Sample 3300026042

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

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Sample 3300026042

3300026042: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_ThreeSqB_D1 (SPAdes)

Overview

Basic Information
IMG/M Taxon OID	3300026042 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116107 \| Ga0208538
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_ThreeSqB_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	38900910
Sequencing Scaffolds	6
Novel Protein Genes	6
Associated Families	6

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2

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 → 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)	terrestrial biome → wetland area → soil
Earth Microbiome Project Ontology (EMPO)	Free-living → Saline → Water (saline)

Location Information
Location	USA: Fairfield, San Francisco Bay, California
Coordinates	Lat. (^o)	38.209766	Long. (^o)	-122.033424	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Associated Families

Family	Category	Number of Sequences	3D Structure?
F007558	Metagenome / Metatranscriptome	349	Y
F014394	Metagenome / Metatranscriptome	263	Y
F024001	Metagenome / Metatranscriptome	208	Y
F034114	Metagenome / Metatranscriptome	175	Y
F073725	Metagenome / Metatranscriptome	120	N
F081923	Metagenome / Metatranscriptome	114	N

Associated Scaffolds

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208538_1000020	Not Available	3056	Open in IMG/M
Ga0208538_1002358	All Organisms → cellular organisms → Bacteria	860	Open in IMG/M
Ga0208538_1003239	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	778	Open in IMG/M
Ga0208538_1003651	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	751	Open in IMG/M
Ga0208538_1007167	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	605	Open in IMG/M
Ga0208538_1011454	All Organisms → cellular organisms → Bacteria	518	Open in IMG/M

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208538_1000020	Ga0208538_10000204	F034114	VPVIMRETSVAAGAVNENLLAGSAFEFARQNSLVSIGINQSATGGFATINSGADVVAEEFAPPINTVYPIIPDGMYFSDVAAAGDRLVIRYRNPTGGALTVRVVCQVTPL
Ga0208538_1002358	Ga0208538_10023582	F073725	MEKRATRRYRISTSIVCSYLNSVDFGKPVDGRMRNCCVNGLYAELGTHYKAGTVLVVRTTGSSCGYSNEKGFRLLAVAEVKWSRPRSIEGGACYATGLKYLML
Ga0208538_1003239	Ga0208538_10032391	F014394	MRAGSRFLATLFAAVVWIYAGMSVASRPVAQEAITPSVLDVAASCAAAVMD
Ga0208538_1003651	Ga0208538_10036511	F007558	MQTIAEIKMLLLEILESAFQSGDVNATQQMGVNMTNAVKREGVVIIQNQNVEVYARIMPLMVKTLKLCDAVESSWRGQATIELEPQQKQLPPPADDDDPDPIEACCSWLYDNHIQWQDMQDLMKARYLAYVIGRFKTKTEAAKWLGVGSTYLCKLSKTTLHAVSQN
Ga0208538_1007167	Ga0208538_10071671	F081923	MKRLIVNISSAIRPVMHRKHFFVMAILGAALAVACTMANTGSIQTSAEVTRQFEGLQVNPNYRYWYLNQENNPFGVIGLDREYGFAGGPVWRAVESDSPIFRKVVGLVESFPVASSLTTGYTIFEQQGRPIGVWYSSIGLGVTIDPATKTVSPATTTPWKSPF
Ga0208538_1011454	Ga0208538_10114541	F024001	AKGSRKNKLAILGVEAPGRQGAKTQEYLDIPSFCNAAGRDALASKMLSYF

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