Sample 3300027580

Overview

Basic Information
IMG/M Taxon OID	3300027580 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0053056 \| Gp0053348 \| Ga0207714
Sample Name	Marine sediment microbial community from Fremont, CA, USA - Pond A23 Sediment 2 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	414290309
Sequencing Scaffolds	14
Novel Protein Genes	14
Associated Families	10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfovibrionales → Desulfovibrionaceae → Desulfovibrio	1
Not Available	9
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Cytophagia → Cytophagales → Hymenobacteraceae → Hymenobacter	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Halanaerobiales	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidetes Order II. Incertae sedis → Rhodothermaceae → Salinibacter → Salinibacter ruber	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Halobacteria → Haloferacales → Halorubraceae → Halorubrum → unclassified Halorubrum → Halorubrum sp. 48-1-W	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
Name	Environmental Microbial Communities From Fremont, Ca And La Paraguera, Puerto Rico
Type	Environmental
Taxonomy	Environmental → Aquatic → Marine → Unclassified → Unclassified → Enviromental → Environmental Microbial Communities From Fremont, Ca And La Paraguera, Puerto Rico

Alternative Ecosystem Assignments
Environment Ontology (ENVO)	marine biome → pond → sediment
Earth Microbiome Project Ontology (EMPO)	Free-living → Saline → Water (saline)

Location Information
Location	Alviso Ponds, San Francisco, CA, USA
Coordinates	Lat. (^o)	37.474067	Long. (^o)	-121.973033	Alt. (m)	N/A	Depth (m)	.075
Location on Map

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Family	Category	Number of Sequences	3D Structure?
F000388	Metagenome / Metatranscriptome	1201	Y
F022890	Metagenome / Metatranscriptome	212	Y
F025922	Metagenome / Metatranscriptome	199	Y
F029285	Metagenome / Metatranscriptome	189	Y
F049200	Metagenome	147	Y
F062484	Metagenome	130	Y
F062489	Metagenome	130	Y
F066493	Metagenome	126	Y
F079661	Metagenome	115	Y
F087432	Metagenome	110	Y

Family

Category

Number of Sequences

3D Structure?

F000388

Metagenome / Metatranscriptome

1201

F022890

Metagenome / Metatranscriptome

212

F025922

Metagenome / Metatranscriptome

199

F029285

Metagenome / Metatranscriptome

189

F049200

Metagenome

147

F062484

Metagenome

130

F062489

Metagenome

130

F066493

Metagenome

126

F079661

Metagenome

115

F087432

Metagenome

110

Scaffold	Taxonomy	Length	IMG/M Link
Ga0207714_1013679	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfovibrionales → Desulfovibrionaceae → Desulfovibrio	3709	Open in IMG/M
Ga0207714_1024218	Not Available	2506	Open in IMG/M
Ga0207714_1039449	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Cytophagia → Cytophagales → Hymenobacteraceae → Hymenobacter	1764	Open in IMG/M
Ga0207714_1039526	Not Available	1761	Open in IMG/M
Ga0207714_1049859	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Halanaerobiales	1473	Open in IMG/M
Ga0207714_1056079	Not Available	1346	Open in IMG/M
Ga0207714_1077986	Not Available	1041	Open in IMG/M
Ga0207714_1082885	Not Available	992	Open in IMG/M
Ga0207714_1105894	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidetes Order II. Incertae sedis → Rhodothermaceae → Salinibacter → Salinibacter ruber	818	Open in IMG/M
Ga0207714_1109821	Not Available	794	Open in IMG/M
Ga0207714_1127011	Not Available	707	Open in IMG/M
Ga0207714_1163167	Not Available	578	Open in IMG/M
Ga0207714_1172786	Not Available	550	Open in IMG/M
Ga0207714_1182572	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Halobacteria → Haloferacales → Halorubraceae → Halorubrum → unclassified Halorubrum → Halorubrum sp. 48-1-W	525	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0207714_1013679

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfovibrionales → Desulfovibrionaceae → Desulfovibrio

3709

Open in IMG/M

Ga0207714_1024218

Not Available

2506

Open in IMG/M

Ga0207714_1039449

All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Cytophagia → Cytophagales → Hymenobacteraceae → Hymenobacter

1764

Open in IMG/M

Ga0207714_1039526

Not Available

1761

Open in IMG/M

Ga0207714_1049859

All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Halanaerobiales

1473

Open in IMG/M

Ga0207714_1056079

Not Available

1346

Open in IMG/M

Ga0207714_1077986

Not Available

1041

Open in IMG/M

Ga0207714_1082885

Not Available

992

Open in IMG/M

Ga0207714_1105894

All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidetes Order II. Incertae sedis → Rhodothermaceae → Salinibacter → Salinibacter ruber

818

Open in IMG/M

Ga0207714_1109821

Not Available

794

Open in IMG/M

Ga0207714_1127011

Not Available

707

Open in IMG/M

Ga0207714_1163167

Not Available

578

Open in IMG/M

Ga0207714_1172786

Not Available

550

Open in IMG/M

Ga0207714_1182572

All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Halobacteria → Haloferacales → Halorubraceae → Halorubrum → unclassified Halorubrum → Halorubrum sp. 48-1-W

525

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0207714_1013679	Ga0207714_10136793	F029285	MKNQADYSKYRCPFDHIEKECGHELHGPEGYQEIYSIWCPCGFRGPVFCLDPEELNLKEKAPA
Ga0207714_1024218	Ga0207714_10242186	F022890	MKSSDHNPYTGKLSESDNVLAAIELAKKFKEFADEGYTDEAMDVESSQWIEVINKLEEKRLNCA
Ga0207714_1039449	Ga0207714_10394491	F062484	GSKSKVEQYIAKVDKHEGFTGNVTKTWAEPKKHPTKSKYACPKKEGIKPDSDMEEVDELPSDWYPKEEI
Ga0207714_1039526	Ga0207714_10395263	F066493	MSQTREWDDGLVDVTDELVKEYSAEGAIERLQRRKESTRSDDLEARCLEAIAYIRREVQDDT
Ga0207714_1049859	Ga0207714_10498593	F087432	MIIYEDGGYTPCTYKVILKNNGKEETHYANFRTYWEDMVAKHDHLTDLAFEEITFTPEQDTRLQEIAELEIPQGFQSEVRQYVEAGEFPEGYQHPLADLKQKKEKEKYDNDLDDAYQMILENEGLI
Ga0207714_1056079	Ga0207714_10560793	F066493	MSEREWHDGVVDVADELVQEHSAEGAIERLQSRRQTSSDELEARCDDAIDYIESEVLADE
Ga0207714_1077986	Ga0207714_10779862	F066493	MSESREFDDGLIDVADELVSEYSAEGAIDRLQRRRESTRSDELADRCLEAIAYIRREVQNNE
Ga0207714_1082885	Ga0207714_10828851	F079661	MGRTTIEIDEDTRDRLREERKPHESNYGDTIDRLLGQSSGGQLWTESEIRDLARDEIRDA
Ga0207714_1105894	Ga0207714_11058943	F049200	MDDLDLGQRLALPYESDDTSISVPAEITGLGLPAVRVETDSGETYIRHAKDVTDWTRHLRHA
Ga0207714_1109821	Ga0207714_11098211	F066493	MSESREFDDGLIDVADELVSEYSAEGAIDRLQRRRESTRSDELEARCLEAIAYIRREVQDNES
Ga0207714_1127011	Ga0207714_11270112	F000388	MKVIKVTKDYFETEDEKVYFFEPLEKEISVEDMQKIVDANEKLVKEMKDGKSSNRL
Ga0207714_1163167	Ga0207714_11631671	F025922	YRVQSLGSTTTFNSEDINELGHLDIIDVVDDVPEVAVTLNTNDFGDVRTLATLAQLDPKKIKMDASADDTNGNLEVVDETGTSTGTYLHGVSVADFAVVCGTLPGVTIWAPVQDECSLGTLDSNIDQTLFLDKVFINSVEFSYDSGANATENYEGETDNKTWFLNKGRFLTMDSFTVSGTDVSNGYVDLSLG
Ga0207714_1172786	Ga0207714_11727863	F062489	MTGPDAIVIRERRPEAPTRRLVYHRLTTGGYDRKTQLWRQAIDGWHTTGTEVVTALRIDCPEGRR
Ga0207714_1182572	Ga0207714_11825722	F062489	VTGPDAIILRERVADGPTRRIVWHPLTAGGYERREQLWRLSIEGWHTRGTEVVESVRINCPEGRR

Scaffold ID

Protein ID

Family

Sequence

Ga0207714_1013679

Ga0207714_10136793

F029285

MKNQADYSKYRCPFDHIEKECGHELHGPEGYQEIYSIWCPCGFRGPVFCLDPEELNLKEKAPA

Ga0207714_1024218

Ga0207714_10242186

F022890

MKSSDHNPYTGKLSESDNVLAAIELAKKFKEFADEGYTDEAMDVESSQWIEVINKLEEKRLNCA

Ga0207714_1039449

Ga0207714_10394491

F062484

GSKSKVEQYIAKVDKHEGFTGNVTKTWAEPKKHPTKSKYACPKKEGIKPDSDMEEVDELPSDWYPKEEI

Ga0207714_1039526

Ga0207714_10395263

F066493

MSQTREWDDGLVDVTDELVKEYSAEGAIERLQRRKESTRSDDLEARCLEAIAYIRREVQDDT

Ga0207714_1049859

Ga0207714_10498593

F087432

MIIYEDGGYTPCTYKVILKNNGKEETHYANFRTYWEDMVAKHDHLTDLAFEEITFTPEQDTRLQEIAELEIPQGFQSEVRQYVEAGEFPEGYQHPLADLKQKKEKEKYDNDLDDAYQMILENEGLI

Ga0207714_1056079

Ga0207714_10560793

F066493

MSEREWHDGVVDVADELVQEHSAEGAIERLQSRRQTSSDELEARCDDAIDYIESEVLADE

Ga0207714_1077986

Ga0207714_10779862

F066493

MSESREFDDGLIDVADELVSEYSAEGAIDRLQRRRESTRSDELADRCLEAIAYIRREVQNNE

Ga0207714_1082885

Ga0207714_10828851

F079661

MGRTTIEIDEDTRDRLREERKPHESNYGDTIDRLLGQSSGGQLWTESEIRDLARDEIRDA

Ga0207714_1105894

Ga0207714_11058943

F049200

MDDLDLGQRLALPYESDDTSISVPAEITGLGLPAVRVETDSGETYIRHAKDVTDWTRHLRHA

Ga0207714_1109821

Ga0207714_11098211

F066493

MSESREFDDGLIDVADELVSEYSAEGAIDRLQRRRESTRSDELEARCLEAIAYIRREVQDNES

Ga0207714_1127011

Ga0207714_11270112

F000388

MKVIKVTKDYFETEDEKVYFFEPLEKEISVEDMQKIVDANEKLVKEMKDGKSSNRL

Ga0207714_1163167

Ga0207714_11631671

F025922

YRVQSLGSTTTFNSEDINELGHLDIIDVVDDVPEVAVTLNTNDFGDVRTLATLAQLDPKKIKMDASADDTNGNLEVVDETGTSTGTYLHGVSVADFAVVCGTLPGVTIWAPVQDECSLGTLDSNIDQTLFLDKVFINSVEFSYDSGANATENYEGETDNKTWFLNKGRFLTMDSFTVSGTDVSNGYVDLSLG

Ga0207714_1172786

Ga0207714_11727863

F062489

MTGPDAIVIRERRPEAPTRRLVYHRLTTGGYDRKTQLWRQAIDGWHTTGTEVVTALRIDCPEGRR

Ga0207714_1182572

Ga0207714_11825722

F062489

VTGPDAIILRERVADGPTRRIVWHPLTAGGYERREQLWRLSIEGWHTRGTEVVESVRINCPEGRR

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300027580: Marine sediment microbial community from Fremont, CA, USA - Pond A23 Sediment 2 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences