Sample 3300025976

Overview

Basic Information
IMG/M Taxon OID	3300025976 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0101404 \| Ga0210093
Sample Name	Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqB_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	108450502
Sequencing Scaffolds	16
Novel Protein Genes	17
Associated Families	16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales → unclassified Ignavibacteriales → Ignavibacteriales bacterium	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales	1
Not Available	6
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Archaea	2
All Organisms → cellular organisms → Bacteria → FCB group	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Candidatus Nitrosopumilus sediminis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	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 → Aquatic → Marine → 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)	Unclassified
Earth Microbiome Project Ontology (EMPO)	Free-living → Saline → Water (saline)

Location Information
Location	USA: San Francisco Bay, California
Coordinates	Lat. (^o)	38.131752	Long. (^o)	-122.266335	Alt. (m)	N/A	Depth (m)	N/A
Location on Map

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Family	Category	Number of Sequences	3D Structure?
F015265	Metagenome / Metatranscriptome	256	Y
F021303	Metagenome / Metatranscriptome	219	Y
F026597	Metagenome	197	Y
F029294	Metagenome	189	Y
F043410	Metagenome	156	Y
F052687	Metagenome	142	Y
F057220	Metagenome / Metatranscriptome	136	Y
F058158	Metagenome / Metatranscriptome	135	Y
F076231	Metagenome	118	Y
F077207	Metagenome	117	Y
F077325	Metagenome	117	Y
F078289	Metagenome / Metatranscriptome	116	N
F078881	Metagenome	116	Y
F084254	Metagenome / Metatranscriptome	112	Y
F099324	Metagenome / Metatranscriptome	103	Y
F103506	Metagenome / Metatranscriptome	101	Y

Family

Category

Number of Sequences

3D Structure?

F015265

Metagenome / Metatranscriptome

256

F021303

Metagenome / Metatranscriptome

219

F026597

Metagenome

197

F029294

Metagenome

189

F043410

Metagenome

156

F052687

Metagenome

142

F057220

Metagenome / Metatranscriptome

136

F058158

Metagenome / Metatranscriptome

135

F076231

Metagenome

118

F077207

Metagenome

117

F077325

Metagenome

117

F078289

Metagenome / Metatranscriptome

116

F078881

Metagenome

116

F084254

Metagenome / Metatranscriptome

112

F099324

Metagenome / Metatranscriptome

103

F103506

Metagenome / Metatranscriptome

101

Scaffold	Taxonomy	Length	IMG/M Link
Ga0210093_1007992	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales → unclassified Ignavibacteriales → Ignavibacteriales bacterium	1056	Open in IMG/M
Ga0210093_1009223	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales	1003	Open in IMG/M
Ga0210093_1014331	Not Available	859	Open in IMG/M
Ga0210093_1016704	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	816	Open in IMG/M
Ga0210093_1016846	All Organisms → cellular organisms → Bacteria	813	Open in IMG/M
Ga0210093_1021404	All Organisms → cellular organisms → Archaea	748	Open in IMG/M
Ga0210093_1023057	Not Available	728	Open in IMG/M
Ga0210093_1024464	All Organisms → cellular organisms → Bacteria → FCB group	713	Open in IMG/M
Ga0210093_1025031	All Organisms → cellular organisms → Bacteria	707	Open in IMG/M
Ga0210093_1025657	Not Available	701	Open in IMG/M
Ga0210093_1028682	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Candidatus Nitrosopumilus sediminis	672	Open in IMG/M
Ga0210093_1037054	All Organisms → cellular organisms → Archaea	613	Open in IMG/M
Ga0210093_1038608	Not Available	604	Open in IMG/M
Ga0210093_1041062	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	591	Open in IMG/M
Ga0210093_1041242	Not Available	590	Open in IMG/M
Ga0210093_1057464	Not Available	521	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0210093_1007992

All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales → unclassified Ignavibacteriales → Ignavibacteriales bacterium

1056

Open in IMG/M

Ga0210093_1009223

All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales

1003

Open in IMG/M

Ga0210093_1014331

Not Available

859

Open in IMG/M

Ga0210093_1016704

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

816

Open in IMG/M

Ga0210093_1016846

All Organisms → cellular organisms → Bacteria

813

Open in IMG/M

Ga0210093_1021404

All Organisms → cellular organisms → Archaea

748

Open in IMG/M

Ga0210093_1023057

Not Available

728

Open in IMG/M

Ga0210093_1024464

All Organisms → cellular organisms → Bacteria → FCB group

713

Open in IMG/M

Ga0210093_1025031

All Organisms → cellular organisms → Bacteria

707

Open in IMG/M

Ga0210093_1025657

Not Available

701

Open in IMG/M

Ga0210093_1028682

All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Candidatus Nitrosopumilus sediminis

672

Open in IMG/M

Ga0210093_1037054

All Organisms → cellular organisms → Archaea

613

Open in IMG/M

Ga0210093_1038608

Not Available

604

Open in IMG/M

Ga0210093_1041062

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

591

Open in IMG/M

Ga0210093_1041242

Not Available

590

Open in IMG/M

Ga0210093_1057464

Not Available

521

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0210093_1007992	Ga0210093_10079922	F026597	MFNMFERHRSLVSVSLALLIIAVVGAAVSSFSPSKKSEYFKELKQIYNTVNTYDNKEINSWEAAKNTIVDLNYWYDFIPRYDVISDEDNDVLILQNKVRDLTIRQQLRTLPEIRKYFGEYLSDKLVGLGYKVTILNDERNKVIVFTHDSFTSRSALEKFHITVTNDLRALGFKQIRYKWFELEKLKDEKYIHYNFSDLPDNEPRKFNLSVIKAN
Ga0210093_1009223	Ga0210093_10092232	F052687	GGTYYLLSMETVEDVKVMGKLQISEQYGSYVMASQSKDANYYAVVEGKVKNNMKKPIKNVFIKYVIAGKETSATIFDLAPGQELHFNTSGVATTGSSPEYDFVGIYYD
Ga0210093_1009843	Ga0210093_10098432	F103506	MGTYMINTESMLETDHFIILDESNTVRGNEFDRSYPKVQIVYPSRMNSHPDNKVTESRPKNGLNYKEKEKHPFTITLSVDAE
Ga0210093_1014331	Ga0210093_10143311	F084254	QSKRHPRADQVASALAMRGLPIAEKDVMIVFDQYDIEKKTPDSHYFDT
Ga0210093_1016704	Ga0210093_10167041	F021303	MTERTISTEVSGLRASVLDHSSEFVELVYRDAPAEYRRLMALERFRQELGRQNRFNHGKLYAYAEFVVFRREFRERFPDASPAACINAFSSLLLKNDISVTNLVEFVEGPDHRGQLLLNQPPAPG
Ga0210093_1016846	Ga0210093_10168462	F057220	MKTCNLSQAKSALGKLADQALKGHPTVIPRGGKLVILQAYELPDHPDEFDALIQAGKESPHRPLTRHVLTG
Ga0210093_1021404	Ga0210093_10214042	F077325	MTSRGNWTEKDEATITAIIVNMINQKQMFQDLGKKNELNNSFGIQNPREYTLGLYTGIVINLFANYWIGEHESGLTPEDLSYLYYEISLFHKEIISGLFD
Ga0210093_1023057	Ga0210093_10230572	F029294	MYQETGETRDAIIEDDNKKIAEIVEANKHLKEPYWIVVFAKPSKSCVDGLPTLVKHIKAYKTQPSSQVGMIAGKVDNAKGTIDWEVNMPQRPFNFDALPGLGAKACNEVVVETTTIPHAYVTQ
Ga0210093_1024464	Ga0210093_10244642	F078881	MSKKIINLFLIVVFLLILLLSGCGTGQFSVGVGVYVPGAWGGPYGGGYYPPVRVGYPVY
Ga0210093_1025031	Ga0210093_10250312	F099324	GEDYRTGYPPRAGYTSTTPHKALVSEACNIEANNLVGDKDFMADDRARRVYFSQCMLRNGYNAAGNYVGIPSK
Ga0210093_1025657	Ga0210093_10256571	F078289	MKTAVSIFILIIVVFPLYGFNSLVRHEDIPKMRELGISQEVIQYIISNQTSSVSSEDVIKMKQSGLNNNDIMSAIKSDLYRPEQKSTSMKEVELIAKLKESGMSDEAVLQFIQTVKSTRRVDSDGNVTKQYTNESQRTQYPTTGATFPKLDNYGYDPSNGRFLFFIKPQNQE
Ga0210093_1028682	Ga0210093_10286821	F015265	VMYPVHMTKNPKLIEKNAIVNLNNVGLPVFLNPIYDIIPIASPTKNPTKLRIFSNKNSND
Ga0210093_1037054	Ga0210093_10370542	F077325	HAIIVNMLNQKQMFQDLGKTTILPNSFNIKNSNEYILGLFTGIVINLFANYWVGEHESGLSPEDLSYLYYKISLFREEIVSGLFD
Ga0210093_1038608	Ga0210093_10386082	F043410	VAQYANLQKMVNAPSEGFDLQGMINKALIGILISKGIITEEEVKIILGNINRQQEIFSKKQNRA
Ga0210093_1041062	Ga0210093_10410621	F077207	RRARRNNLLHTQQGRTSVATPWPIPRPSQAMRFPILPIAIAVLATAGCHDRGARTPAEAHARLQAALAAHDSSLLWRSLDQDTHWSWMTIQRAWREAYDITQSVVPEGQERRHLLARFEPGATSENAETLFAKMLTPGDWAASQALVTAAGTRPPEISSTGESAEIATPAGSLVFHKAHNQHWGWGFSGLASRADR
Ga0210093_1041242	Ga0210093_10412421	F076231	MKIIFIGREHMMNLKPNKGGTADISEFSGFISSKQNSSIMSLTKIVVVISVLLAVLMVVS
Ga0210093_1057464	Ga0210093_10574641	F058158	MSEFTKTEKDDIDIWELHVKEREYILAQIANDRRTSRIRNWIELIFMLGFIWYMLYDIYKDKDLDTIIKFLKA

Scaffold ID

Protein ID

Family

Sequence

Ga0210093_1007992

Ga0210093_10079922

F026597

MFNMFERHRSLVSVSLALLIIAVVGAAVSSFSPSKKSEYFKELKQIYNTVNTYDNKEINSWEAAKNTIVDLNYWYDFIPRYDVISDEDNDVLILQNKVRDLTIRQQLRTLPEIRKYFGEYLSDKLVGLGYKVTILNDERNKVIVFTHDSFTSRSALEKFHITVTNDLRALGFKQIRYKWFELEKLKDEKYIHYNFSDLPDNEPRKFNLSVIKAN

Ga0210093_1009223

Ga0210093_10092232

F052687

GGTYYLLSMETVEDVKVMGKLQISEQYGSYVMASQSKDANYYAVVEGKVKNNMKKPIKNVFIKYVIAGKETSATIFDLAPGQELHFNTSGVATTGSSPEYDFVGIYYD

Ga0210093_1009843

Ga0210093_10098432

F103506

MGTYMINTESMLETDHFIILDESNTVRGNEFDRSYPKVQIVYPSRMNSHPDNKVTESRPKNGLNYKEKEKHPFTITLSVDAE

Ga0210093_1014331

Ga0210093_10143311

F084254

QSKRHPRADQVASALAMRGLPIAEKDVMIVFDQYDIEKKTPDSHYFDT

Ga0210093_1016704

Ga0210093_10167041

F021303

MTERTISTEVSGLRASVLDHSSEFVELVYRDAPAEYRRLMALERFRQELGRQNRFNHGKLYAYAEFVVFRREFRERFPDASPAACINAFSSLLLKNDISVTNLVEFVEGPDHRGQLLLNQPPAPG

Ga0210093_1016846

Ga0210093_10168462

F057220

MKTCNLSQAKSALGKLADQALKGHPTVIPRGGKLVILQAYELPDHPDEFDALIQAGKESPHRPLTRHVLTG

Ga0210093_1021404

Ga0210093_10214042

F077325

MTSRGNWTEKDEATITAIIVNMINQKQMFQDLGKKNELNNSFGIQNPREYTLGLYTGIVINLFANYWIGEHESGLTPEDLSYLYYEISLFHKEIISGLFD

Ga0210093_1023057

Ga0210093_10230572

F029294

MYQETGETRDAIIEDDNKKIAEIVEANKHLKEPYWIVVFAKPSKSCVDGLPTLVKHIKAYKTQPSSQVGMIAGKVDNAKGTIDWEVNMPQRPFNFDALPGLGAKACNEVVVETTTIPHAYVTQ

Ga0210093_1024464

Ga0210093_10244642

F078881

MSKKIINLFLIVVFLLILLLSGCGTGQFSVGVGVYVPGAWGGPYGGGYYPPVRVGYPVY

Ga0210093_1025031

Ga0210093_10250312

F099324

GEDYRTGYPPRAGYTSTTPHKALVSEACNIEANNLVGDKDFMADDRARRVYFSQCMLRNGYNAAGNYVGIPSK

Ga0210093_1025657

Ga0210093_10256571

F078289

MKTAVSIFILIIVVFPLYGFNSLVRHEDIPKMRELGISQEVIQYIISNQTSSVSSEDVIKMKQSGLNNNDIMSAIKSDLYRPEQKSTSMKEVELIAKLKESGMSDEAVLQFIQTVKSTRRVDSDGNVTKQYTNESQRTQYPTTGATFPKLDNYGYDPSNGRFLFFIKPQNQE

Ga0210093_1028682

Ga0210093_10286821

F015265

VMYPVHMTKNPKLIEKNAIVNLNNVGLPVFLNPIYDIIPIASPTKNPTKLRIFSNKNSND

Ga0210093_1037054

Ga0210093_10370542

F077325

HAIIVNMLNQKQMFQDLGKTTILPNSFNIKNSNEYILGLFTGIVINLFANYWVGEHESGLSPEDLSYLYYKISLFREEIVSGLFD

Ga0210093_1038608

Ga0210093_10386082

F043410

VAQYANLQKMVNAPSEGFDLQGMINKALIGILISKGIITEEEVKIILGNINRQQEIFSKKQNRA

Ga0210093_1041062

Ga0210093_10410621

F077207

RRARRNNLLHTQQGRTSVATPWPIPRPSQAMRFPILPIAIAVLATAGCHDRGARTPAEAHARLQAALAAHDSSLLWRSLDQDTHWSWMTIQRAWREAYDITQSVVPEGQERRHLLARFEPGATSENAETLFAKMLTPGDWAASQALVTAAGTRPPEISSTGESAEIATPAGSLVFHKAHNQHWGWGFSGLASRADR

Ga0210093_1041242

Ga0210093_10412421

F076231

MKIIFIGREHMMNLKPNKGGTADISEFSGFISSKQNSSIMSLTKIVVVISVLLAVLMVVS

Ga0210093_1057464

Ga0210093_10574641

F058158

MSEFTKTEKDDIDIWELHVKEREYILAQIANDRRTSRIRNWIELIFMLGFIWYMLYDIYKDKDLDTIIKFLKA

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300025976: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqB_D1 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences