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 3300026048

3300026048: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Sandmound_TuleB_D1 (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300026048 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)
Gs0111376 | Gp0116119 | Ga0208915
Sample NameNatural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Sandmound_TuleB_D1 (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size68332032
Sequencing Scaffolds42
Novel Protein Genes44
Associated Families43

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Alcaligenaceae1
All Organisms → cellular organisms → Bacteria5
Not Available21
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → Acetobacteraceae1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria5
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Beijerinckiaceae → Methylovirgula → Methylovirgula ligni1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → methanotrophic bacterial endosymbiont of Bathymodiolus sp.1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Hyphomicrobiales bacterium1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales1

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)38.000706Long. (o)-121.624306Alt. (m)N/ADepth (m)0
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F000708Metagenome / Metatranscriptome926Y
F003800Metagenome / Metatranscriptome468Y
F005254Metagenome / Metatranscriptome407Y
F006533Metagenome / Metatranscriptome371Y
F007471Metagenome / Metatranscriptome350Y
F009579Metagenome / Metatranscriptome316Y
F013688Metagenome / Metatranscriptome269Y
F014051Metagenome266Y
F017497Metagenome / Metatranscriptome240Y
F023130Metagenome / Metatranscriptome211Y
F024820Metagenome / Metatranscriptome204Y
F026036Metagenome / Metatranscriptome199Y
F027676Metagenome194Y
F027922Metagenome / Metatranscriptome193Y
F028596Metagenome191Y
F030609Metagenome / Metatranscriptome185Y
F031547Metagenome / Metatranscriptome182Y
F031548Metagenome / Metatranscriptome182Y
F033383Metagenome / Metatranscriptome177Y
F037023Metagenome / Metatranscriptome168Y
F038774Metagenome / Metatranscriptome165Y
F040402Metagenome / Metatranscriptome162Y
F040890Metagenome161Y
F041239Metagenome / Metatranscriptome160N
F042409Metagenome / Metatranscriptome158Y
F048394Metagenome / Metatranscriptome148Y
F050453Metagenome / Metatranscriptome145Y
F052015Metagenome / Metatranscriptome143Y
F054674Metagenome139N
F055973Metagenome / Metatranscriptome138Y
F060458Metagenome / Metatranscriptome133Y
F061197Metagenome / Metatranscriptome132Y
F070778Metagenome122Y
F087939Metagenome / Metatranscriptome110Y
F088485Metagenome109Y
F088953Metagenome / Metatranscriptome109N
F091213Metagenome / Metatranscriptome107Y
F092312Metagenome107N
F094058Metagenome / Metatranscriptome106N
F097602Metagenome / Metatranscriptome104Y
F097616Metagenome / Metatranscriptome104Y
F101428Metagenome102Y
F103981Metagenome101N

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0208915_1002244All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Alcaligenaceae1375Open in IMG/M
Ga0208915_1002820All Organisms → cellular organisms → Bacteria1279Open in IMG/M
Ga0208915_1007169Not Available906Open in IMG/M
Ga0208915_1007496Not Available890Open in IMG/M
Ga0208915_1008883Not Available834Open in IMG/M
Ga0208915_1009751All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium805Open in IMG/M
Ga0208915_1009950Not Available799Open in IMG/M
Ga0208915_1010273All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → Acetobacteraceae790Open in IMG/M
Ga0208915_1011417All Organisms → cellular organisms → Bacteria758Open in IMG/M
Ga0208915_1011965Not Available743Open in IMG/M
Ga0208915_1012411All Organisms → cellular organisms → Bacteria732Open in IMG/M
Ga0208915_1013909Not Available699Open in IMG/M
Ga0208915_1014004Not Available697Open in IMG/M
Ga0208915_1014544All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria687Open in IMG/M
Ga0208915_1014934Not Available680Open in IMG/M
Ga0208915_1015294All Organisms → cellular organisms → Bacteria674Open in IMG/M
Ga0208915_1015901All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Beijerinckiaceae → Methylovirgula → Methylovirgula ligni664Open in IMG/M
Ga0208915_1016251All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes658Open in IMG/M
Ga0208915_1016369Not Available656Open in IMG/M
Ga0208915_1016563Not Available653Open in IMG/M
Ga0208915_1016716All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria650Open in IMG/M
Ga0208915_1017313All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria642Open in IMG/M
Ga0208915_1018436All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → methanotrophic bacterial endosymbiont of Bathymodiolus sp.626Open in IMG/M
Ga0208915_1018954Not Available619Open in IMG/M
Ga0208915_1020305Not Available602Open in IMG/M
Ga0208915_1021755Not Available586Open in IMG/M
Ga0208915_1022409Not Available578Open in IMG/M
Ga0208915_1022431Not Available578Open in IMG/M
Ga0208915_1024048All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium562Open in IMG/M
Ga0208915_1024505Not Available557Open in IMG/M
Ga0208915_1024873Not Available554Open in IMG/M
Ga0208915_1025175All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes551Open in IMG/M
Ga0208915_1025226Not Available550Open in IMG/M
Ga0208915_1026132Not Available543Open in IMG/M
Ga0208915_1026503All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria540Open in IMG/M
Ga0208915_1026984All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Hyphomicrobiales bacterium536Open in IMG/M
Ga0208915_1027912Not Available528Open in IMG/M
Ga0208915_1028160All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria527Open in IMG/M
Ga0208915_1030954All Organisms → cellular organisms → Bacteria507Open in IMG/M
Ga0208915_1031326Not Available504Open in IMG/M
Ga0208915_1031476All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria503Open in IMG/M
Ga0208915_1031984All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales500Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0208915_1002244Ga0208915_10022441F028596LAMGVQVMDMSQAEFAAYVRADYEKWLKVAREGNIVVE
Ga0208915_1002820Ga0208915_10028202F017497VRQASPAALRLSVWAYAHLLWAYPASFRAEFGGEMALLFSDCCRDEWRSAGPAGVCRLLARAALDTLVSAPPLWAERLEETMKGHSADRRWGFWLADHGLAIGGLALLAVGAATSWWAMSLGWAALAIAFFAWVAETDGLAVPRPGRVAIRRGGFDIPLAFKVRRGERVLLFVCEEDPERGGWSDVYTVLDQPKGTDGSDGFEPLYCVPPATLPSGWSLRGRVPVDDLRFEHHERVVYVTRGSLERSLSAAGM
Ga0208915_1007169Ga0208915_10071691F042409TLIPLLFSSCGGGYAAQRKSYNEWLNSNIGIATLDDLISSMGPPQQSIETPEGIWYTWRKVSSGAVSGGVSMGFFGLGMTTPTDTGEELNCLFDRNTGRLRNYNYRDW
Ga0208915_1007496Ga0208915_10074961F033383ANLVWGDSLRRCSGGAVSHEIEYTVLSAGNGDRDGLEIKFVNIQKWMKKENSGLARTTLELAKYTERAGHSVCVKEPGDGKVLYGMARDPDLHTIHSQLNPDAFFDKKPKMMWMHGEPLSSVGNGVSMKAICDLAPKVDAFMCMRKDEYPIWSSIKRTYLVDKGIDLEFYFPIAGSEKLDGEPSVLYCENWRRERNPLYLCMAMEKVWQKLPRARLHLYNCTDQKMQQTFHALSKNNKWWAFLGSLKGPVDIKEINALYNRADIVVSCLFPLYARSIEAFGAGKAFIGPGYKEHDY
Ga0208915_1008883Ga0208915_10088831F050453NGTVDYGTFTTAPQQKRGALGGEQVWAIREVTAAWFTRGGVVARSMLGRMTVCLIALTGVVAPAEAQRPDSTRLRPTVVIVKISKDPASDYNGTYRASGMSTKCGLADYGYPHRLNSFAVMFPDDTATIAVTSVNFDADTLKSGTTVNSFYLSVGIRVGQHGTPPAYVVRANQPQFNEPGTATHTRTSNGSDSLTVKGAATKGTKVDVEMTLVCQP
Ga0208915_1009278Ga0208915_10092781F027676MSMDDRVAIRAKFERFPAAIKGAFLLRGADGLPHQVHVVQVRAAELAGGEPRPVGVETVVLDVSPTQETFVPFEISTIEMPSGWYCLECDVAVDGEARLVRPGDRFSMPWPRAAVRRGSVTIGAKVAGVSIETLECLGDSIRIAFAADALPRFSLDVDGRPHAVLEVEFDEVSGRGRVIAYPVLRADQRLSIDLGAGTAVEVVLP
Ga0208915_1009751Ga0208915_10097511F101428LILFLSISIFLATAIGSIGLYLWLEARKESLPQRFKEIVGEEAGAPRGGIAASAGEWLGKVRKRFAAKAPTEIELLEMLSGKELTGGRLLLNQAGIRSAGAHYAYLVV
Ga0208915_1009950Ga0208915_10099502F030609SNHLHRKSVLNINPFKERHRLIPACRNVFLLVSIGGLLLGLSVAPGCCKRCCGTGERSAQTDNTAGIERAGVPVTKEVPHSSETIPGIKDQEIMNPLPARGDTAIHSHKIPRTGNDNDMRTE
Ga0208915_1010273Ga0208915_10102731F000708MPGMTKPDPILARIAAQFTRHSVEKSGGAYLILDRPTANAIARLRPIPGTDRFELFYWSNLKGRWTTFGNLGRMRLMLETAHEIVEKDPMFHISRAR
Ga0208915_1011417Ga0208915_10114171F005254AHLYRNFTLVTDSAMVHVMLLSRTRRDGDFALTCWDCSRNPVEELQLQITPAPGEPAFAAPGGFLFINWEKSTSRTSAG
Ga0208915_1011965Ga0208915_10119652F048394MNDPLLISLLPPEQIGEAAKAPPDQVTYVIAVLLLAGILLSRWL
Ga0208915_1012411Ga0208915_10124112F054674VARLTLRGLARTLVVRLIGIVAFTGALGIGLSWLLEMAVSEPEWTETAAIAQRAVNRSGLPELLAGQNARSPKRWAEESARFVRELPGVVSIKVWDPQGTVVWAVQA
Ga0208915_1013909Ga0208915_10139092F023130MTRRFWVPATALFLSSIMAMIGSVSQDAMAGIVVLSQSTGAPIVREEVPAKIRSAGDSAPHPQRNVSARYWMRGIVLLLVILLVLWLIYRTFTGWKPMIS
Ga0208915_1014004Ga0208915_10140042F024820SPPKRPVPVRPLSIRYMGFECTSAGRAYRLRVEGPGDPREFTLTIPNVAFEDRKARFQDAPDLCFARLQRELATNAELADGAHLVITPAELDEYRDAQLRRSPDRKTRTLRTWP
Ga0208915_1014544Ga0208915_10145442F031548TLMIFFGAGVSLADDWKGDGGRRGYAYGHYKHGGYPHCQYCAPRPVYVERQYYPVVVERYVYHPPVVYQAPAPSGFSFGMSIADAGSAFSFGMAGR
Ga0208915_1014934Ga0208915_10149341F009579MSGVELALAFLAGVAMGIALDRVVLPMLVDAWIDRLRRHGR
Ga0208915_1014934Ga0208915_10149342F003800MGDERRDADLEHRRADVYSSARIGAAAALTLVLVVLLVLDVAVPDYDISPGILLPLLGAILALLGLEASALWRGVR
Ga0208915_1015294Ga0208915_10152942F097616MNGPLLISLLPPEKLLDSTGAVPVYDPFIAVLLLIGF
Ga0208915_1015901Ga0208915_10159012F103981CPNQVEGLAMSDVAGLNVQVLQDCDLVVTEPGTGEKVVYRKDGDSPVLVMMDSLRADPDAARVRFLVSAWKAAHAKAQQLGWLKS
Ga0208915_1016251Ga0208915_10162511F040890LFWFLVMVSFVAALLAGASWALAYSSVDTLLGAPPPQMGTQSTTFLWDGLPHAPGRPRVWRFAYSPTLIPGAPSVRIYVSTTGRVVQTEPANLPELLNAFRRRGY
Ga0208915_1016369Ga0208915_10163692F031547MRTYIVYRVDYLKSKTVKIGKVLDRREGERNNNPADMLRLAKIKYATSSIDSHIFILRESSN
Ga0208915_1016563Ga0208915_10165631F061197MDDTVLSTLLAEADDDVRSLVVIDKDPVTWLAIDAPGAEDEAMPSEAVTQMGGTVALARSTALLARFPNPAAAIGTWLTLAAWTGQDVCGAAVSGYCHRPELVSATLSQLPDLLSPAAPGELWIDFELTTAVDLNDDRFSVERIDRGSLVPASCKLTLR
Ga0208915_1016716Ga0208915_10167162F026036MKSDSKRETTLPPIAAGRLFLFFLPFAILFSVFAMPFPVNAGVPLTEMARLEASDAVTIDGTRSLFKGYMSLGLLAEAASLLERRVGLGVFPATAAAALFDEIVNAQGRYDDPERLVAVCETAIRSGIRTPLILYSYGTGLRRIR
Ga0208915_1017313Ga0208915_10173132F060458MTARQEVYKNCIGLVCRHSSIQMRLEAVVRKIASLQAFIAKSCSDAAVATAACRKKSGPQCVFEIIQKAEKGVDPLFIKRVTGFKEQKIANILHRLFKYGEIRIEPGGLYVAVAGR
Ga0208915_1018436Ga0208915_10184361F097602VIILPSEGPSALGRCNCDTLSPKRNSNVDVMNRGSADEAVVIVKFGADEFMVTWRRVKHRISNRTLEVKGGTCKRPWPLIIDRRTEISLTGAVDYSRRKQ
Ga0208915_1018954Ga0208915_10189541F038774MQKYLLAAVFVVALAGPAFAEEFYVAFDPASHKCSMMHSQPASPMKSMGKFGTKAEAEKAMASMKECTAG
Ga0208915_1020305Ga0208915_10203051F027922VSAAVQEKKKKKAPFTFLEQFAQRLDRALQGHNDRDAQVIYAAKPLLQYITLRLHDYLDPRTAEPLSGEDGALLWDPAELKVPDWLYTERGETIAAERRARLAAVLPKAREAAVGFPGERCSECGLPLLSTIRTGDPSYCAVCKGNVLWEWSWMREQVEVAFSSALRSVGPHP
Ga0208915_1021755Ga0208915_10217551F088953MDTSTQAQKRQRATTFPSARGAAPTCGLLEVQWDSPFDRLCFLVSAPDLALKNSRRYTTLLAELIAGSGCTEDEILAHGHKVRAYLFFAQDRLSKDGQLDGLTGKEKRTYRLPAVAPAF
Ga0208915_1022409Ga0208915_10224092F031547MKTYSVYRVEYLKNKTVKIGKVLDRRQRERNNNAADMLRLAQSKYANSSIDSHIFILRESPLQNLPFGGV
Ga0208915_1022431Ga0208915_10224312F041239MPEPGLGLSALWEERDYKACGVSRECRGRFILGKLFDRDTRKLQGAWLAAFGTRVLGPPEIRTSEITKSQWQLILSHMGASPDEIADVQARMSRAGR
Ga0208915_1024048Ga0208915_10240482F094058MQILLNVIFYAFLAFLMYDATVVEHDPWFAFVVGFVIVVAIVCQLMPSMHANKVSPGEFPYDTIGD
Ga0208915_1024505Ga0208915_10245051F037023EVRRVGEYQTVAEAVAVAQNAIEQFLRGEFKRGMDATKLFSLYEERGEHMFIFQDEAKTFNVAGFDHTEYARTRAAEICGGVK
Ga0208915_1024873Ga0208915_10248731F091213VRTNGQMLICNDVGAYREGFGIEGVCLSTPREKLRSGAGQNELAVDQVLANFVAELFVILHPATLPMLERMFEDVKQDAETDGERELKRRAEIGIAAARI
Ga0208915_1025175Ga0208915_10251751F055973MATATPPVNKNAVYPRDEIAKLLAPPEQEHPGTKLRRILHEARDKRSFVHTAGAYDAFTAAIMTRLGFKALYGSGWQLAAVKN
Ga0208915_1025226Ga0208915_10252261F092312MPTFSGKEREMLGRGGWKTALGILVTGAMLLGCFAPVIIYGVYKVYDLGKQQVIALRIMEEPENVYKTSIAVAEERGVKITTRKDKELFLSAVTKSGPEADVKVSSLPKGGSLLTITVDKGKDPKAERQEIVNAVLSVCSKFGTQCTEEKEK
Ga0208915_1026132Ga0208915_10261321F013688HDMSRGKRFGIGALLLAAVCSGVAQAADSPEPTSRPIPDLHLSISEAPGEVSVRLPVPADRHLLYGLLSPYVSLGSSTTLAAPWASALPPGLRRETDGLEDVRLGAGMAMPLSQRTQLYGEYRFLRGRLDAGVGRSPLQREPDTADFRAGFSIRLD
Ga0208915_1026503Ga0208915_10265031F040402MAKNITWVNLAFAAAVAVLISACSMANLGWLRNSEEVGRTFETLHVPPDYRYWYLYLENSPYAVLGLDREYRIEDISWTGVEPGSEVFRKVVGLVESFPVPGSRTYGAYILNSKGERIGVWYSSMSAGITVDPDTKVVSITTGTPWMHGDGN
Ga0208915_1026984Ga0208915_10269841F006533LPGEVQVNIARRVDSYIKIARAAKEETIVATVASTAMEDQAKAIGQGGDTMDPRWAAPAIAEAWCYATISLSKGYLDRLHAEAIIAAIETFTTSRLKGVM
Ga0208915_1027912Ga0208915_10279121F070778MALGACGYAGSDEIEAESATLLARVPVGTSFNDVPAAMEALGFSCTAARRQFPDAKGEVRETEPHLVCERESGDWLICTRRTRAILIQLNGQLSDVLVNVGRFCSKSPITAADGRR
Ga0208915_1028160Ga0208915_10281601F052015MPRHDVTEIYMIKKSAEGFIVSFRRGTDHGVRPGMQLAVVNEDGFRVGVVEVLASTETDSEALVSGESGIKLGCLVSIPQPMRPG
Ga0208915_1030954Ga0208915_10309541F088485VVELTGQGATGAAEARGSRVADAIDVALADLRHAWEHGLARALGQDD
Ga0208915_1031326Ga0208915_10313262F014051IEAVAALMKKIGSIKPDKEPVTYDKFVDKTVWKDANAMVK
Ga0208915_1031476Ga0208915_10314761F007471VDHQKVDDALWAEVRAQFSEAEVIELVAHTTLYIGFGRFNEIVGIEPG
Ga0208915_1031984Ga0208915_10319841F087939TLTHVGLAEDIAKSPLPTGKGFVESLDRPGLGIEVDEDRVRRHRVQIAAQSVA

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