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 3300026033

3300026033: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_CattailNLA_D1 (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300026033 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0111376 | Gp0116070 | Ga0208652
Sample NameNatural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_CattailNLA_D1 (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size87604917
Sequencing Scaffolds14
Novel Protein Genes14
Associated Families13

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius sp. associated proteobacterium Delta 11
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium3
Not Available4
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium1
All Organisms → cellular organisms → Bacteria1
All Organisms → cellular organisms → Bacteria → Terrabacteria group1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
NameNatural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration
TypeEnvironmental
TaxonomyEnvironmental → 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
LocationUSA: Fairfield, San Francisco Bay, California
CoordinatesLat. (o)38.197102Long. (o)-122.010033Alt. (m)N/ADepth (m)0
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F001823Metagenome / Metatranscriptome630Y
F007858Metagenome / Metatranscriptome343Y
F013110Metagenome / Metatranscriptome274Y
F018387Metagenome / Metatranscriptome235Y
F024001Metagenome / Metatranscriptome208Y
F027172Metagenome / Metatranscriptome195Y
F052268Metagenome143Y
F065699Metagenome / Metatranscriptome127Y
F068909Metagenome / Metatranscriptome124Y
F085674Metagenome / Metatranscriptome111Y
F095691Metagenome105Y
F105202Metagenome100Y
F105468Metagenome100Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0208652_1000641All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius sp. associated proteobacterium Delta 14600Open in IMG/M
Ga0208652_1001837All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria2644Open in IMG/M
Ga0208652_1005702All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium1533Open in IMG/M
Ga0208652_1012264Not Available1031Open in IMG/M
Ga0208652_1016160All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium887Open in IMG/M
Ga0208652_1016890All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium865Open in IMG/M
Ga0208652_1017212Not Available856Open in IMG/M
Ga0208652_1017525Not Available847Open in IMG/M
Ga0208652_1021587All Organisms → cellular organisms → Bacteria753Open in IMG/M
Ga0208652_1036796All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria558Open in IMG/M
Ga0208652_1037255All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium554Open in IMG/M
Ga0208652_1041015Not Available525Open in IMG/M
Ga0208652_1041861All Organisms → cellular organisms → Bacteria → Terrabacteria group519Open in IMG/M
Ga0208652_1042513All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria515Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0208652_1000641Ga0208652_10006414F105202QSDLHLDVQQRAHLYLASLYFSPMNPKRDYGLALEHLETYALFDPDFANAVDPRLLLAAIIEIERFSALAEAQTKEIQALSQELNILKRQSLAFRGSRQDIQSANLKLQKRIGQLQKKVRNLERSNAKLNKTIEMLSTLDSRLEEKRINFIKTDSIEEK
Ga0208652_1001837Ga0208652_10018373F018387MIGVEVPLLDQGSVQFILLGVMILAVLALLWITIAK
Ga0208652_1005702Ga0208652_10057022F007858VCRALVVLCVADDREALVALKASTVSAEWELAPGAIDLRSTLDQIDADRPHVMVAFGDHVELVGIVRERFPSMRIVTDRDTPGATVVATSLDEVRGLVLGLPRPGGPVGA
Ga0208652_1012264Ga0208652_10122641F105468ETTPSVREKTLERENRELKEKLAELYLENAQLKKLGDWLRRRRNASTSVITAQSLTRSPKDSKS
Ga0208652_1016160Ga0208652_10161603F013110MSGSRKDTLLRALEAEVGIAPADPGSLFTDDVVGWSPYASVSGLTAVSELAALRDMAFSGVSIS
Ga0208652_1016890Ga0208652_10168902F007858MCRALIVLCVATDVASLSALKQATVSAEWELTPGATNETDALGQVDAERPHVLVAFGPYERLVALCAERFPGMRIVADRDVPGATVVAT
Ga0208652_1017212Ga0208652_10172121F052268PGLPGEWRGTRYDFVKGGAGLTIPGLPDAVRGCLDGT
Ga0208652_1017525Ga0208652_10175252F001823MRAYDRDLIRGGHYGQRPCVPHLKAEHMAAPTNAANVKKALANSEPSTH
Ga0208652_1021587Ga0208652_10215871F095691MLQHDGSIRIAWQADGFEAILVRARFRPASQRDEFARGVADVALLERNLPDLQAALRACYPGAFDLITDRSLSGPGRVIVSFHPPP
Ga0208652_1036796Ga0208652_10367962F068909STKPAPPCPKCGSDEVTRLLSRINTEWLPSDVAWDRVGRSWD
Ga0208652_1037255Ga0208652_10372552F027172MAEKTILVCDACGKPAAETVTMKTSRGNFVKDLCSTHVNELVAGARKPRPGRRKGTTVTAAAKPAAKAATAAPKKRGRPRKKPAS
Ga0208652_1041015Ga0208652_10410151F085674MPGEVMLVGIATIAIAIAGFTAITSALEPPGGSWSPAMRLRQRSIVSTSFNVGLESFAPLIAFAWLEELHSALVVASLVVAIYTTSVVLFRGRQFVRAGGMHTGVAGLTLFALGPTATLLFWANAIVFASLAIFALALLVQLLVAMISF
Ga0208652_1041861Ga0208652_10418612F065699VTEQYIGWALALGLVVGGALVWFAVGRLPRSGEEIPDEERAAEAAWISASIDERGGKAPADLVEEVLELHAEYLDRQSQELA
Ga0208652_1042513Ga0208652_10425131F024001KNKLMILGVEAPGRQGVKPQEYLDIPRFCNAAGRDASATKMAGYF
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