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 3300026061

3300026061: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushSE_TuleB_D1 (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300026061 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)
Gs0111376 | Gp0116115 | Ga0208541
Sample NameNatural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushSE_TuleB_D1 (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size70587126
Sequencing Scaffolds37
Novel Protein Genes40
Associated Families39

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria2
All Organisms → cellular organisms → Bacteria7
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria4
Not Available12
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Nevskiales → Steroidobacteraceae → Steroidobacter → Steroidobacter denitrificans1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium2

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)38.224476Long. (o)-122.019341Alt. (m)N/ADepth (m)0
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F002104Metagenome / Metatranscriptome593Y
F007876Metagenome / Metatranscriptome343Y
F007982Metagenome / Metatranscriptome341Y
F009010Metagenome / Metatranscriptome324Y
F010406Metagenome304Y
F010927Metagenome / Metatranscriptome297Y
F018950Metagenome / Metatranscriptome232Y
F020200Metagenome225Y
F021303Metagenome / Metatranscriptome219Y
F021565Metagenome / Metatranscriptome218Y
F027335Metagenome / Metatranscriptome195Y
F028592Metagenome / Metatranscriptome191Y
F032671Metagenome / Metatranscriptome179Y
F036723Metagenome / Metatranscriptome169Y
F042409Metagenome / Metatranscriptome158Y
F045255Metagenome153Y
F045785Metagenome / Metatranscriptome152Y
F046145Metagenome151Y
F047968Metagenome149Y
F048318Metagenome / Metatranscriptome148Y
F051241Metagenome / Metatranscriptome144Y
F056368Metagenome137Y
F056991Metagenome / Metatranscriptome137Y
F058543Metagenome135N
F061020Metagenome132Y
F067873Metagenome125Y
F068280Metagenome / Metatranscriptome125Y
F073721Metagenome120Y
F073723Metagenome120Y
F081923Metagenome / Metatranscriptome114N
F085771Metagenome / Metatranscriptome111Y
F085853Metagenome / Metatranscriptome111Y
F086748Metagenome / Metatranscriptome110N
F087857Metagenome / Metatranscriptome110N
F100542Metagenome / Metatranscriptome102Y
F102756Metagenome / Metatranscriptome101Y
F103344Metagenome / Metatranscriptome101Y
F104669Metagenome / Metatranscriptome100Y
F105751Metagenome100Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0208541_1000252All Organisms → cellular organisms → Bacteria → Proteobacteria2894Open in IMG/M
Ga0208541_1000286All Organisms → cellular organisms → Bacteria2796Open in IMG/M
Ga0208541_1001126All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria1907Open in IMG/M
Ga0208541_1001567Not Available1715Open in IMG/M
Ga0208541_1001686All Organisms → cellular organisms → Bacteria → Proteobacteria1680Open in IMG/M
Ga0208541_1001818Not Available1637Open in IMG/M
Ga0208541_1003252All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria1355Open in IMG/M
Ga0208541_1003782All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium1284Open in IMG/M
Ga0208541_1004342Not Available1221Open in IMG/M
Ga0208541_1004554All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium1200Open in IMG/M
Ga0208541_1004687All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria1187Open in IMG/M
Ga0208541_1004927All Organisms → cellular organisms → Bacteria1164Open in IMG/M
Ga0208541_1007810All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium973Open in IMG/M
Ga0208541_1009404All Organisms → cellular organisms → Bacteria906Open in IMG/M
Ga0208541_1011503Not Available834Open in IMG/M
Ga0208541_1011731All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium827Open in IMG/M
Ga0208541_1012228All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales814Open in IMG/M
Ga0208541_1014622Not Available754Open in IMG/M
Ga0208541_1016388All Organisms → cellular organisms → Bacteria718Open in IMG/M
Ga0208541_1019009All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Nevskiales → Steroidobacteraceae → Steroidobacter → Steroidobacter denitrificans673Open in IMG/M
Ga0208541_1019364All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria668Open in IMG/M
Ga0208541_1019803All Organisms → cellular organisms → Bacteria662Open in IMG/M
Ga0208541_1020029Not Available658Open in IMG/M
Ga0208541_1023132Not Available618Open in IMG/M
Ga0208541_1026611Not Available581Open in IMG/M
Ga0208541_1026749All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria579Open in IMG/M
Ga0208541_1028111All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium566Open in IMG/M
Ga0208541_1028115Not Available566Open in IMG/M
Ga0208541_1028255All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium565Open in IMG/M
Ga0208541_1029029Not Available558Open in IMG/M
Ga0208541_1029225All Organisms → cellular organisms → Bacteria556Open in IMG/M
Ga0208541_1029717Not Available552Open in IMG/M
Ga0208541_1031306Not Available539Open in IMG/M
Ga0208541_1031400All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium538Open in IMG/M
Ga0208541_1031663All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria536Open in IMG/M
Ga0208541_1032488All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium530Open in IMG/M
Ga0208541_1033764All Organisms → cellular organisms → Bacteria520Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0208541_1000252Ga0208541_10002521F010927KARLVIEQGRDSILVMRVVVAQNETVALAVGGRLESTTGFLRIRERKDERGRNENKAVGSIVFVPAVGDGDERSPANFQINISMSAAKFEALLKVAISGRLPSKFFVNAGERASARETRGMGYVIRAGVRTKFWDNKRYRTLPVTNFSVILPITVPETPESPAFEEDRAIAESIASNDQVAELADEFAVFQGETKNALTAVVSVVAVIGVLLLFINLVLIIK
Ga0208541_1000286Ga0208541_10002861F100542MRVDYAFAKGTLFEGLVATFRYAWTHQDGTLQNGHQLRAYLNYEVRF
Ga0208541_1001126Ga0208541_10011262F085771YAGALELSVARVPVALASAGPGAMQWSTEQEYIYALLIQQLNMGSLSPVEIDWASAQMRAWGRKLEFQAIPRSTEGFYVDLASKRGLVRRTGGEAGPTMHFLDTTPLADQLERAIHALRQADIGEPGAAAALSQQRIGVLEKVRPVVAPNLYGDLRRAPRTPVTMAAKVRIGLARICAELSPKAVVEPANDPDAGNEQIEVYAVADRPRNRPHVADEHDSLSASIAPVADPAWQIKDRSVAGLRISAAGGIGQSLVLGALVAVRQSDAIDWVLGAVRRLNKVSNDEVEAGVSIIADRIVPITVHAKRPTQDDLGMVVNGVDVSVMGTRFDALYLPPPSRPERPLAVKTLIVPTSEYADGRNVILTTGHSVYTIALRHLVEQRAEWSWAAFQIIDKKPTDI
Ga0208541_1001567Ga0208541_10015674F058543KVEFFQTIESLLGIVKSQCNDIEIRVKDDNSLMIEIIFDGKDQMERIFYNNEFTIIKGTVKSLCKDVIIKVNDSIVSHN
Ga0208541_1001686Ga0208541_10016862F032671MPAHAVPLTAEELTKLCAEADDAAHCGRLVEELQLQRLPNLAVRDRSALRVSLYPSGTTTFTDTEAIDGGRSYSLWDFMSEINAVVLYVTEGDDATFTLLQRTTGRKVELPSDPKLSPDRARLVTADFCASRCSNELALWRVTRDGVRKESTWRPRANWSDVVATWKDAETVVVEYSVAGTQARSRISRRLADAEWVRAQAP
Ga0208541_1001818Ga0208541_10018181F047968MGTEKVDRHKAKMDNMIKDEVTRMFEKVLDYAEVAVPNGEQYRKLRSKILRIGNNCIRNIQKDVEKHFDVRYKATSETIVEVIQR
Ga0208541_1003252Ga0208541_10032521F067873SPMALNLSLSPVDLNPASPPETRPAQVAAWLDQALTRHAIEAARVVGDALAATNAVAVGGTRRLELADKYWHTAEILWPRLELYFASATHPLRGEPLEAAKATLFLAQELFVAYKRVLEHEANKRVLFGGNRALGALVHRCMQCLWRILVNSYVAYAPVLPRTWLDAHRIYAFAHERDVHQRAIAGDDPAATPERVYVQALLLALANPYGFLQGQFDTVIRYVQEHSHWVTLTDVAPVHRMAKAVAVVPVGHDFPPFSASKGGTIEGSKFYLLTFDLAFQIQEQVHKLEAGGEFPAGIGRDPASRRRYLTLLKRLLRQWAIPPARQFNRLPSQARVVMCTELLGVWQYSRGRHSGVTVSTKAMPPLMHCQVINHTPAGYALRQMDAQPPPLRIGELLALRSEGRAGPQVAIVRWFRNTMRGTGLEFGCEVLSDHPEAAAAALETAPEGKRV
Ga0208541_1003782Ga0208541_10037822F020200MCWVCERLEHLITSWNEEQEFQEQTSSDDYHRGLSKGFSECVKALSEAVASMRLKGICEKFPEYERALNDKQRLDILEDLLKLRDEDTNQE
Ga0208541_1004342Ga0208541_10043421F045255MLWACLLLPSLPLDVFARAASPADAAKPFAVGSGGRTPR
Ga0208541_1004554Ga0208541_10045542F002104MKSKNVSSIAANQSEAQLLERLRQHPEMMERVQSILDIAYNTEGPLKSADQVEELLIQEMRRLGNTSMHQWATQAEQRVSRELKAQDGTVRSRKKKR
Ga0208541_1004687Ga0208541_10046872F081923MYRRSSIFLLIIAAALAAACTMANIGSVRTSPEVTRQFESLQIHPNYRYWYLNQENNPFGVIGLDREYEFDGGPVWRAVEPDSPTFKKVVGLVASFPMPSSMTTGYTIFEHQGRPIGVWYSSIGLGVTIDPATKTVSPATTTPWKSPF
Ga0208541_1004927Ga0208541_10049272F021303MKERPVSTDVLSLRANVLNHSSEFVELVYRDAPAEYRRLMTLERFRRELGQQTRFNHGKLYAYAEYVVFRNEFRERFPDASPAACINAFSSLFLKNDISITNLVEFVEGPDHRGQLLLKRRPEPG
Ga0208541_1007810Ga0208541_10078101F087857VPLLVIAFVAIQIVPPAHAEPITLTIMAIAGITTVMTAACTDMAVHGEHIVQANSPNEKPAEVFASERSADSSNNHDVQVTTAR
Ga0208541_1009404Ga0208541_10094043F051241PRQQYWDRLYQMLEEEAEKRGRTPPPAPLVYALDHEPTENDKIERLQEQVAWADRNQLLHRVQMFFDAMPASAWNHLER
Ga0208541_1011503Ga0208541_10115032F021565MAIKYYAHFLVEEPDPRGLQEYRGVVELDGQPRRTGRELREAAHIIARNMGRQLRDVKVLQWARLH
Ga0208541_1011731Ga0208541_10117312F056991MKTRLVIGIAMVCLTAGMWALPACGDESSADHQKNYYLKCIKAEIDNYSCKVAFTTSRSKNLQAYGESAARRAAFLSQNRDALVQEMFAQKVSMRPHAVQQYLGQRFTQENQVQLALERP
Ga0208541_1012228Ga0208541_10122281F007876MATGVNLSNLASALDGADFVLFDGVVFAKEYTRVPDERTVADDVVLEATHGDTEITFTRQEMEGAEHLGEGVYRLRSGAELRFLSTATIH
Ga0208541_1013728Ga0208541_10137281F085853MECRLRQYMEARAAQYQKILANEIAAPLEKLNIKEFDQWKAELQAGMKKYAERFRSEMTTNPSFWRNFNQKAPIYQSMIEGVHRFWSDHQFEEIGRRMEQAAAASQAEVEQLNQKKEQIQKGKEGLNNALKNIKTRFGKLGLEAEDAILLAPIAFAALFLFASLNLCQNIQLRKSFHRLFQARDPQKVAITDSEIALAMPLWVDPLAPPIQRRLKLAVMMIPAIASVLALAVVFYCWTIPDA
Ga0208541_1014622Ga0208541_10146222F105751PPGELEAGCLRRAWTRFQTRVSTLKEAFGLLIASVTSGAADLWKQMRLAKETLAGILGFLAQTRKVSLLGDYRCLRLPT
Ga0208541_1016388Ga0208541_10163881F073723LERLLLPLVRRFVALWVRPSILPDDLGGSFESGRPVVYVLEKRSVVDVA
Ga0208541_1016388Ga0208541_10163882F007982MRPVASWMLSAVVMALLVACTERAPQDKEEARAKGRDTDETVFDDMIQTQDRARAVEDLTLGRKAEMDAAIEQSEGDAATDEP
Ga0208541_1019009Ga0208541_10190091F068280MNNGSFASWIVDRPGPAVLVTGLLGLLPLLGLGFAFFRP
Ga0208541_1019364Ga0208541_10193641F046145VCLNFYWKLFEWITARYEKTISDELECDHMALIPKSFLKAKTDFFIMSRYLRVLSEK
Ga0208541_1019803Ga0208541_10198031F009010MPEVPKFLYLLVDNPLLIALPIVGFAALALWSRSNTAAVAAVAWNLYLIYELGMKAEEFCSGLDCMKRTPLYGVYPLLALVSLLALVQAYVHIRDDRRSERFR
Ga0208541_1020029Ga0208541_10200291F086748AGQDTDAARQIGNWFRDTGFPGFFRVGVPDAKILREAPGQIAGQPAWIAVAYLPNSSPLGLNVRNSYEVIRNDSWRGLAVVARGKRYYVLQTELRIEKLAPPDFRFDHEAADWNAFVPELDALYHRIEFLKP
Ga0208541_1023132Ga0208541_10231321F073721GEPGVALGFASDMLRIGGSTTPLADYTVGALISVRHAAGVNHWAFGIASEAWARPGARSLLVGVEAAVINEEPDNLYPKIASNAVIKNRSDGAPQVDVPMNANSIAYWVSAQPGTGFERGLAFDRHSLLAVGKRSAAIDLSDLPDEAIAQVDLIRIRKDVALRYDPSTRQLVLHVDPPAAAAP
Ga0208541_1024182Ga0208541_10241821F104669TLARKGGLWIVVGTATGTAVGVVFGVASVGLALGFAVGILGGCLARR
Ga0208541_1026611Ga0208541_10266112F036723WRPDRVHDQVRTIDFDDLPTHFDPYIKGMVRGRTVVRIAPDSHP
Ga0208541_1026749Ga0208541_10267491F028592QWCQPLRLTLEPSSASSFYIDLGGREGLKRRAAAPLEGKVLFLDTRPLHAVLMQNIVVLEQNLRMQPLSERAPKLTEQLALLTKVAAQADPEFRPFARRGERVAAAGIVDAIVGFNSIAGYLRDAERAPLRHAESDHGYGDTMELAVFGRLRNEEDRLAEQARRRLAAFSARGGPWQVKDVSQTGFRLIAST
Ga0208541_1028111Ga0208541_10281111F045785MLEPALTWIRSLKDPFRNANAAAQWIAALPASDALALQKEALELVAKFPGSRHVAGYAQAEALLRIDARFEPVLAQLAQQYATNYQKSTDVETRLWHAVFDLVKAFVAAYGAVLRAGYPRADQKRWHALLPWILVRLVHYKGIDGKFRLFRYGTWVPAQW
Ga0208541_1028115Ga0208541_10281152F021565MAIKYYAHFLVDEPDPRGLQEYRGVVELDAQPRRGGRELREAAHIIARNMGRQLRDVKVLQWARLH
Ga0208541_1028255Ga0208541_10282552F102756LTPPASPAPPLHRLHDEEVERLLASGEHRRELIALFGEAGYRELSGLARRAAAVRRRGVAVYVLPGLMGSRIGARGRLVDDV
Ga0208541_1029029Ga0208541_10290291F061020FAAQASAGAVTDLYRSGAYGLPWNATKDAIQAKYPGGKWAQNDKGQEQYCAASKQTLLKLPAPHQSRELCFVMGSDGTLASATAVMDASLPSLLAIVNRCRTTFGDFDAVVRDQQAIQSRSTAMLWTKDKQFVVRIVSENDTDGRPLMVSYTVADEPGMYTDGAAKVSNIPGSR
Ga0208541_1029225Ga0208541_10292251F056368MNSFRNRLLVLIIGLIAVTQTVTLVAVLESTRRSVEARAAEQLTA
Ga0208541_1029717Ga0208541_10297171F018950AALLGTPWTAVAAVSGSFLQLRVEYTATSLIGADARAMPGRLWRTRSALRHEGKRQGRSLTVIARLDRNLCWLVMADSRFTIETDLSAFDLPLDVLNGGGDMRQIREGRERANGLDTMRIRVERNAGSGSRFTGHVWATDQGVIARLSGEGESRGRRGRTLMNFRDVRIGPLEPGLFEAPRGVQ
Ga0208541_1031306Ga0208541_10313061F042409VAKLPFPIPPRPKLILMLCALIPLLFFSCGGGKAAQRNSSNEWLSSNIGIATLDDLIPTMGPPQQSIDTPEGIWHTWRKVNFGTVSGGVSMGFLGMGMTTPAETGEELNCLFDRNTGRLRNYNYREW
Ga0208541_1031400Ga0208541_10314001F048318MATVENVRLDITASTTKPGYSKIAYSYELHPSEMDCAWQREYTVCVDFWGEDLIDDDLLAWGKDEHTVKFDDSGPCEPKKVERVFEVETKILDEDLFGDDEVYLIVEASSGLGSDEAGEDPVVGRSNTVIGDF
Ga0208541_1031663Ga0208541_10316631F010406MTPLRTIVFLLLLANLTFLGYTRLDSAGGGEAARLAQQVQPDKIKLLTPQQVAALGPGKVAALA
Ga0208541_1032488Ga0208541_10324881F027335LEENMIVACEINHYPVKLEHLLRVTKDGPEILSEYPVDPELVPA
Ga0208541_1033764Ga0208541_10337641F103344TTPAIMPFRQRGSILGSILGILVCGVGGGFAAWASVTALGVGGVLGAILAAVIGMVVATALWTGGTTLLRALGWVR

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