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 3300025943

3300025943: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_CattailNLA_D2 (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300025943 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)
Gs0111376 | Gp0101367 | Ga0210125
Sample NameWetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_CattailNLA_D2 (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size146313507
Sequencing Scaffolds41
Novel Protein Genes44
Associated Families40

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
Not Available16
All Organisms → cellular organisms → Archaea → Euryarchaeota → Methanomada group → Methanobacteria → Methanobacteriales → Methanobacteriaceae → Methanobacterium1
All Organisms → cellular organisms → Bacteria3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium1
All Organisms → cellular organisms → Archaea1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Nevskiales → Steroidobacteraceae → Steroidobacter → Steroidobacter denitrificans1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Patescibacteria group → Microgenomates group → Candidatus Woesebacteria → Candidatus Woesebacteria bacterium1
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria5
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin0381
All Organisms → cellular organisms → Bacteria → PVC group → Lentisphaerae → unclassified Lentisphaerota → Lentisphaerae bacterium RIFOXYA12_FULL_48_111
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon RBG_13_46_16b1

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 → Aquatic → Marine → 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)Unclassified
Earth Microbiome Project Ontology (EMPO)Free-living → Saline → Water (saline)

Location Information
LocationUSA: San Francisco Bay, California
CoordinatesLat. (o)38.209923Long. (o)-122.033409Alt. (m)N/ADepth (m)N/A
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F000233Metagenome / Metatranscriptome1512Y
F002467Metagenome / Metatranscriptome557Y
F004287Metagenome / Metatranscriptome445Y
F004454Metagenome / Metatranscriptome437Y
F016394Metagenome247Y
F017852Metagenome / Metatranscriptome238Y
F019578Metagenome229Y
F021446Metagenome / Metatranscriptome219Y
F022119Metagenome / Metatranscriptome216Y
F022216Metagenome / Metatranscriptome215Y
F025793Metagenome / Metatranscriptome200Y
F029006Metagenome189Y
F029140Metagenome / Metatranscriptome189Y
F031548Metagenome / Metatranscriptome182Y
F031716Metagenome182Y
F032323Metagenome180Y
F033941Metagenome176Y
F034974Metagenome / Metatranscriptome173Y
F037907Metagenome / Metatranscriptome167Y
F040767Metagenome / Metatranscriptome161Y
F041845Metagenome159Y
F046145Metagenome151Y
F047153Metagenome150Y
F049737Metagenome / Metatranscriptome146Y
F049781Metagenome / Metatranscriptome146Y
F051787Metagenome / Metatranscriptome143Y
F052017Metagenome / Metatranscriptome143N
F053661Metagenome141Y
F058543Metagenome135N
F061018Metagenome / Metatranscriptome132Y
F061952Metagenome131Y
F066901Metagenome126Y
F069625Metagenome123Y
F073725Metagenome / Metatranscriptome120N
F076055Metagenome / Metatranscriptome118Y
F088148Metagenome / Metatranscriptome109Y
F098776Metagenome / Metatranscriptome103Y
F099498Metagenome103Y
F102455Metagenome / Metatranscriptome101Y
F105454Metagenome100N

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0210125_1000915Not Available3603Open in IMG/M
Ga0210125_1004217All Organisms → cellular organisms → Archaea → Euryarchaeota → Methanomada group → Methanobacteria → Methanobacteriales → Methanobacteriaceae → Methanobacterium1910Open in IMG/M
Ga0210125_1004385Not Available1880Open in IMG/M
Ga0210125_1005552All Organisms → cellular organisms → Bacteria1703Open in IMG/M
Ga0210125_1006235All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium1625Open in IMG/M
Ga0210125_1006287All Organisms → cellular organisms → Archaea1620Open in IMG/M
Ga0210125_1008661All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales1411Open in IMG/M
Ga0210125_1009481All Organisms → cellular organisms → Bacteria1356Open in IMG/M
Ga0210125_1011646All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium1240Open in IMG/M
Ga0210125_1012179All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Nevskiales → Steroidobacteraceae → Steroidobacter → Steroidobacter denitrificans1215Open in IMG/M
Ga0210125_1012279All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Patescibacteria group → Microgenomates group → Candidatus Woesebacteria → Candidatus Woesebacteria bacterium1210Open in IMG/M
Ga0210125_1017803Not Available1024Open in IMG/M
Ga0210125_1018985All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota995Open in IMG/M
Ga0210125_1021108Not Available950Open in IMG/M
Ga0210125_1021340Not Available945Open in IMG/M
Ga0210125_1025798All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria870Open in IMG/M
Ga0210125_1028392All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia834Open in IMG/M
Ga0210125_1029880All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium816Open in IMG/M
Ga0210125_1030429Not Available810Open in IMG/M
Ga0210125_1033879All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium773Open in IMG/M
Ga0210125_1037809Not Available737Open in IMG/M
Ga0210125_1038655All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria730Open in IMG/M
Ga0210125_1040395Not Available716Open in IMG/M
Ga0210125_1044963All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038684Open in IMG/M
Ga0210125_1046008All Organisms → cellular organisms → Bacteria → PVC group → Lentisphaerae → unclassified Lentisphaerota → Lentisphaerae bacterium RIFOXYA12_FULL_48_11677Open in IMG/M
Ga0210125_1049351All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria657Open in IMG/M
Ga0210125_1050258All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon RBG_13_46_16b652Open in IMG/M
Ga0210125_1051256All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium647Open in IMG/M
Ga0210125_1052881Not Available639Open in IMG/M
Ga0210125_1058107All Organisms → cellular organisms → Bacteria614Open in IMG/M
Ga0210125_1062507All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria596Open in IMG/M
Ga0210125_1066000Not Available583Open in IMG/M
Ga0210125_1066611All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria581Open in IMG/M
Ga0210125_1067231Not Available578Open in IMG/M
Ga0210125_1067671Not Available577Open in IMG/M
Ga0210125_1081672Not Available533Open in IMG/M
Ga0210125_1082305All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria531Open in IMG/M
Ga0210125_1089005Not Available513Open in IMG/M
Ga0210125_1090186All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria510Open in IMG/M
Ga0210125_1091253Not Available508Open in IMG/M
Ga0210125_1092836Not Available504Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0210125_1000915Ga0210125_10009154F066901MNHPWEAQVAWQICKLISELDVLLWDLFWDEFEAIYNEEAEKYWNSNIHTNTYTPHT
Ga0210125_1004217Ga0210125_10042173F053661VVDMKDYYQTNKGRLLGIGGILIVVGLVLYFARSHNTFVLVLPIVGVVLFIAGVIYKPRKKIENVTSDAQ
Ga0210125_1004385Ga0210125_10043852F102455LANELNYRLALTLNTLVQLTSDSATGVDSSVNIPLANGSYLTANNVRSAAQSLVSVNARPLYTDGFFGGVIHPNVVKDVLNDTSWNGLTDILKRGDNGREMLLAPVSNEDAITFAGVKFKQTSTAPTVTIGGNTYYNTYIYGDDALFAIFLGRNPETNERNYKLLVQEAPQQGSVSDPARQIGGWVAYNVYVKLGVV
Ga0210125_1004704Ga0210125_10047043F105454MAVAAVWFGRGPTVRTMSDSKDPTGPQLPIDAGANPEVERRRAKFGTASEGWEAYNTWLDRVRAQPGPVSRQAVIAKALYSVSSYKTWAGKARGAFDKPK
Ga0210125_1005552Ga0210125_10055522F076055MRMKRITVDVDDLALAAAGEQLGTTGLGETVNAALRDAARRRTLAKFDVLTDIDGTPEEIAAGRELS
Ga0210125_1006235Ga0210125_10062351F040767MIRVNFTTFERNPDTKQWVELPVAQLLADGDEVSISGPHADWINPDLAIVDPETAERVTRADGAERWARLQPFGYRSGDLRVKVAEVAAAEPVAASFRYSTAA
Ga0210125_1006287Ga0210125_10062872F022119MKCPACGQILKRIEGVCGEYTCINPECLENKKAHVQAHAEFYGLTQADINANYRIALAKK
Ga0210125_1008661Ga0210125_10086611F073725MEKRATRRYRISTSIVCSYLNSVDFGKPVNGRMRNCCVNGLCAELGAHYKAGTVLVVRTTGSSCGYSDEEGFRSLAVAEVKWSRPRSIEGGACYATGLKYLML
Ga0210125_1009481Ga0210125_10094812F066901MKHPCDAQVAWQICKLISELDVLLWDLYWDEFEAIYEREETEKYWGSTIHTDQDESHT
Ga0210125_1011646Ga0210125_10116461F037907GRLWPQIAALGLFAVVLLPLSFVVFAWALRRTKINGTLTHF
Ga0210125_1012179Ga0210125_10121792F022216VSNTRANGPTEQQRRRIRRGALALALLAIGIYVAFIASGVLGWRG
Ga0210125_1012279Ga0210125_10122792F046145VSLNFYWKLFEWITARYEKTFPDWLECDHTALKPKPFSEAKISFFITSRYLRVLSEKI
Ga0210125_1017803Ga0210125_10178031F004454QGCEGLAVDENRRKIIEVRADLHQQIRKLALLNDLKIYVLANAVIEEALNDKERIAALIKKLKV
Ga0210125_1018985Ga0210125_10189851F022119MKCPACGQILERIEGVCGEYTCINPECLENKKAHVQAHAEFYGLTQADINAN
Ga0210125_1021108Ga0210125_10211081F052017MKRGCLTKDDVERFEGELGKLIVVKKALELALINPAIKDDQKQMYGVALTQCERTLREFRGALIAMKV
Ga0210125_1021340Ga0210125_10213401F021446MKTLSIALMAAFMLVLAATSTGQAQSAEDCYNDPNPGGKYVYRGCNLAEVIFIRGDKLSKINELTLIIEVQGGQNSHTTRLTFPILAKRQEGDKLILDYQWPLGGDTYEATIIGDTLTNRKTKGYLAGIREEVFTRE
Ga0210125_1025798Ga0210125_10257981F019578MEKRPNGSWRVKKKGEAVGVIAANSSVVAVLPRKKAGEDTRLKEAYLLAAAPLLFDACSKINSILESSLIVTPEGIKINCTDIKKSLSDALLRAMGYRKSPEEP
Ga0210125_1028392Ga0210125_10283921F069625VNRLAQFLQHSTKVFGLKGLLRSVREGRVEPRVPLLPLALCLVLGVVTRIGSYLDLAQQTKDRRRWRHLCGLKAPVQHEIFGYVTERMDPEDWRQNQARVAKQLKRNKRLESAKIKGLLFVSIDANEHFASFSRTCPCC
Ga0210125_1029880Ga0210125_10298803F046145WKLFEWITARYEKTISDELECDHMALIPKSFLKAKTDFFIMSRYLRVLSEKI
Ga0210125_1030429Ga0210125_10304291F049781NTGTIGFALAKDTNGNYPNNDEFYGNDCEAASTSFGQICFNIVNAQSTVIGPNNRCENVYNCFQFPSDGSAVGIHLLDPYISISSNTSVKPNEPASAMVAIDNNGHNWLPSMHFGMNDLAGPNLLGNAGFEGWQNSTTLDYWGGVSGTNINQAGSGIYQQQSSASAPTDSTTQGSYSVAIGDNVTAGLGIDSGCIQVDSTLNYTLAFRIAAASTSVNFRPGFRFYSDANCTEADRITSVATNARVLTPANYAGVSTLAGTGANWQSTNA
Ga0210125_1033879Ga0210125_10338791F031716MSRFTPGPWHVEEEKGSYGVFSNDALLAITLSDDLPDKGAAKANANLMATAPRLLEIIKDIKEHLDNNMIVTGEGLKINDSHLRESIIDAIMRAEGYRL
Ga0210125_1036349Ga0210125_10363492F000233KIRKSKFQADLAPSEDSMVRALKTELQMTSNTDFLSDALALFRWAVSERKRGHVIVSESSTGERNILVFPRLERVAPEVALPHVDIQWNDTELESLAQLASGQAAEPTKALIRAMRH
Ga0210125_1037809Ga0210125_10378091F041845MPLELSVLEKLEIAHRLVAEALGQTPQLYDCRLDQALLVLELSIKRAHRSPHMRLRLHRDHREEQFLF
Ga0210125_1038655Ga0210125_10386551F033941YPRCAVKTIEESGNVGTVAKIAIRLQIYCLLREWHARQFNRLPSRARVVMCAGLSGAWQYSRGTHAGVAAAPAGLPAMSKCQVINHTPAGYALRQADTSPPALRIGELIALRVEGRGGVQVAMVRWFRNTWKGSGLEFGCEIVSDAPEAGVAAAEDAPAGALAPVVVVPEDPVPGAGHESLPPQLIVPADTFQLEQALTLKRAGSESFVVLTKLAEKGPGFEIYEYVPVG
Ga0210125_1040395Ga0210125_10403951F004287AAPAGRTDTAATVSIASISDQDWYVSRTHGVYHIPACPKAGPGESSQPYALLLITSRGDALDLGDNRRFPFTISAREIAEDLLQDLHDHGAFVCAGARPTADEIAAATARRETYYHRLIAEGDTLWARGHSFREISDMHRRAAIALGVEREWAYVPMRTGECPACGEKIKLGVAVCKHCHAILDAEKAAKHGLVASSSGASERQDSTESTTDNKRESREQRR
Ga0210125_1044963Ga0210125_10449631F061952MKKTSPWFILLFPIAIPAMIVLDYFGYRIIALMILVALVLSFAYCMYSLFTKFRSLRGAFATLAQALCDPGSSSVRHYPYHHTLSGSVAGRRFHFSLLGHDERALCQLFLEYPVGRDFLMEAGDDAAQNARDLPQDVGAIHRLPGFRSLRALSRRVPFFSRFLSGLAGSGGPGLVLRKQGDDPLSPPVLKRDLEMLLRLAESLGEVPPSGRKDR
Ga0210125_1046008Ga0210125_10460082F088148ADAAHTTKANCRQLTQNNGAEFLLFLKANQPLALAKAEQLLPGKLPPSGQHAG
Ga0210125_1049351Ga0210125_10493512F046145MLQVCLNFYWKLFEWITNRYEKTIQNLLECDHMALKPKPFSEAKTGFFIMSRYLRVLSEK
Ga0210125_1050258Ga0210125_10502581F017852PAKLGGLEKKHCVKRVGAWTVIPEHLLVWVYEAPSSEALQNFSLEPEMVKWMAWNTSEIKLAMSLEESIHLLNKPNMNRTLET
Ga0210125_1051256Ga0210125_10512561F061018MNGYSLGKGSDFCVANKKAPKDEWAKIIDKVEAAILMSLANKVLADAVDRQDQIDEHRRQLKLVELKDFSRRNSAG
Ga0210125_1052881Ga0210125_10528811F047153VGNSAFIYDTEHSRWASLLVGLNYGQVVTWSGHKWRPNFEVDYDFRDTRGNQQWVIRAGIVLLLPR
Ga0210125_1058107Ga0210125_10581071F034974DKRQGELGNFVDQLFETAVFLSPLFDLGNQIHRDVSGVGFGFELPGQIVTQVLFASGTPAVGIAASATNGDEAGGQDRALGLELFLTSLEEAADQGGVFGCFHMFTRVTCQAGTTE
Ga0210125_1062507Ga0210125_10625071F098776MSATYFDFTTPKFFLFRNQSKRLSIPQCHILILFWCALVILYDVT
Ga0210125_1066000Ga0210125_10660001F032323MSHLELRLKNEVSLKSRLLRSLLSENPSYSVKEYREEPDPTDNNYQIISFTAYEKGPYCPIWNTLSEFIKNNEVEHLNDSSADRSS
Ga0210125_1066611Ga0210125_10666111F099498IIQNQNVEVYARIMPLMVKTLKLCDAVESSWRGQATIELEPQQKQLPPPADDDDPDPIEACCSWLYDNHIQWQDMQDLMKARYLEYVIGRFKTKTEAAKWLGVGSTYLCKLSKTTLHAVSQN
Ga0210125_1067231Ga0210125_10672311F049737MIEQAALKKEISSAKSNLEMDLDEVIRSLEEAAQEIEKVDWEHGGLADDDR
Ga0210125_1067671Ga0210125_10676713F016394YLAKKVRNSHPNVESFPIATIYTTIKEQEKTKLNLPDFKQLIYHLTGWDISFQVIRRQLEINQIVCRAHTSIG
Ga0210125_1081672Ga0210125_10816722F025793MSEITDKTDELFMAASRSDDDLGYPADVAFVPSDEEWTDDVLWRNLIEGQATVLVGEDTELLLVPLRRGMIDRLRGRVPVSVAPRTHGHASSYATLSRLGRHPVRQMRALAHA
Ga0210125_1082305Ga0210125_10823051F002467DDGRAAAERPFFGLYIPAHGENRQSAQRSLVGPDDKFSPGAMIELDTGSARYLVRFTQMLERQAGWSWALFSAVRKLSG
Ga0210125_1087604Ga0210125_10876041F051787QQVAERLESARKSFQDKELKNEYVFKEIREKVTKIWPQASQEIIPGVPNIDLISSDEALLSLIRDGLKFRDKPTTKSAGASVAALTSRRGSSTNNRSGDDNIEKLRAQAKAGDKKAAENLLIARLQSIRGSRGR
Ga0210125_1089005Ga0210125_10890051F029006MNKLIMALMAIYFIGDPGLQYLAWLGELKVYAVAAAVALVSMPWIASQLDG
Ga0210125_1090186Ga0210125_10901861F031548MKTNIMKIFAIAALMIFVGAGVSMAGGWKEYGGKRGNAYGHYKGRQYNHYEYCTPRPVYVEHHYRPVVVERRVYHPPVVYQAPAPSGYFLGMSVVEQGMAFSFGMSGH
Ga0210125_1091253Ga0210125_10912531F058543METVTISASISEKKKVEFFQTIESLLGIVKSQCNDIEIRVKDDNSLMIEIIFDGKAQMERIFYNNEFTIIKGTVKSLCKDVIIKVNDSIVSHN
Ga0210125_1092836Ga0210125_10928361F029140MKDASKEILRFWKTQWEAYMKSMMAMQEQGETMLDMIQKSGVLQEGSLNMVRDWAKKYKSIQKSYLDAVEEHFEKLDDIIGGTP

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