Sample 3300026135

Overview

Basic Information
IMG/M Taxon OID	3300026135 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0114514 \| Gp0125944 \| Ga0209939
Sample Name	Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_A_D1_MG (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	220557608
Sequencing Scaffolds	16
Novel Protein Genes	16
Associated Families	14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	4
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	3
Not Available	2

Ecosystem and Geography

Ecosystem Assignment (GOLD)
Name	Salt Pond Water, Soil And Salt Crust Microbial Communities From South San Francisco Under Conditions Of Wetland Restoration.
Type	Environmental
Taxonomy	Environmental → Terrestrial → Soil → Wetlands → Unclassified → Soil → Salt Pond Water, Soil And Salt Crust Microbial Communities From South San Francisco Under Conditions Of Wetland Restoration.

Alternative Ecosystem Assignments
Environment Ontology (ENVO)	terrestrial biome → wetland area → soil
Earth Microbiome Project Ontology (EMPO)	Free-living → Non-saline → Soil (non-saline)

Location Information
Location	South San Francisco, USA
Coordinates	Lat. (^o)	37.4962	Long. (^o)	-122.1329	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Family	Category	Number of Sequences	3D Structure?
F002483	Metagenome / Metatranscriptome	555	Y
F005815	Metagenome / Metatranscriptome	389	Y
F018541	Metagenome / Metatranscriptome	234	Y
F019205	Metagenome / Metatranscriptome	231	Y
F026568	Metagenome / Metatranscriptome	197	Y
F030933	Metagenome / Metatranscriptome	184	Y
F048318	Metagenome / Metatranscriptome	148	Y
F048673	Metagenome / Metatranscriptome	148	Y
F053306	Metagenome / Metatranscriptome	141	Y
F087388	Metagenome	110	Y
F095691	Metagenome	105	Y
F096759	Metagenome / Metatranscriptome	104	Y
F098275	Metagenome / Metatranscriptome	104	Y
F105198	Metagenome / Metatranscriptome	100	Y

Family

Category

Number of Sequences

3D Structure?

F002483

Metagenome / Metatranscriptome

555

F005815

Metagenome / Metatranscriptome

389

F018541

Metagenome / Metatranscriptome

234

F019205

Metagenome / Metatranscriptome

231

F026568

Metagenome / Metatranscriptome

197

F030933

Metagenome / Metatranscriptome

184

F048318

Metagenome / Metatranscriptome

148

F048673

Metagenome / Metatranscriptome

148

F053306

Metagenome / Metatranscriptome

141

F087388

Metagenome

110

F095691

Metagenome

105

F096759

Metagenome / Metatranscriptome

104

F098275

Metagenome / Metatranscriptome

104

F105198

Metagenome / Metatranscriptome

100

Scaffold	Taxonomy	Length	IMG/M Link
Ga0209939_1000256	All Organisms → cellular organisms → Bacteria	9234	Open in IMG/M
Ga0209939_1000442	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	7453	Open in IMG/M
Ga0209939_1000492	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	7140	Open in IMG/M
Ga0209939_1001427	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	4474	Open in IMG/M
Ga0209939_1003425	All Organisms → cellular organisms → Bacteria → Proteobacteria	3012	Open in IMG/M
Ga0209939_1011032	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1738	Open in IMG/M
Ga0209939_1011901	All Organisms → cellular organisms → Bacteria	1674	Open in IMG/M
Ga0209939_1012254	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	1651	Open in IMG/M
Ga0209939_1015401	All Organisms → cellular organisms → Bacteria	1483	Open in IMG/M
Ga0209939_1035905	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	958	Open in IMG/M
Ga0209939_1037613	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	934	Open in IMG/M
Ga0209939_1043037	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	870	Open in IMG/M
Ga0209939_1049399	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	809	Open in IMG/M
Ga0209939_1053354	Not Available	776	Open in IMG/M
Ga0209939_1062391	All Organisms → cellular organisms → Bacteria	713	Open in IMG/M
Ga0209939_1073115	Not Available	654	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0209939_1000256

All Organisms → cellular organisms → Bacteria

9234

Open in IMG/M

Ga0209939_1000442

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

7453

Open in IMG/M

Ga0209939_1000492

All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria

7140

Open in IMG/M

Ga0209939_1001427

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

4474

Open in IMG/M

Ga0209939_1003425

All Organisms → cellular organisms → Bacteria → Proteobacteria

3012

Open in IMG/M

Ga0209939_1011032

All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria

1738

Open in IMG/M

Ga0209939_1011901

All Organisms → cellular organisms → Bacteria

1674

Open in IMG/M

Ga0209939_1012254

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

1651

Open in IMG/M

Ga0209939_1015401

All Organisms → cellular organisms → Bacteria

1483

Open in IMG/M

Ga0209939_1035905

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

958

Open in IMG/M

Ga0209939_1037613

All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria

934

Open in IMG/M

Ga0209939_1043037

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

870

Open in IMG/M

Ga0209939_1049399

All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria

809

Open in IMG/M

Ga0209939_1053354

Not Available

776

Open in IMG/M

Ga0209939_1062391

All Organisms → cellular organisms → Bacteria

713

Open in IMG/M

Ga0209939_1073115

Not Available

654

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0209939_1000256	Ga0209939_10002566	F098275	MAPGNEAEWARLNAEKREALTPPPDTPIGELLRRGQHLSAQGANLQRAVERANGDRRS
Ga0209939_1000442	Ga0209939_10004428	F048673	MRTYAFILILVAIAASQPHHWLSAVMTAITHCMGR
Ga0209939_1000492	Ga0209939_10004923	F048318	MASVENVRLAITASTIKPGHSDIAYSYELHPSELDCGWKREYTISAVLYGEDMIEDDVLAWGKDEHKVRFEDSRPGEPIKVERVFEVETKVLDEDLFGDDEVYLMVEARSGLRADAAGENLVMSRSNTVIGNF
Ga0209939_1001427	Ga0209939_10014274	F002483	MAIGFLRRRPKKRQQRTAAPWPSTPLPPRRPASYYLVAGVALDRELERLCGLPVFADGALATRRPQLKVRRASKRPNKLGFAVPAEFRLQVTAYPGIGPGDILETLLHELTHLHVGRAAEAHAWHGRTFKRALANAMEQAYGVEIPPPPHTRHGVYAAAIDASRSPAQSGGEG
Ga0209939_1003425	Ga0209939_10034253	F026568	MHKPSPHREFYDPLYHYTRGVLYFDEEEFTFTAYRMPYLALDKKSWKTEKAFTEDYRRMIQSKYS
Ga0209939_1011032	Ga0209939_10110322	F053306	MDCMMQLLARIKGNYLFATTVLLTLSACGQPEPITYESLVWVNNYYVEHPVASLSATAGGWLFRGAREFGPEIRIGFLIPGPMNPDPAKRQAVLESICPAKSEPIWQTLTSDNKLVINVWTEDKKFKDSKTC
Ga0209939_1011901	Ga0209939_10119013	F026568	MHKPSPLKEMYDPYYHYTRGVLYYDENHFTFTAYRMPYLELDSKSWETEKAFKADYRRVVNKKYAT
Ga0209939_1012254	Ga0209939_10122543	F018541	RKNNMYTPKMRSFWVDFPLTDEQYSKLELRWRRRQNFYEIKNEPPADIRIRSFCSFGGEDYKILSLEARGDIDVYNETLKIMDQWIIDTLGEF
Ga0209939_1015401	Ga0209939_10154013	F019205	MFDSRKSFSHKAADAADLVIDFATLGEYGLEPVEQQPRACEGRNRISRPRSTGAWSAAIARFATQA
Ga0209939_1035905	Ga0209939_10359051	F048318	MATVENVHLAITASSTKPDYSDIAYSYELHPSELDCAWKREYTMTAVLCGEDVIEDDVLAWGLDEHKVKFDDTGPCEPKKVGRVFEVETKVLDEDWFGDDEVYLIVEARSGLRPDAAGESMVMRKSNTVIGD
Ga0209939_1037613	Ga0209939_10376132	F030933	MINDHQTDELRHKRAQAVKTAWILGIIALVIFATFIGSAIIGR
Ga0209939_1043037	Ga0209939_10430372	F105198	KKFLIALCLVLFSAQAPAYFTWGIGEMPCNRFVSAKIEFEHARDQRTHPAQLNWIKGFITGINWSHDSNIARDLTIETVDNWIDDYCRNNLNDSIAEASAALVIYLEGDSD
Ga0209939_1049399	Ga0209939_10493991	F005815	MTMNTTRLTMYWTAGEAATVIDFLDTLRETLWETYGEQITRMHREIYDDCTPDTNQCEFEFNDDIPF
Ga0209939_1053354	Ga0209939_10533541	F096759	AFAIRSIFHTTLKQSPGQLVFGRDMIFNIKHTANWEYIRQRKQQLINTNNRRENSKRVEHVYQVGDKVMLRRGTENKYEAPYQGPFEILKVNDNGTVRLMVKSVEDSYNIRRLMPYHSETDPNHGGECNMRVTRSRRKN
Ga0209939_1062391	Ga0209939_10623911	F095691	MLQQDGSIRIAWQADGFEAIYVRARFRPAPDLDGFARTVADVALLERTLPELRTALRKEYPGQFDLVTDEPISKPGRVIISFHPPPGQPNPDPW
Ga0209939_1073115	Ga0209939_10731152	F087388	MAKTVSELAREIISRLDQGEPLESAISMVLTGEGVEDDVLVELQVAGLRDAVVHESFHELLDWHANFGGLAEFLEIDEAIHRTAERIGHDFDGDLPDHPAESGPRLVH

Scaffold ID

Protein ID

Family

Sequence

Ga0209939_1000256

Ga0209939_10002566

F098275

MAPGNEAEWARLNAEKREALTPPPDTPIGELLRRGQHLSAQGANLQRAVERANGDRRS

Ga0209939_1000442

Ga0209939_10004428

F048673

MRTYAFILILVAIAASQPHHWLSAVMTAITHCMGR

Ga0209939_1000492

Ga0209939_10004923

F048318

MASVENVRLAITASTIKPGHSDIAYSYELHPSELDCGWKREYTISAVLYGEDMIEDDVLAWGKDEHKVRFEDSRPGEPIKVERVFEVETKVLDEDLFGDDEVYLMVEARSGLRADAAGENLVMSRSNTVIGNF

Ga0209939_1001427

Ga0209939_10014274

F002483

MAIGFLRRRPKKRQQRTAAPWPSTPLPPRRPASYYLVAGVALDRELERLCGLPVFADGALATRRPQLKVRRASKRPNKLGFAVPAEFRLQVTAYPGIGPGDILETLLHELTHLHVGRAAEAHAWHGRTFKRALANAMEQAYGVEIPPPPHTRHGVYAAAIDASRSPAQSGGEG

Ga0209939_1003425

Ga0209939_10034253

F026568

MHKPSPHREFYDPLYHYTRGVLYFDEEEFTFTAYRMPYLALDKKSWKTEKAFTEDYRRMIQSKYS

Ga0209939_1011032

Ga0209939_10110322

F053306

MDCMMQLLARIKGNYLFATTVLLTLSACGQPEPITYESLVWVNNYYVEHPVASLSATAGGWLFRGAREFGPEIRIGFLIPGPMNPDPAKRQAVLESICPAKSEPIWQTLTSDNKLVINVWTEDKKFKDSKTC

Ga0209939_1011901

Ga0209939_10119013

F026568

MHKPSPLKEMYDPYYHYTRGVLYYDENHFTFTAYRMPYLELDSKSWETEKAFKADYRRVVNKKYAT

Ga0209939_1012254

Ga0209939_10122543

F018541

RKNNMYTPKMRSFWVDFPLTDEQYSKLELRWRRRQNFYEIKNEPPADIRIRSFCSFGGEDYKILSLEARGDIDVYNETLKIMDQWIIDTLGEF

Ga0209939_1015401

Ga0209939_10154013

F019205

MFDSRKSFSHKAADAADLVIDFATLGEYGLEPVEQQPRACEGRNRISRPRSTGAWSAAIARFATQA

Ga0209939_1035905

Ga0209939_10359051

F048318

MATVENVHLAITASSTKPDYSDIAYSYELHPSELDCAWKREYTMTAVLCGEDVIEDDVLAWGLDEHKVKFDDTGPCEPKKVGRVFEVETKVLDEDWFGDDEVYLIVEARSGLRPDAAGESMVMRKSNTVIGD

Ga0209939_1037613

Ga0209939_10376132

F030933

MINDHQTDELRHKRAQAVKTAWILGIIALVIFATFIGSAIIGR

Ga0209939_1043037

Ga0209939_10430372

F105198

KKFLIALCLVLFSAQAPAYFTWGIGEMPCNRFVSAKIEFEHARDQRTHPAQLNWIKGFITGINWSHDSNIARDLTIETVDNWIDDYCRNNLNDSIAEASAALVIYLEGDSD

Ga0209939_1049399

Ga0209939_10493991

F005815

MTMNTTRLTMYWTAGEAATVIDFLDTLRETLWETYGEQITRMHREIYDDCTPDTNQCEFEFNDDIPF

Ga0209939_1053354

Ga0209939_10533541

F096759

AFAIRSIFHTTLKQSPGQLVFGRDMIFNIKHTANWEYIRQRKQQLINTNNRRENSKRVEHVYQVGDKVMLRRGTENKYEAPYQGPFEILKVNDNGTVRLMVKSVEDSYNIRRLMPYHSETDPNHGGECNMRVTRSRRKN

Ga0209939_1062391

Ga0209939_10623911

F095691

MLQQDGSIRIAWQADGFEAIYVRARFRPAPDLDGFARTVADVALLERTLPELRTALRKEYPGQFDLVTDEPISKPGRVIISFHPPPGQPNPDPW

Ga0209939_1073115

Ga0209939_10731152

F087388

MAKTVSELAREIISRLDQGEPLESAISMVLTGEGVEDDVLVELQVAGLRDAVVHESFHELLDWHANFGGLAEFLEIDEAIHRTAERIGHDFDGDLPDHPAESGPRLVH

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026135: Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_A_D1_MG (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences