859	All Organisms → cellular organisms → Bacteria	2127	Open in IMG/M
Ga0208292_1002557	Not Available	1893	Open in IMG/M
Ga0208292_1005538	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium	1445	Open in IMG/M
Ga0208292_1005984	All Organisms → cellular organisms → Bacteria → Proteobacteria	1405	Open in IMG/M
Ga0208292_1006128	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1392	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0208292_1000185

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria

4310

Open in IMG/M

Ga0208292_1000267

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria

3905

Open in IMG/M

Ga0208292_1000531

All Organisms → cellular organisms → Bacteria

3207

Open in IMG/M

Ga0208292_1001139

All Organisms → cellular organisms → Bacteria → Proteobacteria

2515

Open in IMG/M

Ga0208292_1001241

All Organisms → cellular organisms → Eukaryota

2441

Open in IMG/M

Ga0208292_1001859

All Organisms → cellular organisms → Bacteria

2127

Open in IMG/M

Ga0208292_1002557

Not Available

1893

1445

All Organisms → cellular organisms → Bacteria → Proteobacteria

1405

Open in IMG/M

Ga0208292_1006128

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria

1392

Open in IMG/M

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208292_1000185	Ga0208292_10001851	F081923	MKRMIVNISAAIRPVMYRKHFFVMAILGAALAVACTMANTGSIQTSAEVTRQFEGLQVNPNYRYWYLNQENNPFGVIGLDREYGFAGGPVWRAVEPDSPIFRKVVGLVESFPVASSLTTGYTIFEQQGRPIGVWYSSIGLGVTIDPATKTVSPATTTPWKSPF
Ga0208292_1000267	Ga0208292_10002678	F073725	MEKRATRRYRISTSIVCSYLNSVDFGKPVNGRMRNCCVNGLCAELGAHYKAGTVLVVRTTGSSCGYSDEEGFRSPAVAEVKWSRPRSIEGGACYATGLKYLML
Ga0208292_1000531	Ga0208292_10005311	F041286	MSETDKDLQKAVDEHLKRLHERYKSNAKVFTATHIGHISLSIVFVLSILFPFLYLQIDARETNSELEHLSLGIAQLDQRAATYRQAMTGLKKVFGAVEDTPKPLEGYIQALEKEAAGGPVVPLPEGLKPVQESCGSPSDKDPWMECRLRQYMEARAAQYQKILANEIAAPLEKLNIKEFDQWKAELQAGMKKYAERFRSEMTTNPSFWRNFNQKAPIYQSMIEGVHRFWSDHQ
Ga0208292_1001139	Ga0208292_10011391	F063813	EILPIIHKDALMSLVRWSQAHGQKLKPSECESKFQPLAEPSHPSKKPSDQLGSGTGSAPIDETNSIERGLS
Ga0208292_1001241	Ga0208292_10012414	F053088	MDQPIEYFLTQAKRISGASPTTKIHGVLFNVTIGVVAAGTVYGHKSARNGSDIRTSLIVDAYVINGFYIIGTRTGSNYLLARVGPSRIFRDQWGILQEHLGKNHKALAGLPKSDFSTFGPGFMHATCPAQIKDFDRLRREAA
Ga0208292_1001859	Ga0208292_10018595	F073723	MSGMTLLERLLLPLVRRFVSFWVRPSILPDSLAERFQQGRPVVYVLEKRSII
Ga0208292_1002557	Ga0208292_10025572	F009010	MPEVPKFLYLLVDAPLLIAIPIVIFAALAFWSRSKTAAVAAIAWNLYLIYELGMKAEEFCSGLNCVKRTPLYGVYPLLALVSMLALVQGYVHVRDNRRSGRLR
Ga0208292_1005538	Ga0208292_10055381	F016687	IALCAGSASAWDTRWQFKQEAPSNSYGSGTRDIEMQKRFDYNSMNKFKGTIETSSGYTIMRNLNGDTMRGYIDKDGSGLLRDQNGNFHNVNTRW
Ga0208292_1005984	Ga0208292_10059843	F024001	MFTGTVFIVDAKGSRKNKFAILGVEALAWQGAKTQEYLDIPSFRNAARRDASASKM
Ga0208292_1006128	Ga0208292_10061282	F031716	MSRYTPGHWHVKEENGSYGVFSDDDALLAVTLPDDIKDKNAVKANAILMASAPLLLKLIIEIKEHLDNNMIVTQEGLKINDSHLRDSIIDAILRAEGYRL
Ga0208292_1006147	Ga0208292_10061471	F049598	MKKLLLVALVAGAVLAFCAPALAWPVALPWWQPSQHFTCVGKIQAVDTTTSAVTVRVHLASRGAADYLGEDLTVAVAANARIYKAVGARLTPIALGDLVVGEKLRVEGAIEYATGSAVYVGKRLVMRRLPLNQIKRFAFRGPVTQIDADARTLTATMNRVTRALSPYYHRTCDFAVAPDARVWVMKDGWPVRATLADVVVGDRVYAQGGADRSTPSAPVFTIRWMVVRHAVPAPVTP
Ga0208292_1007656	Ga0208292_10076561	F087857	TMKRNFIVVPLLVIAFVAIQIVPPAHAEPITLTIMAIAGITTVMTAACTDMAVHGEHIVQANSPNEKPAEVFASERSADSSNNHDVQVTTAR
Ga0208292_1010642	Ga0208292_10106421	F069000	LSVPLALLLWSLRSAGEDVRTSVAIVAVLLALPWVVPAMVLVAALSVPVYMWLHTQGPVPPVLQWLGGTVLVAAVIGAHVNAALGWVWMHRGKAVPEPGIGDFLKRHSAGAQQRTDDAR
Ga0208292_1012166	Ga0208292_10121661	F093898	MMRFLVARAVNPQLGLFDGLRQWNGIAAALRESPRKRTYQTDDLDQFLS
Ga0208292_1012812	Ga0208292_10128122	F087402	MARAKVVEFDYYQFLRIMQRAGNAGQRIDKTDSRWGEYVRENKINEVAATAIARQKFENATPVIIAEGGDADGLYFFSKDDEACLRLTALE
Ga0208292_1015803	Ga0208292_10158032	F037791	LVLLRMEVAAFHPLPCDRKRLVSVALFLAFIGRANGDL
Ga0208292_1017213	Ga0208292_10172132	F047153	SALVYDFEKSRWASLLTSINYGQVIGLWDHKWRPNVEAGYDFKDDAGNQRWVFRAGITLLLPQ
Ga0208292_1017690	Ga0208292_10176901	F000982	LHYQIRGKAYPAPRYWERLSQMLDEEAEKRGKTPPPPPLTHGLESDPTDEDKTERLREQIAWADRNQLLHRVQMFFEAMPPSGWVRGEKR
Ga0208292_1018196	Ga0208292_10181962	F016687	MKTPKYLAGLVIISMIALCAGSAFTWDTRWQFKQDAPPNNYGSGTRDIEMQKKHDYNSMNKFKGTTDSSNGYTVMRNLNGSTMRGYFDKDGSGLLQDQNGNFYRVNTHW
Ga0208292_1019159	Ga0208292_10191592	F007038	MTRRVFLDTEWTAPPWSDRTELMWIGLADEGGRSWYGISSEVVIDPSTNAFISGAFGLIDPAEPRLSRAQLAAAVMDFCGAVDEFWVWIPTLESFSAWSGLGDGAPESYAKCRDIDLRMLRALLNPWPAGWPKSVHDLNAAAVAAAVEIPPRASNHLHPQVHADWNRRLFDLIQAAPRS
Ga0208292_1020360	Ga0208292_10203601	F000690	FAVPGITFEQEYLKALLLMRLDSGNFTPDQVEWVAGHLDDWVPSLSLVPPPGEGAGFYVDLTGSQGLRRREKRALAGRVQMLDTGPAYTRVVEQLRWLPEQDDAVPKAGELPAREQRLLLMRLASLFGPEAIAHAPRAERIAVDGQVRVVVGLIALTHAVAEIDQPAAGERPPRAPSFDEPTHAPDPTADAESVARRIQGFTWRIADRSETGCRLIAPAREAPTHLGELLAIRDGEAWILGVVRRMQRGPAEEVTVGVEIVARRLVRVLMRTWSAPADDGR
Ga0208292_1026647	Ga0208292_10266472	F049078	MKVHVKHSLKADVASVFKLCTEQKSQEAIYAGLGGSDVKIKREGRAPNVKLKISRREPANPPAAIRRIVPS
Ga0208292_1027705	Ga0208292_10277051	F076224	QKVKEFTLNLKYDSTFKYYSELNSGHPFTVVIDSNICRVDIPDFPNPEISIPEIASIDPLIEQATNNIHFYAYKIPKIEKSKSEIKIEYYNDDSVYSYVVNYNMLDIDSIVQANAGTDFYNLERLKETRPFDDTMLIKYQFDRDYYNRYYSDDEFKKQMEELQKELQQLSKEVKNQKIRVHSEVTKSPKK
Ga0208292_1028972	Ga0208292_10289722	F033859	MLPRFQKLLAPLAISAAIAAPGAASAQDLSPPASEWRSYCQTYLKALDGDTTASDLDVTYCLGVTKGLLNGMRVGSQIGALSFASRVAVQYKLDPDEVFQLFQTQEPSRLLGICSPAASAAPEFVRAVLAHLEKNPGNLQRPIAEVFYEGLQ
Ga0208292_1031206	Ga0208292_10312061	F026705	MLDALKTRYEAFANRVLCSLSEIEREDVRSFDRWFYQGGGWRWLVGIIALTTGVAFVASKLPWNMRFIEAAVLFNVVVLTLLWSGLTAWFGYRKFSGKLFRYIVVGPLLALVGAFAGASIAGLVTGVDPLAWLQDSTKVRHIVTAGLV
Ga0208292_1032067	Ga0208292_10320671	F089119	MSPRAAAGMMEGQAPIALVGLLAIGVIIAVNYFARPQPGAANRAPVATDCRQCGTVVAVRRSAHSIPVTFVEVQMTDGSVRTLRAPARQFSVGDAVEV
Ga0208292_1052478	Ga0208292_10524781	F047753	MKKIIGILEELRIDDAWLRVAPFALAGCRKESYGKLTRLCRRKETLMAVVVAGVIGLYSAKKHIGLCKKAVKAGKNAYRDSDRELNKYLDAIWRVYILDNSIDKQRLIEKAIGCLSGKLDQELSHSLTEAKKEYKAMIQQIIGAVQADTGHSENAVH
Ga0208292_1053862	Ga0208292_10538621	F103189	GDDATFTLLQRTTGRKVELPADPKLSPDRARLVTADFCASRCSNELALWRVTRDGVRKESTWRPRASWSDVVATWKDAETVIVEYSVAGTQARSRISRRLADAEWVRAQAP
Ga0208292_1055771	Ga0208292_10557711	F077451	GLGGLFGRNSPGRWAGLAASFTELGVDLDTAKKFGPIVIDYVAHHGGEDLVDKIRSALKI
Ga0208292_1056121	Ga0208292_10561211	F043793	MLALRTLTVKMTVNFGGAASGALQINSLEGSLMIEWE
Ga0208292_1057134	Ga0208292_10571341	F076231	MERTMMHSKSGRTGTANMSEFSGFVSTKQSGIISITKVVILISVLLAVLMVVSK
Ga0208292_1058736	Ga0208292_10587362	F044151	MFLSVAFAGVLYFLEPMLFEQGLGTSLGGRDRLASDEPEAKLTSPT

Showing 1 to 32 of 32 entries

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026072: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_CattailNLC_D1 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences