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 3300026069

3300026069: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushSE_CattailNLC_D1 (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300026069 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)
Gs0111376 | Gp0116113 | Ga0208539
Sample NameNatural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushSE_CattailNLC_D1 (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size84500455
Sequencing Scaffolds36
Novel Protein Genes39
Associated Families38

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiaceae1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium2
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Pirellulales → unclassified Pirellulales → Pirellulales bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria1
All Organisms → cellular organisms → Bacteria3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria5
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium2
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium 13_1_20CM_4_56_71
Not Available11
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium3
All Organisms → cellular organisms → Bacteria → PVC group1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Alteromonadales → Pseudoalteromonadaceae1
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae1

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: Fairfield, San Francisco Bay, California
CoordinatesLat. (o)38.224518Long. (o)-122.019257Alt. (m)N/ADepth (m)0
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F001196Metagenome / Metatranscriptome749Y
F006851Metagenome363Y
F007982Metagenome / Metatranscriptome341Y
F011594Metagenome289Y
F016540Metagenome / Metatranscriptome246Y
F017154Metagenome / Metatranscriptome242Y
F018947Metagenome232Y
F020201Metagenome / Metatranscriptome225Y
F021129Metagenome220Y
F021563Metagenome / Metatranscriptome218Y
F022216Metagenome / Metatranscriptome215Y
F023130Metagenome / Metatranscriptome211Y
F023894Metagenome / Metatranscriptome208Y
F031676Metagenome / Metatranscriptome182Y
F031715Metagenome / Metatranscriptome182Y
F031901Metagenome / Metatranscriptome181Y
F034234Metagenome / Metatranscriptome175Y
F037274Metagenome / Metatranscriptome168Y
F041849Metagenome159Y
F041952Metagenome159Y
F043121Metagenome / Metatranscriptome157N
F044014Metagenome155Y
F048318Metagenome / Metatranscriptome148Y
F051241Metagenome / Metatranscriptome144Y
F053367Metagenome141Y
F054979Metagenome / Metatranscriptome139Y
F061085Metagenome / Metatranscriptome132Y
F065171Metagenome / Metatranscriptome128Y
F069000Metagenome124Y
F069003Metagenome124Y
F073725Metagenome / Metatranscriptome120N
F080203Metagenome115Y
F082882Metagenome / Metatranscriptome113Y
F085865Metagenome / Metatranscriptome111Y
F087402Metagenome / Metatranscriptome110Y
F091236Metagenome / Metatranscriptome107Y
F097621Metagenome / Metatranscriptome104Y
F101435Metagenome / Metatranscriptome102Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0208539_1003208All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiaceae1292Open in IMG/M
Ga0208539_1003237All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium1289Open in IMG/M
Ga0208539_1006803All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium995Open in IMG/M
Ga0208539_1007429All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Pirellulales → unclassified Pirellulales → Pirellulales bacterium965Open in IMG/M
Ga0208539_1007965All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria940Open in IMG/M
Ga0208539_1008576All Organisms → cellular organisms → Bacteria915Open in IMG/M
Ga0208539_1009546All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria879Open in IMG/M
Ga0208539_1010888All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales836Open in IMG/M
Ga0208539_1011401All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria822Open in IMG/M
Ga0208539_1011988All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium806Open in IMG/M
Ga0208539_1013122All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium 13_1_20CM_4_56_7777Open in IMG/M
Ga0208539_1013228Not Available775Open in IMG/M
Ga0208539_1013492All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium770Open in IMG/M
Ga0208539_1015826Not Available724Open in IMG/M
Ga0208539_1015980All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium721Open in IMG/M
Ga0208539_1016062Not Available720Open in IMG/M
Ga0208539_1016360Not Available714Open in IMG/M
Ga0208539_1017644All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium693Open in IMG/M
Ga0208539_1018265All Organisms → cellular organisms → Bacteria684Open in IMG/M
Ga0208539_1020385Not Available653Open in IMG/M
Ga0208539_1021231All Organisms → cellular organisms → Bacteria643Open in IMG/M
Ga0208539_1022660All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria626Open in IMG/M
Ga0208539_1022675All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium626Open in IMG/M
Ga0208539_1022692All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium625Open in IMG/M
Ga0208539_1023266All Organisms → cellular organisms → Bacteria → PVC group619Open in IMG/M
Ga0208539_1023804All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria614Open in IMG/M
Ga0208539_1024280Not Available609Open in IMG/M
Ga0208539_1024751Not Available604Open in IMG/M
Ga0208539_1028554All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Alteromonadales → Pseudoalteromonadaceae570Open in IMG/M
Ga0208539_1029875All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae560Open in IMG/M
Ga0208539_1031498Not Available548Open in IMG/M
Ga0208539_1032662Not Available539Open in IMG/M
Ga0208539_1032790Not Available539Open in IMG/M
Ga0208539_1036154Not Available517Open in IMG/M
Ga0208539_1037783All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria507Open in IMG/M
Ga0208539_1038131All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium505Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0208539_1003208Ga0208539_10032082F069000MRAPLALWPRRLQWLPGLLLSVPLALLLWSLRSAGEDVRTSVAIVAVLLALPWVVPAMVLVAALSVPVYMWLHTQGPVPPVLQWLGGTVLVAAVIGAHVNAALGWVWMHRGKAVPEPGIGDFLKRHSAGAQQRTDDAR
Ga0208539_1003237Ga0208539_10032371F011594MTYAELENHILLADRMVVSCAPRKAEYGRGYTEGIKFHFNNPQATSPPDHYSIAEIARRNGSRDVHAYARGYRDGCKGLKPEYTG
Ga0208539_1006803Ga0208539_10068031F085865DARETNSELEHLSLGIAQLDQRAATYRQAMTGLKKVFGAVEDTPKPLEGYIQALEKEAAGGPVVPLPEGLKPVQESCGSPSDKDPWMECRLRQYMEARAAQYQKILANEIAAPLEKLNIKEFDQWKAELQAGMKKYAERFRSEMTTNPSFWRNFNQKAPIYQSMIEGVHRFWSDHQFEEIGRRMEQAAAASQAEVEQLNQKKEQIQKGKEGLNNALKNIKTRFGKLGLEAEDAILLAPIAFAALFLFASLNLCQNIQLRKSFHRLFQARDPQKVAITDSEIALAMPLWVDPLAPPIQRRLKLAVMMIPAIASVLALAVVFYCWTIPDAFPG
Ga0208539_1007429Ga0208539_10074291F091236MKYRSTTSRLIEVQTDPAGNNVLGEHLVTGREEHPTTRSRLAIWVAVLALVIALHPGAASAQGDGTVTISGRFSMDYLSGERDLEYFDPELLWVYYNGHEHTWTLTLHGTTQSHFTFSAFGVKRATQIHATSFDLEFFGPDAATLNGIVSEHIAGGEVRIELDNGYSSWIGDDFATIYIAAYGPDVSFEAGDSWGSFTLFPSDVDGYPVVGPEPFSIWAEYSDLWDGRTGNGGAIGSDYSLVTFQVMPALPRLTITSSNNA
Ga0208539_1007496Ga0208539_10074962F080203AGIGLQAAGLYERVDLVPDGEIYSVSLSVGGPTPVGTLTLGVAGSEDSWGFWLSLGRPVGTGSILNDGLFR
Ga0208539_1007965Ga0208539_10079651F087402RILQRAGNAGQRIDKTDSRWGKYVTEKKINEVAATAIARQKFENATPVIIAEGNDTDGLYFFSKDDEACLRLTALE
Ga0208539_1008576Ga0208539_10085761F007982MRPVASWMLSAVVMALLVACTERAPQDKEEARAKGRDTDETVFDDMIQTQDRARAVEGLTLGRTGELDAAIERSEGET
Ga0208539_1009546Ga0208539_10095461F006851MSRPARIDLRLFQQELATRLASKTTAQVESSRLGLSCAGE
Ga0208539_1010888Ga0208539_10108881F073725QRFQEGLIMEKRATRRYRISTSIVCSYLNSVDFGKPVDGRMRNCCVNGLYAELGTHYKAGTVLVVRTTGSSCGYSDEEGFRSPAVAEVKWSRPRSIEGGACYATGLKYLML
Ga0208539_1011401Ga0208539_10114011F065171TDAKLRSFRHERWIPAKWTNVHQLYAGALELSVARVPVALASAGPGAMQWSTEQEYIYALLIQQLNMGSLSPVEIDWASAQMRAWGRKLEFQAIPRSTEGFYVDLASKRGLVRRTGGEAGPTMHFLDTTPLADQLERAIHALRQADIGEPGAAAALSQQRIGVLEKVRPVVAPNLYGDLRRAPRTPVTMAAKVRIGLARICAELSPKAVVEPANDPDAGNEQIEVYAVADRPRNRPHVADEHDSLSASIAPVADPAWQIKDRSVAGLRISAAGG
Ga0208539_1011988Ga0208539_10119882F020201MRIVSRTTRSLLEQKREKSLRRRVAAGTIAKAFPRVEQIRLQLRFLPTAGSVPAAQMHALYPSAPAYFEFACPYGDCDGSFDLNSVVLPLLADNGARADGTMLCSGTRTAAGMTRQPCKLRADYWVSAQHQSIVRAAG
Ga0208539_1012332Ga0208539_10123321F080203IKNQSIYAGFGLQAAGLYGRVDSQVPDDEVYSASAYLAGPTPIGTFTLGAGASADDWNFWLSLGRRIGKGSILDDGLFR
Ga0208539_1013122Ga0208539_10131221F061085MEDIRLTDSWIGNVSMGQMPMGTPPEVTQDRFRSVWANTTKAWSRVQNTGAGCSGNPCDPTANQIGWGADRLTYFAQQATWETPLLCYDQEMHVTHAEQHLSQIINEILRPNTQNIFSMFARKNALYWAKYRQMANSLLSSFSYQWTSVDLDGDGIADDEI
Ga0208539_1013228Ga0208539_10132281F044014MAEDYRPRFGFEITEAQKKRADKILNTYGLRKAIFGPILDDVLDMIEEYGGVAIGVLMSGKAKPRD
Ga0208539_1013492Ga0208539_10134921F021563MEDLKLLLIDRLKSQGMDSSLIPSFLKALTSIISSEPGIEPAQANLKLNSLGWNEVAIDYHCLQIAIAC
Ga0208539_1015826Ga0208539_10158261F023894MEYGNHGNGNIGWVFGILVIAGALMLLACDQPSGQSDLSKKAPPSLGAIANVDGSDDEKKDGKKAQAGSEQAPAQSPAGGQPAQAAPKQ
Ga0208539_1015980Ga0208539_10159801F054979TMQNLLELSAKKFGVPSEVLDLIGRQFISQIIDEFPTLLLPPIMNTLKQEYVENGLEWIKQNVMSLREQFLLLKKLYGPSWILA
Ga0208539_1016062Ga0208539_10160621F051241AEKRGKTPPPPPLTHGLERDPTDEDKTERLREQIAWADRNQLLHRVQMFFEAMPPSGWVRGEKR
Ga0208539_1016360Ga0208539_10163602F101435MIEQIQDFVSEQTAAITSKVKQIRDESTTTVRDAVVESAGNIKSLKSPVRVIARSGVKLTSVSQTAVASLIELQSDVLTSALSDVALRLERAARADGIVDLVRDQYELAHATRGRVVEDAQRAMQIFKV
Ga0208539_1017644Ga0208539_10176442F016540MSQSLDAIPVLTDIVEDDLGAVATIDSTMLFLGELEAHLTAAIHEQADELVHNACREMEALLLEQVSDRLRAQLPALVARIVDEHFHGPARTN
Ga0208539_1018265Ga0208539_10182651F023130MTRRFWVPATALLLSSILVMTGSISHDAMAGIFVLSQSSGSSIVEGEGPATMKMGPAEEFETHSQRDVSSRYWMRGIVLLLLILLILWLIYRTFTGWKPMLSRSVGFLPELQACAW
Ga0208539_1020385Ga0208539_10203852F037274KIYTVYRLGYWNNKLELLGKVVERRKEERKNNAADMLRWAQKIYAASSIDSSIFIVKEGSSEGAIFGGA
Ga0208539_1021231Ga0208539_10212312F053367LWAAERAGWRFDWRFCRDLDPAFDSIRDDPEFKAIFADIERDMARQRAELAQRPKDAPLNLGAAD
Ga0208539_1022660Ga0208539_10226602F041952IVPTSEYADGRQVILATDRSVYTVALKNLVEQRSEWSWAAIQIVEKQVRE
Ga0208539_1022675Ga0208539_10226751F031715DPALASIRDEPEFKAVFADIERDMALERAKLAKLPKDAPRDLAGD
Ga0208539_1022692Ga0208539_10226922F069003AGLSGGLAGVLWSSLVTTPWLARGGSVGVDDRTESATRVFAGAALRAAAGAALGFLFWLGWGLIALVGFPWYVVGPLYGVVTWAALAAPALGTLLLRSHGPAKPVLAHTVEWLATCLAIGLMCAWAWDRYA
Ga0208539_1023266Ga0208539_10232661F031676MKTPQQLSQEAINEFKAIYQEEFGEVLTDDEVKIIATRLLRFFSILNRSNSDQEHQ
Ga0208539_1023804Ga0208539_10238042F018947YVAIRHGLALRIPHPEGFDHPNLLIVLGAAKLGNTRLIDNVDVVPKHNED
Ga0208539_1024280Ga0208539_10242802F017154SCDMTNPYLEPVASVWGRIAGIALLVAGAGLTLVLGHSLFGLLGDEERRRSFTSSSMIFGLVLLALCGICWQAGYRLAFQRPDRTGTLFSRPAWLAIGTGLVVITASMVVAISQVRQMTLLDLQVLLFLGGIGVWCLVLSFRGGGGTR
Ga0208539_1024751Ga0208539_10247511F097621PWNATKDAIQAKYPGGKWAQNDKGQEQYCAASKQTLLKLPAPHQSRELCFVMGSDGTLASATAVMDASLPSLLAIVNRCRTTFGDFDAVVRDQQAIQSRSTAMLWTKDKQFVVRIVSENDTDGRPLMVSYTVADEPGMYTDGAAKVSNIPGSR
Ga0208539_1028554Ga0208539_10285542F041849QLMGLWLAIVGIAIVFGVLYAMGSALSHWKQHRNRADQGRRAG
Ga0208539_1029875Ga0208539_10298751F043121VSCLTQLPASIHDSDCTETLQILGLLLVIGFFILRWLYRKWTEKHSYAVYFGEGDDLVNVGADCKTVEIGEHVLDVMIRAKRTVEVGSANLRFVVDTKHLKSPRSDVEKSIIALVEAKDLDIGAPHCSSKHDKAGGYDLKYSPSYKRVAGSFLRIRI
Ga0208539_1031498Ga0208539_10314981F022216RRGTGGQVSDPRVSSGPTDEQRRRIRRNAIVLALVALGIYVAFIASGVMQARQ
Ga0208539_1032662Ga0208539_10326621F001196GVLSTLLAGLATAGPVGDQYRGGAFGLPWNAGKSAIEAKYPGGNWAQDGKGREQYCSASRQSLLKLPAQHQTKELCFVIGSDGTLASVTARMDASLPALLAVVNRSRTIFGDFDAVQRDENSIQSRSTAMLWTREKPYVVQVASTNDPDGRPMEVTFTVADEAAMYADGAAKVSNKPAP
Ga0208539_1032790Ga0208539_10327901F082882MYRKRDAKNDFFYAFVMFAVFAVVVFNVAAEFVAYYPEAYFVDFNEAVEPRVMTAEADAHAFVAMRAA
Ga0208539_1034064Ga0208539_10340641F031901MRVAFLLIVLGFPLVDLYATVRFARWTGVPTYAWLGLAAIAGLYLLRNERSTFRASTVAAMHGEQPLL
Ga0208539_1036154Ga0208539_10361541F034234MQSEVIALLFPAPSSSADGSTPLVTALLRDAEGLMELRNLRPDKALLRAARLAGRLNSGKPILDPHTREVIGYEIEPMAVPAA
Ga0208539_1037783Ga0208539_10377831F021129HIGHLAMLRALIRDGARDGSFQPELAWDSAASERFFAELKQALKSGYFVVQDRETREVRTVAVPGYVYWADETVGAEPPAGFGLFRAVQGGGFELWLAGLEGALRGKGHGRAMLEALFETPTGRATRFARVRRSGRYAEAVARLLEVHGFTATRETSHETWFVRATPV
Ga0208539_1038131Ga0208539_10381311F048318MATVENVHLDITASTTKPGYSKIAYSYELHPSELDCAWQREYTVSADFWGEDLIDDDLLAWGKDEHKVKFDDSGSCEPIKVERVFEVETKILDEDLFGDDEVYLIVEAHSGLGSDAAGEDPVIGRSNTFVGDF

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