Sample 3300026055

Overview

Basic Information
IMG/M Taxon OID	3300026055 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116125 \| Ga0208003
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - WestPond_TuleB_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	41009351
Sequencing Scaffolds	13
Novel Protein Genes	13
Associated Families	13

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea → Euryarchaeota	1
Not Available	7
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	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: Twitchell Island, San Francisco Bay, California
Coordinates	Lat. (^o)	38.107521	Long. (^o)	-121.649681	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Family	Category	Number of Sequences	3D Structure?
F000982	Metagenome / Metatranscriptome	814	Y
F002104	Metagenome / Metatranscriptome	593	Y
F008255	Metagenome / Metatranscriptome	336	Y
F011624	Metagenome / Metatranscriptome	289	Y
F016394	Metagenome	247	Y
F021446	Metagenome / Metatranscriptome	219	Y
F049732	Metagenome / Metatranscriptome	146	Y
F049734	Metagenome	146	Y
F050029	Metagenome / Metatranscriptome	146	Y
F053838	Metagenome / Metatranscriptome	140	Y
F060094	Metagenome	133	Y
F063812	Metagenome	129	N
F071802	Metagenome / Metatranscriptome	122	N

Family

Category

Number of Sequences

3D Structure?

F000982

Metagenome / Metatranscriptome

814

F002104

Metagenome / Metatranscriptome

593

F008255

Metagenome / Metatranscriptome

336

F011624

Metagenome / Metatranscriptome

289

F016394

Metagenome

247

F021446

Metagenome / Metatranscriptome

219

F049732

Metagenome / Metatranscriptome

146

F049734

Metagenome

146

F050029

Metagenome / Metatranscriptome

146

F053838

Metagenome / Metatranscriptome

140

F060094

Metagenome

133

F063812

Metagenome

129

F071802

Metagenome / Metatranscriptome

122

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208003_1000207	All Organisms → cellular organisms → Archaea → Euryarchaeota	2507	Open in IMG/M
Ga0208003_1000908	Not Available	1375	Open in IMG/M
Ga0208003_1001988	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1050	Open in IMG/M
Ga0208003_1003498	Not Available	843	Open in IMG/M
Ga0208003_1004595	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula	759	Open in IMG/M
Ga0208003_1005013	All Organisms → cellular organisms → Bacteria → Proteobacteria	737	Open in IMG/M
Ga0208003_1005126	Not Available	731	Open in IMG/M
Ga0208003_1008524	Not Available	610	Open in IMG/M
Ga0208003_1009002	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	598	Open in IMG/M
Ga0208003_1009207	Not Available	593	Open in IMG/M
Ga0208003_1009636	Not Available	584	Open in IMG/M
Ga0208003_1010756	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	562	Open in IMG/M
Ga0208003_1012040	Not Available	540	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0208003_1000207

All Organisms → cellular organisms → Archaea → Euryarchaeota

2507

Open in IMG/M

Ga0208003_1000908

Not Available

1375

Open in IMG/M

Ga0208003_1001988

All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales

1050

Open in IMG/M

Ga0208003_1003498

Not Available

843

Open in IMG/M

Ga0208003_1004595

All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula

759

Open in IMG/M

Ga0208003_1005013

All Organisms → cellular organisms → Bacteria → Proteobacteria

737

Open in IMG/M

Ga0208003_1005126

Not Available

731

Open in IMG/M

Ga0208003_1008524

Not Available

610

Open in IMG/M

Ga0208003_1009002

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

598

Open in IMG/M

Ga0208003_1009207

Not Available

593

Open in IMG/M

Ga0208003_1009636

Not Available

584

Open in IMG/M

Ga0208003_1010756

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038

562

Open in IMG/M

Ga0208003_1012040

Not Available

540

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0208003_1000207	Ga0208003_10002072	F063812	MSTKHHDSKKHDDAKPAPDCHFCKEKYVYPEHPTPSGICHKCQTKIGVIILIIFVILGGIVFFGLI
Ga0208003_1000908	Ga0208003_10009081	F002104	SGECCGIKCTNLAKSLNRVGMKQNHALAKAITPQEIHLLEQLRQHPELFDRVQSLLEIVGHAEGPLQTADQVEAALIEEMRRLGSVTMHQWAIQAEARVSTELQHQNPTVLSRKKKRSNGGVSSGSCR
Ga0208003_1001988	Ga0208003_10019881	F011624	ATYAPGFVGDARRSRDGVNYGLGLRYDMNASLGLRLEYGRYGRYTGDLASGLLESDQVSVGLQFLF
Ga0208003_1003498	Ga0208003_10034981	F049734	MSESKNYGFQTQFTVVKKYHRHVLWLILGLLFALDIFTTSMSLHLGNFEKNPLMIPFAGNPALHGIVKLLAYIFLFFVIEKAVIFIQERKPEKTPFWIKLNFQTLYGLIIFVLIYLIWLYLYVVASNILIIS
Ga0208003_1004595	Ga0208003_10045952	F053838	MRWNFWSLCGPLIAAHFGASAKPAGRALFFLGVKRNFTTAPAGDVGELVHLSH
Ga0208003_1005013	Ga0208003_10050133	F050029	MATIVIHWKDKNLPPMEIKNAAYKGADSSIIKITSGGKEYWFNWNECWFLETTSTQ
Ga0208003_1005126	Ga0208003_10051261	F060094	RCGLVLCGFPAFMFAAALLLSCTAQQPEGVPVYRSERGFAIGLPAQWLAVNPLELGGKENPLGTHNPQIRGLFTAEGLKALKEKALSGGVELFVNLETSDETFMESINIQVAPGSVVVEDSDVVPACAETEKSLAALYGNPVKMDACKALKIRRIPAFFMEYRVEKLALAHAQYLIQLKADRYVVMTLTCRPKNLPKLRPEFDAIAASFRAT
Ga0208003_1008524	Ga0208003_10085241	F008255	MIEQIQDFMSEQTAAISSQVKKFRKDSVETVRDAVSVSADNIKSLKTPVRVIARSGVKVTNVSQTAVASLIELQSDILTSTLTGMALRLERAARADGIVELVRDQFELTQATRSRVVEEAQRAAEIFKVASRDLKTVATHAYERFSETAEAKAPAVKTAKRKAKRAVRKTTTRARRAVAA
Ga0208003_1009002	Ga0208003_10090022	F000982	MPQLRFTSRADRLLLHYRIRGKAYPSPRYWERLSQMLEEEAEKRGKTPPPPPLTYSLDHDPTDEEKTERLREQVVWADRNQLLHRVQMFFEAMPPSG
Ga0208003_1009207	Ga0208003_10092072	F016394	MQKEELANLAKKVRNHLPNVESFPIATIYTTIKEQEKTKLNLPDFKQLIYHLTGWDISFQIIRRQLEINQIVW
Ga0208003_1009636	Ga0208003_10096361	F071802	MGTKTSKPNYASLITKILIVLVILNIAGDVLAAAFFLWDPSLGELSVYGGLIASFAGKNGAVMITSAILLGYAVVYAVSVFGLLRKLKWAPPLVIAVSIVNRALALGVIFEPNVAWLIWSAWKLVIIALAFYLWRKT
Ga0208003_1010756	Ga0208003_10107561	F049732	MDVLRILLNIFLFTASLFAAALFVEKIYAGRWKWVAFGILMSFIIGFVLFPATLIAVLEALPGNITLSNAATLVLGGIAAGFLAT
Ga0208003_1012040	Ga0208003_10120401	F021446	MKTLSIALMAAFMLVLAATSTGQAQSAEDGYNDPSPGGKYVYRGCNLAEVIFIRGDKLSEINELTLIIEVQGGKNSHTTRLTFPILAKRQEGNKLILDYQWPNGGDTYEATIIGGTLINRKTKGYLAGIREEL

Scaffold ID

Protein ID

Family

Sequence

Ga0208003_1000207

Ga0208003_10002072

F063812

MSTKHHDSKKHDDAKPAPDCHFCKEKYVYPEHPTPSGICHKCQTKIGVIILIIFVILGGIVFFGLI

Ga0208003_1000908

Ga0208003_10009081

F002104

SGECCGIKCTNLAKSLNRVGMKQNHALAKAITPQEIHLLEQLRQHPELFDRVQSLLEIVGHAEGPLQTADQVEAALIEEMRRLGSVTMHQWAIQAEARVSTELQHQNPTVLSRKKKRSNGGVSSGSCR

Ga0208003_1001988

Ga0208003_10019881

F011624

ATYAPGFVGDARRSRDGVNYGLGLRYDMNASLGLRLEYGRYGRYTGDLASGLLESDQVSVGLQFLF

Ga0208003_1003498

Ga0208003_10034981

F049734

MSESKNYGFQTQFTVVKKYHRHVLWLILGLLFALDIFTTSMSLHLGNFEKNPLMIPFAGNPALHGIVKLLAYIFLFFVIEKAVIFIQERKPEKTPFWIKLNFQTLYGLIIFVLIYLIWLYLYVVASNILIIS

Ga0208003_1004595

Ga0208003_10045952

F053838

MRWNFWSLCGPLIAAHFGASAKPAGRALFFLGVKRNFTTAPAGDVGELVHLSH

Ga0208003_1005013

Ga0208003_10050133

F050029

MATIVIHWKDKNLPPMEIKNAAYKGADSSIIKITSGGKEYWFNWNECWFLETTSTQ

Ga0208003_1005126

Ga0208003_10051261

F060094

RCGLVLCGFPAFMFAAALLLSCTAQQPEGVPVYRSERGFAIGLPAQWLAVNPLELGGKENPLGTHNPQIRGLFTAEGLKALKEKALSGGVELFVNLETSDETFMESINIQVAPGSVVVEDSDVVPACAETEKSLAALYGNPVKMDACKALKIRRIPAFFMEYRVEKLALAHAQYLIQLKADRYVVMTLTCRPKNLPKLRPEFDAIAASFRAT

Ga0208003_1008524

Ga0208003_10085241

F008255

MIEQIQDFMSEQTAAISSQVKKFRKDSVETVRDAVSVSADNIKSLKTPVRVIARSGVKVTNVSQTAVASLIELQSDILTSTLTGMALRLERAARADGIVELVRDQFELTQATRSRVVEEAQRAAEIFKVASRDLKTVATHAYERFSETAEAKAPAVKTAKRKAKRAVRKTTTRARRAVAA

Ga0208003_1009002

Ga0208003_10090022

F000982

MPQLRFTSRADRLLLHYRIRGKAYPSPRYWERLSQMLEEEAEKRGKTPPPPPLTYSLDHDPTDEEKTERLREQVVWADRNQLLHRVQMFFEAMPPSG

Ga0208003_1009207

Ga0208003_10092072

F016394

MQKEELANLAKKVRNHLPNVESFPIATIYTTIKEQEKTKLNLPDFKQLIYHLTGWDISFQIIRRQLEINQIVW

Ga0208003_1009636

Ga0208003_10096361

F071802

MGTKTSKPNYASLITKILIVLVILNIAGDVLAAAFFLWDPSLGELSVYGGLIASFAGKNGAVMITSAILLGYAVVYAVSVFGLLRKLKWAPPLVIAVSIVNRALALGVIFEPNVAWLIWSAWKLVIIALAFYLWRKT

Ga0208003_1010756

Ga0208003_10107561

F049732

MDVLRILLNIFLFTASLFAAALFVEKIYAGRWKWVAFGILMSFIIGFVLFPATLIAVLEALPGNITLSNAATLVLGGIAAGFLAT

Ga0208003_1012040

Ga0208003_10120401

F021446

MKTLSIALMAAFMLVLAATSTGQAQSAEDGYNDPSPGGKYVYRGCNLAEVIFIRGDKLSEINELTLIIEVQGGKNSHTTRLTFPILAKRQEGNKLILDYQWPNGGDTYEATIIGGTLINRKTKGYLAGIREEL

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026055: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - WestPond_TuleB_D1 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences