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 3300026058

3300026058: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNW_TuleA_D1 (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300026058 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)
Gs0111376 | Gp0116089 | Ga0208421
Sample NameNatural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNW_TuleA_D1 (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size64856408
Sequencing Scaffolds41
Novel Protein Genes44
Associated Families43

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria3
All Organisms → cellular organisms → Bacteria7
Not Available7
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium15
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Rhodothermaeota → Rhodothermia → Rhodothermales → unclassified Rhodothermales → Rhodothermales bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria1
All Organisms → cellular organisms → Archaea2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → unclassified Acidimicrobiia → Acidimicrobiia bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Rhizorhabdus → Rhizorhabdus wittichii1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Anaeromyxobacteraceae → Anaeromyxobacter1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon1

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 biomewetland areasoil
Earth Microbiome Project Ontology (EMPO)Free-living → Saline → Water (saline)

Location Information
LocationUSA: Antioch, San Francisco Bay, California
CoordinatesLat. (o)38.05246563Long. (o)-121.76914021Alt. (m)N/ADepth (m)0
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F000925Metagenome / Metatranscriptome832Y
F002252Metagenome / Metatranscriptome578Y
F003187Metagenome / Metatranscriptome502Y
F003255Metagenome / Metatranscriptome497Y
F003627Metagenome / Metatranscriptome476Y
F003912Metagenome / Metatranscriptome462Y
F006079Metagenome / Metatranscriptome382Y
F006851Metagenome363Y
F010354Metagenome / Metatranscriptome305Y
F017250Metagenome / Metatranscriptome242Y
F019205Metagenome / Metatranscriptome231Y
F020203Metagenome / Metatranscriptome225Y
F021102Metagenome / Metatranscriptome220Y
F021418Metagenome / Metatranscriptome219Y
F021619Metagenome / Metatranscriptome218Y
F025512Metagenome / Metatranscriptome201Y
F027211Metagenome / Metatranscriptome195Y
F027905Metagenome / Metatranscriptome193Y
F028853Metagenome / Metatranscriptome190Y
F031150Metagenome / Metatranscriptome183N
F035704Metagenome171N
F037757Metagenome / Metatranscriptome167Y
F038132Metagenome166Y
F040782Metagenome / Metatranscriptome161Y
F041850Metagenome / Metatranscriptome159Y
F041902Metagenome159Y
F045206Metagenome / Metatranscriptome153Y
F054295Metagenome140Y
F055518Metagenome / Metatranscriptome138Y
F057190Metagenome136Y
F058251Metagenome135Y
F063008Metagenome130Y
F067213Metagenome / Metatranscriptome126Y
F070289Metagenome / Metatranscriptome123N
F072476Metagenome121Y
F072481Metagenome / Metatranscriptome121Y
F073898Metagenome120Y
F074523Metagenome / Metatranscriptome119Y
F075472Metagenome / Metatranscriptome119Y
F079375Metagenome / Metatranscriptome116Y
F090229Metagenome108Y
F097998Metagenome / Metatranscriptome104Y
F101965Metagenome102Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0208421_1000120All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria3892Open in IMG/M
Ga0208421_1000801All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria2154Open in IMG/M
Ga0208421_1001069All Organisms → cellular organisms → Bacteria1946Open in IMG/M
Ga0208421_1003496Not Available1260Open in IMG/M
Ga0208421_1003939All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium1204Open in IMG/M
Ga0208421_1004093All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium1185Open in IMG/M
Ga0208421_1004289All Organisms → cellular organisms → Bacteria1161Open in IMG/M
Ga0208421_1005189All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium1073Open in IMG/M
Ga0208421_1006617All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Rhodothermaeota → Rhodothermia → Rhodothermales → unclassified Rhodothermales → Rhodothermales bacterium969Open in IMG/M
Ga0208421_1008562All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium871Open in IMG/M
Ga0208421_1009536All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium834Open in IMG/M
Ga0208421_1009647All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria829Open in IMG/M
Ga0208421_1010062All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium815Open in IMG/M
Ga0208421_1010215All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium810Open in IMG/M
Ga0208421_1011679Not Available765Open in IMG/M
Ga0208421_1011855All Organisms → cellular organisms → Archaea760Open in IMG/M
Ga0208421_1012365All Organisms → cellular organisms → Bacteria746Open in IMG/M
Ga0208421_1012712All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium736Open in IMG/M
Ga0208421_1013298All Organisms → cellular organisms → Archaea723Open in IMG/M
Ga0208421_1013705All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium714Open in IMG/M
Ga0208421_1014483All Organisms → cellular organisms → Bacteria697Open in IMG/M
Ga0208421_1014486Not Available697Open in IMG/M
Ga0208421_1014632All Organisms → cellular organisms → Bacteria694Open in IMG/M
Ga0208421_1014747All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria692Open in IMG/M
Ga0208421_1015624All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium675Open in IMG/M
Ga0208421_1017968All Organisms → cellular organisms → Bacteria637Open in IMG/M
Ga0208421_1018676Not Available626Open in IMG/M
Ga0208421_1019564Not Available613Open in IMG/M
Ga0208421_1021489Not Available589Open in IMG/M
Ga0208421_1022124All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → unclassified Acidimicrobiia → Acidimicrobiia bacterium582Open in IMG/M
Ga0208421_1022848All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium573Open in IMG/M
Ga0208421_1023537All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium565Open in IMG/M
Ga0208421_1023577All Organisms → cellular organisms → Bacteria565Open in IMG/M
Ga0208421_1024626All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium554Open in IMG/M
Ga0208421_1024812All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Rhizorhabdus → Rhizorhabdus wittichii552Open in IMG/M
Ga0208421_1024947All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium551Open in IMG/M
Ga0208421_1026659All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Anaeromyxobacteraceae → Anaeromyxobacter535Open in IMG/M
Ga0208421_1027322Not Available530Open in IMG/M
Ga0208421_1027651All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium527Open in IMG/M
Ga0208421_1028964All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon517Open in IMG/M
Ga0208421_1030322All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium507Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0208421_1000120Ga0208421_10001202F019205MFDTRKTFSIKAADATDLIIDFATLGEYGLEPVNTASGRACEARLRAGARRRSTGAWTAAISRFTVPA
Ga0208421_1000269Ga0208421_10002696F021102VRRESPVKRRNPSGKVVWVAGYTGRDGKHHIAKPAWNRGKGTFERKADAQQAIEEAYGVADKPDILGAYATSWTERHPRSARTNATNTHRIGRVLDIDVEGIGLKDWPMRELRRRHALVLVDHMLRVQGRATTGVVGILRSLSARSCPFAARTSTARP
Ga0208421_1000801Ga0208421_10008012F090229MPLEGHYERQTTPLYKLSSREIKTATVVLLVTVVAMLGVVVATAGDSNPPTPIGCIRANVAGVVGAETISGCGAEAEAKCAHAALFESPRAHGVVAECERQGIEF
Ga0208421_1001069Ga0208421_10010693F027211MVRTYWLVPVFYEASGNLDLQPFARTDQIEACRPRAMWLPSVRRRVGWGK
Ga0208421_1003496Ga0208421_10034962F028853MTSLEPKGAVHWIDHYVVGTNDLPNWSYWALNATGLPIRPINGLTTNMRKKN
Ga0208421_1003939Ga0208421_10039391F017250RLPSTTPTAEKPALSEAQRIERLRLLAKRLRRPDGLDRDVLKRIEHLTGDEQ
Ga0208421_1004093Ga0208421_10040932F006079MARRKPGKIVEGPELTAVTAEKVFGWMGVHKENGELIGKKQDKAGRWRSARVPAYSTDPVHAYAIDERMKQLKRWERYERELSRVTKAQNLPSEWATPEQRSRAAI
Ga0208421_1004289Ga0208421_10042891F038132EGQMAYQRIFTEGNDGPDSMRVDIPKDKVPRGNRRPQGDPNRYLFVDRAEWMDQAPIRKFVKEALAERKK
Ga0208421_1004644Ga0208421_10046442F035704MALHIKDSEFYAIDAHSHLGRRKTPLGHGVASFLGEDLVRNLDEAGLDCAV
Ga0208421_1005189Ga0208421_10051892F055518MVNYIQNKWKLSPKVAEESYRVWLNGFTSDGKIPVKGLQEIYGEAFAAKLIPTAVPVAKVMDYTFVDQVLKEKDRPLRSRKWLARHLLIL
Ga0208421_1006617Ga0208421_10066172F003255MPVTLSIHHLKDFDAWLKVFKENPPPPVGRWRVFRGADDRNRVHVVGEVAASEVQTVKDFLASDRMRDVFRRVNAMSTAPVEFVWLEEQTP
Ga0208421_1008562Ga0208421_10085621F101965ANPRHEPQIGFDRVQSAEDRYLFGADGRLVYEVGHVFALQMHIVDKTHTRGLFLADFFAIEENGPRCLNKLPCEMVRAGS
Ga0208421_1009536Ga0208421_10095362F073898MTQASISYHQQLRSIGQTLEAQRINVFELSCRGERIIVKGQPDKETSLLGALRKWQKQRRSEGLNSSLTFTQQDIDEIDRQGRTHRSQGNRLPDFYSLPNTLRTVGSYLDLKGAQLIEIHKQPLSLTMLSRNQAGHPEYEERSIASF
Ga0208421_1009647Ga0208421_10096472F002252MTFADVLAWCKRNQADVRGVYRGKDISISHNDTALPSVLPPISAIFHWDVKMRELNHYVSSSDFERIVTGKLT
Ga0208421_1010062Ga0208421_10100622F072476MALRVKSRKILIPDVPPVGESTTYQGLVIAGIGVFCGSVVIAAVLFV
Ga0208421_1010215Ga0208421_10102151F079375MAEIEKEYLVGTVRPTNRPEAGQELDLDTLIPAKIKFVYLTMNFTRGTEEEFSTS
Ga0208421_1011679Ga0208421_10116792F000925MQSPEDRNYAAIERLERLLDEIRSDPSKPRETEAIREIGFEIAIAVREVGAMLTKDVGWEETFVAGQRARQAGSEPAAHD
Ga0208421_1011855Ga0208421_10118551F074523IASDFIEAEKQVIGSFQSQIDRNSGGVWDLYNPQKIAENHAVAVNNFTSYLLNTADLVNNALLSNIRVYNTALEQTRDNLKACAKTNTNYIQAVSGNSQNRETNTTSP
Ga0208421_1012365Ga0208421_10123652F057190MSANNGGKSALHVATFSGWYRFEQNGKDLKQTKRDLTYWTLTCMSVDPDNPQKIYAGSEHSGLFYTDNGGARWKRAEPNTPKMMLFSALALNDGVMVGTIPSAVYRSKNGGWEELAGVRINSAGANFPP
Ga0208421_1012712Ga0208421_10127122F097998VALFFHSDDVDQLIPFKEAVQITEFALRDLVSPKGVNAPRKRLNLHRDIGEASF
Ga0208421_1013298Ga0208421_10132982F072481MYYAGSKQCDDMIARKNETKPPFRPDLESEKQVLCEHCGETYKEKEIKWDKVRERWVCKNHPKCDGSVSHLDIRHVD
Ga0208421_1013705Ga0208421_10137052F063008ANVEHLRQSFSQESRRLSKCLEEIDDNILACRQYLQDYERIRSSLCGLNEKLTQLGAQSIQVPDGLPATDLGEIVRERIDFLRSQGKI
Ga0208421_1014483Ga0208421_10144831F058251QPVASVVIGCEQLAPLEQNVQAAMNFRPISESGKQRLQEKVAPSRSAWENFLRTHEDSVA
Ga0208421_1014486Ga0208421_10144861F027905NAPADEVLRRAEADDAPFAKSDELRAWVTQGLEELPELGR
Ga0208421_1014632Ga0208421_10146321F031150MAEFIIDADGHIMEDPKDIFAHIKGNFSEMNWHSTWPMFDADGWQRG
Ga0208421_1014747Ga0208421_10147472F040782WPAWRGTFVEPLACVLRGASRLPRGRVLIVGNGFVGQLFGAVLARRGDDVFSVDSDPRRSGRAPDGPVDAAVLCGPGGTDTALDAVAPGGTVLAFADAGSIPLADVYRRELTVVGARSAAPPYMPEAVALLHDLDVPEPTVLPLERFADGLELYRRRDATKVVFTA
Ga0208421_1015624Ga0208421_10156242F041902MADWRMIDADGHIREVESDVFEYLPDYYKSRREAVLYFPLLPHHGWHRQAGRGGMGASFLIPTLEDWRAALEQD
Ga0208421_1017968Ga0208421_10179681F025512LDRTVRLLQRAFEVPGLRLELAVLLVEYHIRRNEVARRSHAKTWWARHKGVKLLPL
Ga0208421_1018676Ga0208421_10186762F003627VDRESARANITAGLVAGGIAVGVFALCFVVAMLYIAS
Ga0208421_1019564Ga0208421_10195642F037757MTTAAVRRSAPFWISIFAGLALWEIAGRSTSAAFMVPFSETLVRLKQLVVGADFIAQFLDSAQLFLTGFVLALVVGMP
Ga0208421_1019741Ga0208421_10197411F003187VMKKFLVIVCSLALALGVASCAGKGKAPIGKGKAPVVTKG
Ga0208421_1021489Ga0208421_10214892F006851MSRAARLDLRSFQQELASRLASKTAAQVESSRLGLACGERRFLIRLSDAGE
Ga0208421_1022124Ga0208421_10221241F045206IIEEIPGDELDELRIVEAMVRGPGLSKAGRSPLGVAMPKTPSPNGGP
Ga0208421_1022848Ga0208421_10228482F067213HHDVVVRLIKSTVEGIRYAISNEDATKRIISKYLGVTDSDLLRQSYLYVADTFVREPFVPESVMQSMVQRMVQVNMIDAKSAQTTPTSAYFDNSYVAALKQAGVLDKIWK
Ga0208421_1023537Ga0208421_10235372F021418ALYDTGDLSGYHDIVIERTLRVGKELVEHGAEAIIPLGGKIYPYVVTPEELAPHLGVPVINTKAVGVSYAELMARNKIQHSIKAYPCPTGLDPETVSQRSQ
Ga0208421_1023577Ga0208421_10235772F054295FLEAKWGIKETDVRESIYRDMVGLFSRNGVASDETMNNVVQLVRDTRKSKDDKTLADIVDWSFAKKAQAELKIK
Ga0208421_1024626Ga0208421_10246261F041850DHSKLVVICESTGVWDILPPALKGLVQEVESYRSMNMTLTEPASSESCAAQLQRYFFIARRLIDYMEFHVIGNDSVLKRLKVA
Ga0208421_1024812Ga0208421_10248122F075472MSRIARLSLVDRAEVGLSIAAQCRLLKIARSTLYWRAVPVSEDDLRLMRRI
Ga0208421_1024947Ga0208421_10249471F003912ARLAPAKMRYSSMLRCIGQALSDMQLKAVEVRTHGEDLIVQAWNRGTSMAMDFEKHYTPEDLRLLEAESRAKRRVFAGPPDFLSVSQVLRMAGNHVDRMCGRLLRVSWQDQSDKIQSVTVQWESGQPGRDRSESPLTVVEELCIHIYKQRKKINLVSERQANRPFVSVVKSL
Ga0208421_1026659Ga0208421_10266592F021619LQAYAGEMRDDESVLDLRLTQLLAVDASLSDARRALLRAARIPSAFSAEVRALLALVADIDRRVMLEVAQ
Ga0208421_1027322Ga0208421_10273221F070289PQRLVLTGANVSPQFLQGTCGDVNGAIVNSFLATAWTFLPKSNPVRKQAALLRKILRRPVSNFDGDAAGALWAYKAAIERGGATRARIRDALETKLRGLVTPAGKIFLSRKNHQGLQLDSMWVGRIDNCKVKPLFGKAFAKKK
Ga0208421_1027651Ga0208421_10276511F020203VIIDCDTHLMPRDAFEAVGGNLAALKPILKFDSQGLYTDVDFPGYRDIAGTSPLLAPGSGAMFKSLWEPQARMKDYDDRLGIEQHVVLPQFSGWWSYLLEAELACHMARSH
Ga0208421_1028964Ga0208421_10289641F010354MSNDTGPKSSSKKSTKNITTAKKVKETKSVPITVQLNILKVLINERSLIPLLRILKKNKELHTRELLITMGSWGYGQSLMKKATNLGLIERKVKKEKSPGRGKPRIYNSLTNKGRDVVGLADKVVYTK
Ga0208421_1030322Ga0208421_10303221F038132TEGNDGPDSMRVDIPKDKVPRGNRRPQGDPNRYLFVDRAEWMDQAPIRKFVKEVLAARKK

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