Sample 3300026047

Basic Information
IMG/M Taxon OID	3300026047 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116117 \| Ga0208658
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Sandmound_ThreeSqA_D1_rd (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 | Gp0116117 | Ga0208658

Sample Name

Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Sandmound_ThreeSqA_D1_rd (SPAdes)

Sequencing Status

Permanent Draft

Sequencing Center

DOE Joint Genome Institute (JGI)

Published?

Use Policy

Open

Dataset Contents
Total Genome Size	63153588
Sequencing Scaffolds	36
Novel Protein Genes	39
Associated Families	38

Dataset Contents

Total Genome Size

63153588

Sequencing Scaffolds

Novel Protein Genes

Associated Families

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	2
All Organisms → cellular organisms → Bacteria	3
Not Available	19
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → Rhodoplanes piscinae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1

Dataset Phylogeny

Taxonomy Groups

Number of Scaffolds

All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium

All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium

All Organisms → cellular organisms → Bacteria

Not Available

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales

All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria

All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae

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

All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria

All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → Rhodoplanes piscinae

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria 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: Antioch, San Francisco Bay, California
Coordinates	Lat. (^o)	38.000637	Long. (^o)	-121.624207	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Location Information

Location

USA: Antioch, San Francisco Bay, California

Coordinates

Lat. (^o)

38.000637

Long. (^o)

-121.624207

Alt. (m)

N/A

Depth (m)

Location on Map

Zoom:

Family	Category	Number of Sequences	3D Structure?
F001574	Metagenome / Metatranscriptome	669	Y
F001984	Metagenome / Metatranscriptome	608	Y
F002389	Metagenome / Metatranscriptome	565	Y
F003307	Metagenome / Metatranscriptome	494	Y
F006263	Metagenome / Metatranscriptome	377	Y
F006520	Metagenome / Metatranscriptome	371	Y
F007886	Metagenome / Metatranscriptome	343	Y
F008969	Metagenome / Metatranscriptome	325	Y
F016461	Metagenome / Metatranscriptome	247	Y
F017505	Metagenome / Metatranscriptome	240	N

Family

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208658_1002231	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1493	Open in IMG/M
Ga0208658_1004899	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	1022	Open in IMG/M
Ga0208658_1005111	All Organisms → cellular organisms → Bacteria	1001	Open in IMG/M
Ga0208658_1005350	Not Available	980	Open in IMG/M
Ga0208658_1005497	Not Available	968	Open in IMG/M
Ga0208658_1006269	All Organisms → cellular organisms → Bacteria	909	Open in IMG/M
Ga0208658_1007211	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	855	Open in IMG/M
Ga0208658_1007462	Not Available	841	Open in IMG/M
Ga0208658_1009598	Not Available	752	Open in IMG/M
Ga0208658_1009953	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	739	Open in IMG/M

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208658_1002231	Ga0208658_10022312	F008969	MTDASEVTGRDSYVIAQALYEFIRLEQSKPIAERRGSDERDAKAILHARFDDELELLVQSDEAAGRKPPDCKRRVTIGG
Ga0208658_1004899	Ga0208658_10048992	F003307	MADSLLDNVDVHDAGDKIILSSPDEMTLNAVLQQMKKEGAQGIQQPMKVGRKWIASFEHPGLGQCKVEKIGFQIVITGMSEGAVVARSGEFREKGALVTRGPEQEDGAWKLYLDDAGARTGNMVTG
Ga0208658_1005111	Ga0208658_10051112	F016461	MYHPTIFFDPQFTVGVMAGWLLQAAGVGALLLAGLWFSIAGEWRRGTPAPTAFRALAGLGLAMFLGGILWQFVGYFRTGTLSW
Ga0208658_1005350	Ga0208658_10053502	F006263	MGTGWQLLEGVGTLLVSIALTYWLFVAPSRIKREQRQKARDLRDPRNR
Ga0208658_1005497	Ga0208658_10054971	F091213	MGRAVQMLICNEDAPRRETRGIGRETLGIQSVGLSTPREKLRSGVGQKELAVDQVLANFVAELLVVLHPATLPMLERMFEDVKQDAETDGEWELKRRAEIGIAAARVAAREQEAIEN
Ga0208658_1006269	Ga0208658_10062691	F037023	MTFYVEGVSKHDEPEPEVRRIGEYESLTEAIAVAQKAIEKFLRDAHRRGMTAKRLFTVYEEEGEHMFIFQDEAGTFNVPSFDHTDYARTMAATICGRLK
Ga0208658_1007211	Ga0208658_10072111	F001984	MNRFRRTATDIAAVIFVLVLPACGIFQETYGIQEVDNWVRSNEPLAESGQMKWSVYYAGYFEKVAATPVISEGPVMEGAGIMLTAALFFEQGRLDRAGFDSVRGVMRKYQTVDDAAANLLAREALVRALEQKDKVAPRSSP
Ga0208658_1007462	Ga0208658_10074621	F091213	VRTSGQMLICNDVGAYREGFGIEGVCLSTPREKLRSGAGQNELAVDQVLANFVAELFVILHPATLPMLERMFEDVKQDAETDGEWGLKRRAEIGIAAARIAAREQEAIET
Ga0208658_1009598	Ga0208658_10095982	F041796	MARRSFLRACGGSAALLVPLLRDIEARADGAGAPLRFLIIHKPLGVQWPLWRPAVFP
Ga0208658_1009953	Ga0208658_10099531	F031088	MKLNVLAVAVAATAIGAFSTNAQVVIEERRDPAVVIEHDRPDTSVTIEKRDGFLGTEKKTITKETTGSGDCTSKTVHKEDITGSEIQKTNCN
Ga0208658_1011801	Ga0208658_10118012	F021258	VQVEFGRAGFFDRMDLRAQVIRAQEVVGYPEPAGRVAF
Ga0208658_1011917	Ga0208658_10119172	F089000	MGEPTPETPASKYFVATVAMIAGAFFFAVGAGLLPIPGGPSNLHGPLWLVLCVGLAFFLTGGAIILQLLGHANDSGDRPAGAPLWLRAVQYLIDLCIFVCFGAISSWVAFGP
Ga0208658_1012281	Ga0208658_10122811	F070780	MSAFFESLARRRAALVQRSTRQRGDIAAAVASVRRASAEPLLLGAGIAATVLTSSPKLRG
Ga0208658_1012667	Ga0208658_10126672	F017505	VKARFAVAPNFHCSGSWKDRLLVAEGSGWCAPHDDELASLTLTKPGSDPACCCLFSVPAHMRNRFWAMLNEEAAEGTGDFDEFSEDLANFLTFKELPPPKDSVSELLIQSPDGKVETGDVWALINFGEEPVLLTWPQFQLRLGPAQGCRMAVGLPPNVVPPPKDELNVLLAIRLGPA
Ga0208658_1013435	Ga0208658_10134352	F044348	ADYASGRDLFSEGQWDWLIAASYSDFALIEPERVTIVYPASYEIRDRDYRLVAHPTPPRDSLRAAQKEMSRFFR
Ga0208658_1013566	Ga0208658_10135662	F070242	KIARMLPRRQRRAFEQAALSFRDGGMFEADRWRAGLLHTAHRAALVASGDVLGAFDQIVREDRHLAGDVARGGEALLKAARENREIVEMINFAVSDDLSTMNRRLGID
Ga0208658_1013695	Ga0208658_10136951	F007886	YLVVEGGDAVVAVFEVLEVVLAGVLAGGDTAVEAGVEGAVDVVCSDVLGADSFLSPVRGAGASLPGDGFSLSE
Ga0208658_1015237	Ga0208658_10152371	F027190	RAHLNGRVQVPDLADTVGPVTESNCAGAISPGGEQLEVNYQSVTKSGIPDEVNSIRSAVLTSLLGKERSPNKIVPPALREWIAAGGEPQMVGDGMVGSSSDVNQGTTAGGQRAGRGQSPRSSEEAGNDRGAKEGRNVVLGVVGVSSQKDPGSAVRLCARMLRKTGLELLLRPGNGPPETQVSGAQACAAGATLPKALSRVPEPVH
Ga0208658_1015537	Ga0208658_10155372	F062737	TLWKNTRQVVHTAAEPPNHGRICLAMMGWTRNSRNDERKIVAAYGRVAARGARITWA
Ga0208658_1016259	Ga0208658_10162592	F006520	MWILIVYVFIAAVGEAVVIAIGLTLDRIYPLASLPISLSLFFAVLAFGWPLAVRSTKPNHAKSEKLAN
Ga0208658_1017101	Ga0208658_10171012	F034962	MRALVVTSNPATASSEPETPAAALSDLGCEVVAVGYDVDQLPEDIELQRPSVVVVDAGA
Ga0208658_1017937	Ga0208658_10179372	F093175	GDGWHLVGLDAEGRVWFGSPRRTAKGRMLAWALMDESVESEDAPQAPITAPERIEALVPERHWPTKPRA
Ga0208658_1018761	Ga0208658_10187611	F049465	MSLQRELPRMDLRFAKLCIELDCSTVFDSAIFRHCPTCGSVECYPVESWLNRERSETAPVVIGNGNMDRAARVADMPRPVWLERLRAKRVEGDA
Ga0208658_1019088	Ga0208658_10190882	F068886	LGRSSSSRWRWIVLCDRAALGGLALGLALYVMPLWREGRLRVAFWITLLSTLA
Ga0208658_1020539	Ga0208658_10205392	F035133	TRHMNSEQLEAPMANAFIDWTSRAAIATRIAEEQRHPVESWKELIVPEDYDLSLEKIEYQIKPAKWPWLVHII
Ga0208658_1021118	Ga0208658_10211181	F002389	MAAGDAAGGPLARLAADPRDPEAALQAVRFELYRENIYGALEMLEAAHAAHPHPGYAEQAARIRSWLVHLASREAYISAQDEQYRRLRWRGGLKLIEKRIRMMLGRKTRKMIER
Ga0208658_1021635	Ga0208658_10216351	F098734	MKKKPPGVFSLIVTAFTGFGSHIMTLCVTGRDRLLAL
Ga0208658_1021670	Ga0208658_10216701	F023288	MGGLALLAVGAATSWWAMSLGWAALVIAFFARVAEADGFAVPRPGRVAIRRGGFDIPLAFKVRRGERWLLFVCEEDPERGGWSDVYTVLDQPKGTDGSDGFEPLYSLPPASPPSGWSLRGRVPVDDLRFEYHERSTYVTRGSLERSLSAAGM
Ga0208658_1022004	Ga0208658_10220041	F036745	GFPLTVPAPNGQGTVVATGNAFAGLRIFEAPGAAGMSTINGFVAWQNAQNGLRLYGGEKVKVRNSVFLANVLNGVYVTGYDASAAGNDLSQVDLGSVSDAGRNVLQASVGSMPDLAGLCVGMSPSRGLLTLSARGNVFAGPTDCTTSTAGIVRSAVCGGFVDLGVVSAAGTTVNVD
Ga0208658_1022186	Ga0208658_10221861	F100042	VSLMSRLMTLARPTGVGHAISTYTIPIDGRDEWIAAARRQA
Ga0208658_1022728	Ga0208658_10227281	F029270	MAQELIIDVHGHEISVHVRGTSLRTTYRKGDAPWLVCTELRADDPDAIFTRDEFKAMAWNTANATARKLGWLV
Ga0208658_1022834	Ga0208658_10228342	F103796	ESDHAGAEPWQYMVCYEFDSEASLQAFVRSDTLRAMTRDYNARFGGAGDRARLAYRQIYP
Ga0208658_1022912	Ga0208658_10229121	F021571	QGKKLPHCKIVNAYDPTIAPIMKGKSNCPAQFGRKPGLLSEPTAGFIFATAVPVGNPSDASYVLPLLDKVQHAIARVRGPKTPAIHSVAGDLGVNDTALRQALHDRGILSVGIPKTVAPINPEPRPEAILDLLNEAGLNRKRTPHQVQLACACGYSRPVVESHIASLLARGAGQ
Ga0208658_1023050	Ga0208658_10230502	F028610	PRPAFVYDDAIQHHAVDPTLPLPAEKILWIQDQMVKAGKLKAPLDLKTVTAPEYRERALKVIGH
Ga0208658_1023232	Ga0208658_10232322	F061029	MADTNTNCPVCKLPVGDSKFRCHLCRAAGKDVRFDSGPCEAEHLTKAHTKAEIERFDVEQTIRKP
Ga0208658_1023719	Ga0208658_10237191	F001574	VNRYVAIPKRGVNVMTSLRLGTSVLDFMNPNGLVRPAIEKFAGAWLACFVVMAHGDFANALSLDHAQLASICGTIGALVAVALLAQMDRTTNSLPRQMTISAFATFIGDVFAHPSHFPPQWGEPLVTAVVSAVIAVAVWHAKRLVFSR
Ga0208658_1023781	Ga0208658_10237812	F063749	MKNLFAVILALTAATAAVAKPSPIEPVRSANPIALARVSAEFNIGPAGATLERNYFRAPESDSHSGLYLCRFEPSMFAKVRLTQSCK
Ga0208658_1024082	Ga0208658_10240821	F023433	MNLLRSICCLFGSRCEGEEPKPTKETIRDEPSADLGQKEAKLEKTGKEQMGHMEGGDASKTAQQPT
Ga0208658_1024616	Ga0208658_10246161	F025363	GVQTWGDRTEPSITVIPRSGSAVTVSVSGTGLRSNDHLVVEVDQLLRSPDEDGQPSWTRGQPLYGASLGPNGAGEIEHTVTLTLPAGDFDDLGARAWVGAEPEPCYGHGNTTGCVRVHIPRPQERPQLSVTWETFVKVPRLLVRLKARNLAQRPSRWMTLRAYGLLAA

Showing 1 to 39 of 39 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

3300026047: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Sandmound_ThreeSqA_D1_rd (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences