Sample 3300003160

Basic Information
IMG/M Taxon OID	3300003160 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0110115 \| Gp0061294 \| Ga0006779
Sample Name	Avena fatua rhizosphere microbial communities - H4_Bulk_Litter_22 (Metagenome Metatranscriptome, Counting Only)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Basic Information

IMG/M Taxon OID

3300003160 Open in IMG/M

GOLD Reference
(Study | Sequencing Project | Analysis Project)

Gs0110115 | Gp0061294 | Ga0006779

Sample Name

Avena fatua rhizosphere microbial communities - H4_Bulk_Litter_22 (Metagenome Metatranscriptome, Counting Only)

Sequencing Status

Permanent Draft

Sequencing Center

DOE Joint Genome Institute (JGI)

Published?

Use Policy

Open

Dataset Contents
Total Genome Size	5678828
Sequencing Scaffolds	28
Novel Protein Genes	32
Associated Families	24

Dataset Contents

Total Genome Size

5678828

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
Not Available	20
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → Flavobacteriaceae → Joostella → Joostella marina	1
All Organisms → cellular organisms → Eukaryota → Sar → Rhizaria → Endomyxa → Phytomyxea → Plasmodiophorida → Plasmodiophoridae → Spongospora → Spongospora subterranea	2

Dataset Phylogeny

Taxonomy Groups

Number of Scaffolds

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

Not Available

All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila

All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia

All Organisms → cellular organisms → Bacteria

All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes

All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → Flavobacteriaceae → Joostella → Joostella marina

All Organisms → cellular organisms → Eukaryota → Sar → Rhizaria → Endomyxa → Phytomyxea → Plasmodiophorida → Plasmodiophoridae → Spongospora → Spongospora subterranea

Ecosystem Assignment (GOLD)
Name	Avena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa, For Root-Enhanced Decomposition Of Organic Matter Studies
Type	Host-Associated
Taxonomy	Host-Associated → Plants → Rhizosphere → Soil → Unclassified → Avena Fatua Rhizosphere → Avena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa, For Root-Enhanced Decomposition Of Organic Matter Studies

Ecosystem Assignment (GOLD)

Name

Avena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa, For Root-Enhanced Decomposition Of Organic Matter Studies

Type

Host-Associated

Taxonomy

Host-Associated → Plants → Rhizosphere → Soil → Unclassified → Avena Fatua Rhizosphere → Avena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa, For Root-Enhanced Decomposition Of Organic Matter Studies

Alternative Ecosystem Assignments
Environment Ontology (ENVO)	terrestrial biome → rhizosphere → soil
Earth Microbiome Project Ontology (EMPO)	Host-associated → Plant → Plant rhizosphere

Alternative Ecosystem Assignments

Environment Ontology (ENVO)

terrestrial biome → rhizosphere → soil

Earth Microbiome Project Ontology (EMPO)

Host-associated → Plant → Plant rhizosphere

Location Information
Location	Hopland, California, USA
Coordinates	Lat. (^o)	38.97364	Long. (^o)	-123.117453	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Location Information

Location

Hopland, California, USA

Coordinates

Lat. (^o)

38.97364

Long. (^o)

-123.117453

Alt. (m)

N/A

Depth (m)

Location on Map

Zoom:

Family	Category	Number of Sequences	3D Structure?
F000817	Metagenome / Metatranscriptome	879	Y
F000864	Metagenome / Metatranscriptome	855	Y
F001233	Metagenome / Metatranscriptome	741	Y
F001418	Metagenome / Metatranscriptome	698	Y
F001633	Metagenome / Metatranscriptome	660	Y
F004796	Metagenome / Metatranscriptome	423	Y
F007777	Metagenome / Metatranscriptome	345	Y
F014312	Metagenome / Metatranscriptome	264	Y
F026174	Metagenome / Metatranscriptome	198	Y
F027072	Metagenome / Metatranscriptome	195	Y
F030647	Metagenome / Metatranscriptome	184	N
F037587	Metagenome / Metatranscriptome	167	Y
F038031	Metagenome / Metatranscriptome	166	Y
F039900	Metagenome / Metatranscriptome	162	Y
F040967	Metagenome / Metatranscriptome	160	Y
F043602	Metagenome / Metatranscriptome	156	Y
F054015	Metagenome / Metatranscriptome	140	Y
F067018	Metagenome / Metatranscriptome	126	Y
F076910	Metagenome / Metatranscriptome	117	N
F077592	Metagenome / Metatranscriptome	117	Y
F079443	Metagenome / Metatranscriptome	115	Y
F079670	Metagenome / Metatranscriptome	115	N
F083529	Metagenome / Metatranscriptome	112	Y
F104228	Metagenome / Metatranscriptome	100	Y

Family

Scaffold	Taxonomy	Length	IMG/M Link
Ga0006779J45831_100003	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	519	Open in IMG/M
Ga0006779J45831_100010	Not Available	877	Open in IMG/M
Ga0006779J45831_100020	Not Available	729	Open in IMG/M
Ga0006779J45831_100265	Not Available	641	Open in IMG/M
Ga0006779J45831_100298	Not Available	601	Open in IMG/M
Ga0006779J45831_100331	Not Available	534	Open in IMG/M
Ga0006779J45831_100377	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	773	Open in IMG/M
Ga0006779J45831_100409	Not Available	587	Open in IMG/M
Ga0006779J45831_100940	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia	657	Open in IMG/M
Ga0006779J45831_101097	Not Available	644	Open in IMG/M
Ga0006779J45831_101334	Not Available	544	Open in IMG/M
Ga0006779J45831_101390	Not Available	609	Open in IMG/M
Ga0006779J45831_102052	Not Available	565	Open in IMG/M
Ga0006779J45831_102091	Not Available	599	Open in IMG/M
Ga0006779J45831_103122	Not Available	521	Open in IMG/M
Ga0006779J45831_103364	All Organisms → cellular organisms → Bacteria	882	Open in IMG/M
Ga0006779J45831_103638	Not Available	588	Open in IMG/M
Ga0006779J45831_104129	Not Available	1113	Open in IMG/M
Ga0006779J45831_105119	Not Available	693	Open in IMG/M
Ga0006779J45831_105286	Not Available	685	Open in IMG/M
Ga0006779J45831_106013	Not Available	500	Open in IMG/M
Ga0006779J45831_106353	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes	1689	Open in IMG/M
Ga0006779J45831_106940	Not Available	566	Open in IMG/M
Ga0006779J45831_107050	Not Available	541	Open in IMG/M
Ga0006779J45831_107263	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → Flavobacteriaceae → Joostella → Joostella marina	577	Open in IMG/M
Ga0006779J45831_109726	All Organisms → cellular organisms → Eukaryota → Sar → Rhizaria → Endomyxa → Phytomyxea → Plasmodiophorida → Plasmodiophoridae → Spongospora → Spongospora subterranea	662	Open in IMG/M
Ga0006779J45831_110672	All Organisms → cellular organisms → Eukaryota → Sar → Rhizaria → Endomyxa → Phytomyxea → Plasmodiophorida → Plasmodiophoridae → Spongospora → Spongospora subterranea	701	Open in IMG/M
Ga0006779J45831_110685	Not Available	596	Open in IMG/M

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0006779J45831_100003	Ga0006779J45831_1000031	F014312	RRLRLLRPTKGSANGVVRLWERVKAERFALAMTPLVEAERLARKTERFSERPDKNG*
Ga0006779J45831_100010	Ga0006779J45831_1000101	F079670	LKKGLKVLEMVKRERNKIIIIDNSLKLRTILYFFFKKKYNLS*
Ga0006779J45831_100020	Ga0006779J45831_1000201	F000817	ELRWTAAVNRLKPEVSRIIPGNWGKAESGWLARPLLRRIARFDGGGRIHQFL*
Ga0006779J45831_100265	Ga0006779J45831_1002651	F001418	NRKVCQREAEFTSSSDSVRALSVNAKKGLRDEERLETVPNSVK*
Ga0006779J45831_100298	Ga0006779J45831_1002981	F007777	LTQLRGSVARPVLGVVERKAASRSGLLPVMEADAHLRTDPQLGKTSGGEQRAHVSPDSDATFRPRMPVGEQTARGSLGT
Ga0006779J45831_100331	Ga0006779J45831_1003311	F004796	SYRGICTSQVNSKDDTVNSTSLPLPLQLTKPVLLAGDLDTQVREGLSDAYDSKAQLCSHTQSSAQSKTLNVLGIQVDVNADIVVDDVIA*
Ga0006779J45831_100331	Ga0006779J45831_1003312	F004796	MNTNLPLPLQLTKPVLLAGDLDTQVREGLSASYDAKTQMCSGTHSSTQSKTLNLLGIQVDVNADAVVDDVIA*
Ga0006779J45831_100377	Ga0006779J45831_1003772	F001633	AGGVLPDATLCGMQMFRSHGGTVLTVAGRDLSSEASAPGSDTPCRERRAGRGADTPATFVSSRRHPYHGDGASFWPAVGPALRV*
Ga0006779J45831_100409	Ga0006779J45831_1004091	F037587	FQVTRFTALFTTGMHGTEHCNLGAPSVLPFHSPISDFAVTGSKLRSALQLSPGRGWMLVTAFRSPATVAAFTASIPGSTFLACYFASAPIDSAARSIFGSATGPRFAPRPAASTLQTRCSFLDLDLPHTRPPLPFRTVTSLRIKAFCRICCSSTRLPIPPDLRSLPAAGLYH
Ga0006779J45831_100725	Ga0006779J45831_1007251	F104228	LMVQRVTSVIILLLKRRSYGQCDPYDYWYTNTLSYGGPSNFKQQLSILTNAEYDAGATMTGNASSIRSIIILFSG*
Ga0006779J45831_100940	Ga0006779J45831_1009402	F001633	GGVLPDATLCGMQMFRSHGGTVLTVAGRDLSSEASAPGSDASCRKRRAGRGADTPATFTFSRRHPYHGDGASFWPAVCPALRV*
Ga0006779J45831_101097	Ga0006779J45831_1010971	F054015	MRVTLAVPRKRDLPNERRPTAGQSEHAHREGHKISAGSVKTFRHVSDVEMNTAGL*
Ga0006779J45831_101334	Ga0006779J45831_1013341	F004796	LPGHPFKTRYTKDETVNSTSLPLPLQLTKPVLLAGDLDTQVRDGLSDAYDTKTQLCSHTQSSARSKTLNVLGIQVDVNADIVVDDVIA*
Ga0006779J45831_101390	Ga0006779J45831_1013901	F001233	EQSWTAAVNRLTLDFSRIIPGDWGKVESGWLARLLLSRIARFGSGGRIHQFLWQRSRAVSTREKGTER*
Ga0006779J45831_102052	Ga0006779J45831_1020521	F076910	QARSVQTYQVFRAQAGECRAVATVPYVPKSSRTAGPLMVSRCVSTGAPPVLGGHGDRQLAGSVHTYRVCRGTETLGPSSEVTRLRRSRNPARAILLDLANDTDEHVRPGNPAPANGSPSSNRGRLEEKPITLKARPHRSTVAPITGPRLGGRGSKEAHQKWPDLGVAPRGEGSVLPNVLGAVTEQAIA
Ga0006779J45831_102091	Ga0006779J45831_1020911	F004796	VNSTNLPLPLQLTEPVLLAGDLDTQVRDGLSDKYDTKTQLCSHTQSQARSNTLNVLGIQVDVNADVVVDDVIA*
Ga0006779J45831_102091	Ga0006779J45831_1020912	F004796	MNLPLPLQLTEPVLLAGDLDTQVREGLSDKYDAKAQLCSGTQSQSKSKTLNFLGIQVDVNADLVVDDVIA*
Ga0006779J45831_103122	Ga0006779J45831_1031222	F067018	MTEKQTKPQALSLEVQELESWCNPGCGSSSTDPRCTCPISISTTGSLFTSKTSS*
Ga0006779J45831_103364	Ga0006779J45831_1033641	F083529	MRFILIFGLLLMALATTAFVIGNFKVTSSTKVVDTPSVQASTRQDRIVKVPVFLDAALFLGGLAMVVLGARTN*
Ga0006779J45831_103638	Ga0006779J45831_1036382	F030647	NILGANFLLYLRTPKIRPEIETRLGYPVLNSDHVHLSDMTVFIASSSVHLLFVIQHGGKIKPKIGPKVIHILLALEKLFLL*
Ga0006779J45831_104129	Ga0006779J45831_1041291	F038031	VGFRPRGLRTFGVKVPPALRSRQGWKERSVFSDPFSITYDGNVKSLPRTEVARDYNRYTTADGEFEVLISNNLRKPQNGIATVSFKLARYLPDPTPGDFSNPYRNVRNSFGFSYGFDAITRAEVSVDVPRLRATVNTLIDSAFQGRLLGGER*
Ga0006779J45831_105119	Ga0006779J45831_1051191	F039900	LRNGSSWFRPDEGSQSKDRGPLLGQTHYSSTEKRGGVSGMEQFLSEKDQEVWKYVLSDYRTESERDSEADIPVPDRLLPKRRSQELVRMLKLSQMIGLLLWLNRSELITLGGRERLLYLQAKASFEAIEAGLRFARRLSQEEKLRSDFRHQMRELNRRPQSKHFRQSEARRIGVGYRDKGMLPGSSTGARTRAQKDAYIPSHLVPRILRDALQLVTPACLTADEEWVDLS
Ga0006779J45831_105286	Ga0006779J45831_1052861	F079443	AIPLQVREMMDVREENAEGDVASAVPLSERERICKMRRMRLAWISSAVLALGLMATASWAQEPNPNAPGNEELPGVAIAGVSEEFAPVWGGPFSGSATLTINGQSYPVAVTSNSLDLAPLPDNFGRMVGTTVHVFDFGDGNLLMTSDEVRLTPTQPGWFSVQATLTITSGTGIFSNAAGQIDVYGNLASDGSTATELWLMEGRVMV*
Ga0006779J45831_106013	Ga0006779J45831_1060131	F043602	EAAMCYSRDWETTERRKQREAEAAEAQRKRDGVIKTLLSEAEKAAQARTEKPAAKVTALSKERG*
Ga0006779J45831_106353	Ga0006779J45831_1063535	F027072	MKSLMSLWSRMAEESAIQCCTSASRDINTVSARIEHEGLSFLTITLPSLGKAI
Ga0006779J45831_106940	Ga0006779J45831_1069401	F000864	MQFLVLISLIVAVLGQTKPTLSNDFAANVEYSETFGQRKVDFKGAWYSDFTDGADAYDVTLAGQGDVLIWQNKTSKGMTEYVERKITTPTCTRFDAPTYLPHPFSFLTNAVNNGTCFAANMTGTAWSVYDPRAANITLCASNDGKTPYALTEVRFGTFHSTRTITWNNFISGKPSSRYFVLPAICTTR
Ga0006779J45831_107050	Ga0006779J45831_1070501	F004796	VNSGNLPLPLQLTKPVLLAGDLDTQVREGLSDKYDAKTQLCSHTQSQAKSKTLNFLGVQVDVNADVVVDDVIA*
Ga0006779J45831_107050	Ga0006779J45831_1070502	F004796	MTNLPLPLELTKPVLLAGDLDTQVREGLSDKYDAKAQLCSGTQSQAKSNTLNVLGIQVDVNADLVVDDVIA*
Ga0006779J45831_107263	Ga0006779J45831_1072631	F077592	LGVGMDIPLGAWLNSTALGWTAHGHLGWFPGTSPIGIRIDGDYTGFGARDLDCPNCSSTKLTQLSGSLEWRIPLDRKSKVNPVIYFLGGGGIDWFSDFAPYRKQDDNTIVTAGSNTITNFPGFGNVVSTDDSGTFYHWSVGGGVQFGGLFIESQYKSINTNGASSMHVPVLVGWNWNF*
Ga0006779J45831_109726	Ga0006779J45831_1097261	F040967	MSNQYLTETSILSQVEIDYSTVEPISTDSYDESAVLSSILERNISDLFACALQFAIVGCGNKTLGSVKVSGVEKKVESIVQEHGITINGTLNAKLEPGELTMKRLSRFFRYNIRDYIKERHCESFLYRKYCTQGQPEFVFPGAEYMVDETNCSGILEAYEEMDKVLNTRFLPRIHQILKARKIAY*
Ga0006779J45831_110672	Ga0006779J45831_1106721	F040967	GVDLILCKKLFNLPGVTMSNQYLSEQVILSQVEVDYTAIEPISTDSYDESAVLSSILERDISELFACALQFAIVGCGNKTLGSVKVSGVEKRVESIVQEHGITVNSSLNAKLEPGELTMKRLSRFFRFNIRDYIKERHCESFLYRKYCTQGQPEFVFPGAEYMVDETNCSGILEAYEEMDKVLNTRFLPRIHQILKARKIAY*
Ga0006779J45831_110685	Ga0006779J45831_1106851	F026174	RILAGLPLEWKAIPGDLQERAVIIALHCCLNGPVGVNKQTTFPVVGAAKIKDIFGCTNSSWKGFCYAVATVVAAVDPKIDCGQVRKNGKYWPL*

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300003160: Avena fatua rhizosphere microbial communities - H4_Bulk_Litter_22 (Metagenome Metatranscriptome, Counting Only)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences