Sample 3300026006

Overview

Basic Information
IMG/M Taxon OID	3300026006 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116065 \| Ga0208533
Sample Name	Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_25C_80N_302 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	Y
Use Policy	Open

Dataset Contents
Total Genome Size	31066178
Sequencing Scaffolds	18
Novel Protein Genes	22
Associated Families	22

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	5
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Candidatus Koribacter → Candidatus Koribacter versatilis	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. Root1462	1
Not Available	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → Solibacteraceae → Candidatus Sulfopaludibacter → unclassified Candidatus Sulfopaludibacter → Candidatus Sulfopaludibacter sp. SbA3	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 → Rice Paddy Soil → 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 → paddy field → paddy field soil
Earth Microbiome Project Ontology (EMPO)	Free-living → Saline → Water (saline)

Location Information
Location	USA: Twitchell Island, California
Coordinates	Lat. (^o)	38.1087	Long. (^o)	-121.653	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Family	Category	Number of Sequences	3D Structure?
F001012	Metagenome / Metatranscriptome	806	Y
F002903	Metagenome / Metatranscriptome	522	Y
F006636	Metagenome / Metatranscriptome	368	Y
F008767	Metagenome / Metatranscriptome	328	Y
F010108	Metagenome / Metatranscriptome	308	Y
F011047	Metagenome / Metatranscriptome	296	Y
F011438	Metagenome / Metatranscriptome	291	Y
F011791	Metagenome / Metatranscriptome	287	Y
F014796	Metagenome	260	Y
F016515	Metagenome	246	Y
F019004	Metagenome / Metatranscriptome	232	Y
F020237	Metagenome / Metatranscriptome	225	Y
F028562	Metagenome	191	Y
F040521	Metagenome	161	Y
F045279	Metagenome / Metatranscriptome	153	Y
F050783	Metagenome / Metatranscriptome	145	Y
F053349	Metagenome	141	Y
F057190	Metagenome	136	Y
F072511	Metagenome	121	N
F082358	Metagenome	113	Y
F097106	Metagenome	104	Y
F099198	Metagenome	103	Y

Family

Category

Number of Sequences

3D Structure?

F001012

Metagenome / Metatranscriptome

806

F002903

Metagenome / Metatranscriptome

522

F006636

Metagenome / Metatranscriptome

368

F008767

Metagenome / Metatranscriptome

328

F010108

Metagenome / Metatranscriptome

308

F011047

Metagenome / Metatranscriptome

296

F011438

Metagenome / Metatranscriptome

291

F011791

Metagenome / Metatranscriptome

287

F014796

Metagenome

260

F016515

Metagenome

246

F019004

Metagenome / Metatranscriptome

232

F020237

Metagenome / Metatranscriptome

225

F028562

Metagenome

191

F040521

Metagenome

161

F045279

Metagenome / Metatranscriptome

153

F050783

Metagenome / Metatranscriptome

145

F053349

Metagenome

141

F057190

Metagenome

136

F072511

Metagenome

121

F082358

Metagenome

113

F097106

Metagenome

104

F099198

Metagenome

103

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208533_100072	All Organisms → cellular organisms → Bacteria	1446	Open in IMG/M
Ga0208533_100357	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1068	Open in IMG/M
Ga0208533_100682	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	947	Open in IMG/M
Ga0208533_101562	All Organisms → cellular organisms → Bacteria → Terrabacteria group	787	Open in IMG/M
Ga0208533_102247	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Candidatus Koribacter → Candidatus Koribacter versatilis	722	Open in IMG/M
Ga0208533_102323	All Organisms → cellular organisms → Bacteria → Acidobacteria	717	Open in IMG/M
Ga0208533_102616	All Organisms → cellular organisms → Bacteria	699	Open in IMG/M
Ga0208533_103614	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. Root1462	647	Open in IMG/M
Ga0208533_104083	All Organisms → cellular organisms → Bacteria	628	Open in IMG/M
Ga0208533_105235	Not Available	592	Open in IMG/M
Ga0208533_105535	All Organisms → cellular organisms → Bacteria	583	Open in IMG/M
Ga0208533_106289	All Organisms → cellular organisms → Bacteria → Acidobacteria	564	Open in IMG/M
Ga0208533_106743	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	554	Open in IMG/M
Ga0208533_107920	All Organisms → cellular organisms → Bacteria → Acidobacteria	532	Open in IMG/M
Ga0208533_108255	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → Solibacteraceae → Candidatus Sulfopaludibacter → unclassified Candidatus Sulfopaludibacter → Candidatus Sulfopaludibacter sp. SbA3	526	Open in IMG/M
Ga0208533_109037	All Organisms → cellular organisms → Bacteria	513	Open in IMG/M
Ga0208533_109293	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	510	Open in IMG/M
Ga0208533_109469	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	507	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0208533_100072

All Organisms → cellular organisms → Bacteria

1446

Open in IMG/M

Ga0208533_100357

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

1068

Open in IMG/M

Ga0208533_100682

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

947

Open in IMG/M

Ga0208533_101562

All Organisms → cellular organisms → Bacteria → Terrabacteria group

787

Open in IMG/M

Ga0208533_102247

All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Candidatus Koribacter → Candidatus Koribacter versatilis

722

Open in IMG/M

Ga0208533_102323

All Organisms → cellular organisms → Bacteria → Acidobacteria

717

Open in IMG/M

Ga0208533_102616

All Organisms → cellular organisms → Bacteria

699

Open in IMG/M

Ga0208533_103614

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. Root1462

647

Open in IMG/M

Ga0208533_104083

All Organisms → cellular organisms → Bacteria

628

Open in IMG/M

Ga0208533_105235

Not Available

592

Open in IMG/M

Ga0208533_105535

All Organisms → cellular organisms → Bacteria

583

Open in IMG/M

Ga0208533_106289

All Organisms → cellular organisms → Bacteria → Acidobacteria

564

Open in IMG/M

Ga0208533_106743

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

554

Open in IMG/M

Ga0208533_107920

All Organisms → cellular organisms → Bacteria → Acidobacteria

532

Open in IMG/M

Ga0208533_108255

All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → Solibacteraceae → Candidatus Sulfopaludibacter → unclassified Candidatus Sulfopaludibacter → Candidatus Sulfopaludibacter sp. SbA3

526

Open in IMG/M

Ga0208533_109037

All Organisms → cellular organisms → Bacteria

513

Open in IMG/M

Ga0208533_109293

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

510

Open in IMG/M

Ga0208533_109469

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

507

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0208533_100072	Ga0208533_1000722	F053349	MKTFQDGAYAMAALSASVVAFRILVRKGLVTRDEAVRGLLDEAVQRAIFAESQHEETIGRTTAELNRQSAEILKFIAESL
Ga0208533_100357	Ga0208533_1003571	F050783	MDIETVPTDRSLEENGLLEAQLQLDEGDLIKKLSLSAATAKILCLCYAIEPPVGSEVQVLEGEETEIIKNFWKLAV
Ga0208533_100682	Ga0208533_1006821	F072511	GSEMIDPSEKLSNDHAHDTQSFCLRNAMPELREHGSEPTAIGKLESLAGQLVERLAQRSCVQSVIASAAAVLQSTDEMKMAELNDPALGCTELDNTGNLVGDRGANTSVYRRRNGCEGVGPTLHVLSAFAQHRIEEDGSILMAGFDRHHIQNPIFSSKAKVKSVQDQNQRSFRQGKVPRPRCELSQSRTKPPTQPLRSKAIASSKSFQRACVHKHWAQRSGVRSLTLAASSFLADSPRTRALTALTTSGTEVINFRSATLRVRVPRMHAHELHPD
Ga0208533_101562	Ga0208533_1015622	F040521	MFRRILGELGSSFIVCLGERVLERAVFPGLHLLPGRMIASDPTRADSMTALIAEAIALMGMVWVFVGSLYAIGWLYRRPLRWQVPPIVTIVIVALIFAGSFSQWYTLPAPPQP
Ga0208533_102247	Ga0208533_1022472	F019004	SNTTPDDIDLTFVVMAVPNNGRATAIGYQHFMLHRGTVGKELPFGETLPHGGYVVHVDAVGEVSPKNLIYRDRMQTPGQLQVMVGP
Ga0208533_102323	Ga0208533_1023231	F011791	LYFLYSALTALAAILLLPYWVVQGLRHGKYFSNLGQR
Ga0208533_102616	Ga0208533_1026162	F082358	ISFVYGLTASIFFVIVLMIVGTKWLASEPGAANAPLSRILLGAFLGLFLGALLFGLIYSTVLSFFTAKRRSEI
Ga0208533_103249	Ga0208533_1032491	F020237	MTLGKRLYLNFGFILGMVLLLFVVNYLAVRREHAAKDAAAASLK
Ga0208533_103614	Ga0208533_1036142	F099198	MADAITALIGAIIMIGYMFLIAAKLAAPPLWICVLIGLALMLWGFWWEDWEPVVKRPKK
Ga0208533_104083	Ga0208533_1040831	F014796	FPLLFRPMDSEYGLFPTAVIAARESWLKDPKNRKLAVDFLRALNEGLQLTRESPNAVKQALRKYIRVNDEALLQGSVEYFRDAFPSTLRTREKVMTNALKFIDHPKAKQYDVTQSFDNSLVDEIK
Ga0208533_105235	Ga0208533_1052352	F028562	ERRRAPAARPPAKIRQLEARLAQVEADLARVRSTATRGGLTRVKLAGIEKAMARHVARAQTGLKDSVNRLSRRLQSVRSPKEAARQIAQARENVKESLDRLAQRLGESQKMVTREVSLLTRGLKAGVRAGRAVYRGRRR
Ga0208533_105535	Ga0208533_1055351	F057190	MSANNGGKSALHVATFSGWYRFEQNGKDLKQTKRDLTYWTLTCMSVDPDNPQKIYAGSEHSGLFYTDNGGARWKRAEPNTPKMMLFSALALNDGVMVGTIPSAVYRSKNGGWEELAGVRINSAGANFPPS
Ga0208533_105903	Ga0208533_1059031	F010108	ACETSRHGETVAAGKHGKFHGYLRGTITGGTFNPNATCPADCGFTDVWIATFFGPDATFSCFEDSRACRFDFEYSAPHQGLRWHHWSDKGRGAGALLHERFHGDIANP
Ga0208533_106289	Ga0208533_1062891	F016515	MNQETDVSRVVAELIEAYFGGLRRTVRKNLTRLTGAFLRLALSVRFGYGGLHLTSVARVLPEGKKFKSSYKWLGRFLACKYFDPSSLAECMLALMLGEKP
Ga0208533_106743	Ga0208533_1067431	F001012	VDAKIRDTAAALTLVKKRVSESLAQHYISMREPRIQMPEDLMKEEQSYERLLQALQDMKGEIAKQIRPVEEQIIQANVEHLRQSFSQESRRLSKCLEEIDDNILACRQYLQDYERIRSSLCGLNEKLTQLGAQSIQVPDGLPATDLGEIVRERIDFLRSQGKI
Ga0208533_107920	Ga0208533_1079201	F011438	FDIMPYEMQVVPAGPETAIVTYNVVLRVPAAEDQGPPPRYQHFSSVWVKQGDNWKMKFLQMTASHWGDW
Ga0208533_108255	Ga0208533_1082551	F002903	PHKIVLHRGTCGQCSHGKGRPAGHDANHARWHGPYATVAHAREAAHAMTGVLIRSECKCV
Ga0208533_108543	Ga0208533_1085432	F045279	LKIYVALAWPNSGFAAKPIVLGYQQLSGSAMLLGRLQNPAVPVRISAG
Ga0208533_109037	Ga0208533_1090371	F011047	MRGLRYVLRNFTAQAVKEHLRSQLERPESDGELTPNEVELVRFAAERSAQLTKLANRSPA
Ga0208533_109058	Ga0208533_1090581	F097106	RTNLADACRPPHLRKLMKPGSLRVVTIDDQRWVVRAVRRLDQSVPPLRFFNGAECRYVAEYPEDWPALPESELTSIFQRAHRGA
Ga0208533_109293	Ga0208533_1092931	F006636	TLCLVFMLPNALLAQARPFPGPDVQQIYQRLLPQIEKIPAFDHHAHPGFADDPDVDAMAAPPNASEALRTRSDNPELAAAAKALFGYPYNDLSPEHAKWLLDKKTEVKKQLAGSAYFNSILDKINIESSVANRAIRFALFCRSRKRYSDLWR
Ga0208533_109469	Ga0208533_1094692	F008767	KNMGKASTYHRDLMEACTANPRPQDLPKIVRENEVSVMSEPDAELWYHVGALMAACGQNDAALRLLKAAVQQNYCAHSALLDDPLLKPLRKETAFNEVLTASSNCENVFKEGRQ

Scaffold ID

Protein ID

Family

Sequence

Ga0208533_100072

Ga0208533_1000722

F053349

MKTFQDGAYAMAALSASVVAFRILVRKGLVTRDEAVRGLLDEAVQRAIFAESQHEETIGRTTAELNRQSAEILKFIAESL

Ga0208533_100357

Ga0208533_1003571

F050783

MDIETVPTDRSLEENGLLEAQLQLDEGDLIKKLSLSAATAKILCLCYAIEPPVGSEVQVLEGEETEIIKNFWKLAV

Ga0208533_100682

Ga0208533_1006821

F072511

GSEMIDPSEKLSNDHAHDTQSFCLRNAMPELREHGSEPTAIGKLESLAGQLVERLAQRSCVQSVIASAAAVLQSTDEMKMAELNDPALGCTELDNTGNLVGDRGANTSVYRRRNGCEGVGPTLHVLSAFAQHRIEEDGSILMAGFDRHHIQNPIFSSKAKVKSVQDQNQRSFRQGKVPRPRCELSQSRTKPPTQPLRSKAIASSKSFQRACVHKHWAQRSGVRSLTLAASSFLADSPRTRALTALTTSGTEVINFRSATLRVRVPRMHAHELHPD

Ga0208533_101562

Ga0208533_1015622

F040521

MFRRILGELGSSFIVCLGERVLERAVFPGLHLLPGRMIASDPTRADSMTALIAEAIALMGMVWVFVGSLYAIGWLYRRPLRWQVPPIVTIVIVALIFAGSFSQWYTLPAPPQP

Ga0208533_102247

Ga0208533_1022472

F019004

SNTTPDDIDLTFVVMAVPNNGRATAIGYQHFMLHRGTVGKELPFGETLPHGGYVVHVDAVGEVSPKNLIYRDRMQTPGQLQVMVGP

Ga0208533_102323

Ga0208533_1023231

F011791

LYFLYSALTALAAILLLPYWVVQGLRHGKYFSNLGQR

Ga0208533_102616

Ga0208533_1026162

F082358

ISFVYGLTASIFFVIVLMIVGTKWLASEPGAANAPLSRILLGAFLGLFLGALLFGLIYSTVLSFFTAKRRSEI

Ga0208533_103249

Ga0208533_1032491

F020237

MTLGKRLYLNFGFILGMVLLLFVVNYLAVRREHAAKDAAAASLK

Ga0208533_103614

Ga0208533_1036142

F099198

MADAITALIGAIIMIGYMFLIAAKLAAPPLWICVLIGLALMLWGFWWEDWEPVVKRPKK

Ga0208533_104083

Ga0208533_1040831

F014796

FPLLFRPMDSEYGLFPTAVIAARESWLKDPKNRKLAVDFLRALNEGLQLTRESPNAVKQALRKYIRVNDEALLQGSVEYFRDAFPSTLRTREKVMTNALKFIDHPKAKQYDVTQSFDNSLVDEIK

Ga0208533_105235

Ga0208533_1052352

F028562

ERRRAPAARPPAKIRQLEARLAQVEADLARVRSTATRGGLTRVKLAGIEKAMARHVARAQTGLKDSVNRLSRRLQSVRSPKEAARQIAQARENVKESLDRLAQRLGESQKMVTREVSLLTRGLKAGVRAGRAVYRGRRR

Ga0208533_105535

Ga0208533_1055351

F057190

MSANNGGKSALHVATFSGWYRFEQNGKDLKQTKRDLTYWTLTCMSVDPDNPQKIYAGSEHSGLFYTDNGGARWKRAEPNTPKMMLFSALALNDGVMVGTIPSAVYRSKNGGWEELAGVRINSAGANFPPS

Ga0208533_105903

Ga0208533_1059031

F010108

ACETSRHGETVAAGKHGKFHGYLRGTITGGTFNPNATCPADCGFTDVWIATFFGPDATFSCFEDSRACRFDFEYSAPHQGLRWHHWSDKGRGAGALLHERFHGDIANP

Ga0208533_106289

Ga0208533_1062891

F016515

MNQETDVSRVVAELIEAYFGGLRRTVRKNLTRLTGAFLRLALSVRFGYGGLHLTSVARVLPEGKKFKSSYKWLGRFLACKYFDPSSLAECMLALMLGEKP

Ga0208533_106743

Ga0208533_1067431

F001012

VDAKIRDTAAALTLVKKRVSESLAQHYISMREPRIQMPEDLMKEEQSYERLLQALQDMKGEIAKQIRPVEEQIIQANVEHLRQSFSQESRRLSKCLEEIDDNILACRQYLQDYERIRSSLCGLNEKLTQLGAQSIQVPDGLPATDLGEIVRERIDFLRSQGKI

Ga0208533_107920

Ga0208533_1079201

F011438

FDIMPYEMQVVPAGPETAIVTYNVVLRVPAAEDQGPPPRYQHFSSVWVKQGDNWKMKFLQMTASHWGDW

Ga0208533_108255

Ga0208533_1082551

F002903

PHKIVLHRGTCGQCSHGKGRPAGHDANHARWHGPYATVAHAREAAHAMTGVLIRSECKCV

Ga0208533_108543

Ga0208533_1085432

F045279

LKIYVALAWPNSGFAAKPIVLGYQQLSGSAMLLGRLQNPAVPVRISAG

Ga0208533_109037

Ga0208533_1090371

F011047

MRGLRYVLRNFTAQAVKEHLRSQLERPESDGELTPNEVELVRFAAERSAQLTKLANRSPA

Ga0208533_109058

Ga0208533_1090581

F097106

RTNLADACRPPHLRKLMKPGSLRVVTIDDQRWVVRAVRRLDQSVPPLRFFNGAECRYVAEYPEDWPALPESELTSIFQRAHRGA

Ga0208533_109293

Ga0208533_1092931

F006636

TLCLVFMLPNALLAQARPFPGPDVQQIYQRLLPQIEKIPAFDHHAHPGFADDPDVDAMAAPPNASEALRTRSDNPELAAAAKALFGYPYNDLSPEHAKWLLDKKTEVKKQLAGSAYFNSILDKINIESSVANRAIRFALFCRSRKRYSDLWR

Ga0208533_109469

Ga0208533_1094692

F008767

KNMGKASTYHRDLMEACTANPRPQDLPKIVRENEVSVMSEPDAELWYHVGALMAACGQNDAALRLLKAAVQQNYCAHSALLDDPLLKPLRKETAFNEVLTASSNCENVFKEGRQ

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026006: Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_25C_80N_302 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences