Sample 3300026016

3300026016: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Browns_TuleA_D1 (SPAdes)

Overview

Basic Information
IMG/M Taxon OID	3300026016 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116067 \| Ga0208779
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Browns_TuleA_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	74687304
Sequencing Scaffolds	39
Novel Protein Genes	41
Associated Families	40

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes	2
All Organisms → cellular organisms → Bacteria	8
All Organisms → cellular organisms → Bacteria → Acidobacteria	3
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → Gemmatimonadaceae → unclassified Gemmatimonadaceae → Gemmatimonadaceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1
Not Available	8
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	7
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Candidatus Nitrosotenuis → unclassified Candidatus Nitrosotenuis → Candidatus Nitrosotenuis sp.	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium lablabi	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
Name	Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration
Type	Environmental
Taxonomy	Environmental → 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 biome → wetland area → soil
Earth Microbiome Project Ontology (EMPO)	Free-living → Saline → Water (saline)

Location Information
Location	USA: Browns Island, San Francisco Bay, California
Coordinates	Lat. (^o)	38.04565	Long. (^o)	-121.866287	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Associated Families

Family	Category	Number of Sequences	3D Structure?
F001341	Metagenome / Metatranscriptome	719	Y
F001654	Metagenome / Metatranscriptome	656	Y
F001984	Metagenome / Metatranscriptome	608	Y
F005534	Metagenome / Metatranscriptome	397	Y
F008142	Metagenome / Metatranscriptome	338	Y
F008920	Metagenome	326	Y
F011445	Metagenome / Metatranscriptome	291	Y
F011956	Metagenome / Metatranscriptome	285	N
F013910	Metagenome / Metatranscriptome	267	Y
F014765	Metagenome	260	Y
F015265	Metagenome / Metatranscriptome	256	Y
F018339	Metagenome / Metatranscriptome	235	Y
F018765	Metagenome / Metatranscriptome	233	Y
F018992	Metagenome / Metatranscriptome	232	Y
F019019	Metagenome / Metatranscriptome	232	Y
F019326	Metagenome / Metatranscriptome	230	Y
F020028	Metagenome / Metatranscriptome	226	Y
F026115	Metagenome / Metatranscriptome	199	Y
F031556	Metagenome / Metatranscriptome	182	Y
F032230	Metagenome	180	Y
F034493	Metagenome	174	Y
F036876	Metagenome / Metatranscriptome	169	Y
F041224	Metagenome / Metatranscriptome	160	Y
F044528	Metagenome	154	N
F045819	Metagenome	152	Y
F054961	Metagenome / Metatranscriptome	139	Y
F058268	Metagenome	135	Y
F061025	Metagenome	132	Y
F062080	Metagenome / Metatranscriptome	131	N
F068261	Metagenome / Metatranscriptome	125	Y
F074939	Metagenome	119	N
F078463	Metagenome / Metatranscriptome	116	Y
F082716	Metagenome	113	Y
F085321	Metagenome	111	Y
F086262	Metagenome	111	N
F089147	Metagenome / Metatranscriptome	109	Y
F101108	Metagenome / Metatranscriptome	102	Y
F102738	Metagenome / Metatranscriptome	101	Y
F103989	Metagenome	101	N
F104092	Metagenome	101	Y

Associated Scaffolds

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208779_1000132	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	8317	Open in IMG/M
Ga0208779_1001697	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes	1862	Open in IMG/M
Ga0208779_1001886	All Organisms → cellular organisms → Bacteria	1777	Open in IMG/M
Ga0208779_1001911	All Organisms → cellular organisms → Bacteria	1767	Open in IMG/M
Ga0208779_1003872	All Organisms → cellular organisms → Bacteria	1274	Open in IMG/M
Ga0208779_1004374	All Organisms → cellular organisms → Bacteria → Acidobacteria	1198	Open in IMG/M
Ga0208779_1005294	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → Gemmatimonadaceae → unclassified Gemmatimonadaceae → Gemmatimonadaceae bacterium	1090	Open in IMG/M
Ga0208779_1005911	All Organisms → cellular organisms → Bacteria	1033	Open in IMG/M
Ga0208779_1006602	All Organisms → cellular organisms → Bacteria	983	Open in IMG/M
Ga0208779_1007128	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	951	Open in IMG/M
Ga0208779_1007157	Not Available	949	Open in IMG/M
Ga0208779_1007472	Not Available	930	Open in IMG/M
Ga0208779_1007603	Not Available	923	Open in IMG/M
Ga0208779_1007813	All Organisms → cellular organisms → Bacteria	912	Open in IMG/M
Ga0208779_1008087	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	899	Open in IMG/M
Ga0208779_1008937	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	861	Open in IMG/M
Ga0208779_1008970	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Candidatus Nitrosotenuis → unclassified Candidatus Nitrosotenuis → Candidatus Nitrosotenuis sp.	860	Open in IMG/M
Ga0208779_1009617	All Organisms → cellular organisms → Bacteria → Acidobacteria	833	Open in IMG/M
Ga0208779_1010321	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	808	Open in IMG/M
Ga0208779_1010650	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium lablabi	798	Open in IMG/M
Ga0208779_1010858	All Organisms → cellular organisms → Bacteria	791	Open in IMG/M
Ga0208779_1012137	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	754	Open in IMG/M
Ga0208779_1012186	All Organisms → cellular organisms → Bacteria → Acidobacteria	753	Open in IMG/M
Ga0208779_1012537	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	744	Open in IMG/M
Ga0208779_1013460	All Organisms → cellular organisms → Bacteria	723	Open in IMG/M
Ga0208779_1014217	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	707	Open in IMG/M
Ga0208779_1014955	Not Available	693	Open in IMG/M
Ga0208779_1015208	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	689	Open in IMG/M
Ga0208779_1017189	Not Available	655	Open in IMG/M
Ga0208779_1017482	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	651	Open in IMG/M
Ga0208779_1018211	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Thaumarchaeota incertae sedis → Candidatus Nitrosotenuis → unclassified Candidatus Nitrosotenuis → Candidatus Nitrosotenuis sp.	641	Open in IMG/M
Ga0208779_1019413	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes	625	Open in IMG/M
Ga0208779_1024234	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	571	Open in IMG/M
Ga0208779_1026745	Not Available	550	Open in IMG/M
Ga0208779_1026815	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	549	Open in IMG/M
Ga0208779_1027061	Not Available	547	Open in IMG/M
Ga0208779_1028127	Not Available	539	Open in IMG/M
Ga0208779_1028714	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	534	Open in IMG/M
Ga0208779_1029934	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	526	Open in IMG/M

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208779_1000132	Ga0208779_100013210	F018992	MAPVMQKFDMNAEETCRFAAELSEEYGARGALSFAGRAVASFEADGLPERAAMWRALHAILGDIALRRLDPDAPLVIH
Ga0208779_1001697	Ga0208779_10016972	F036876	DPSSTWEAGTWTYRAYNPQRKLWEMQGINTNNGAWQAGLMWSDGADRLLTEWYGPMLVRFRYFAIQQDHFLWRADATFDRGKSWIRDYWTMEVHRISR
Ga0208779_1001886	Ga0208779_10018862	F089147	LSGIHARRDKSPSIAYSEELIFTISATLQSTDRRHGIVEQERCHFQLDS
Ga0208779_1001911	Ga0208779_10019112	F085321	MKIFGIVFASLGAGMVLFALVYLNGLLFGLVNSMVTLMAGPLVDRILARRKQ
Ga0208779_1003872	Ga0208779_10038722	F104092	MSELQVAEDGRYLSGEIPFGYALWGDRLVEVPAELDACVTAIRLVKQGKPYPEIAAALRQEHGVTLSQQRFDSLMESVYRRYGPI
Ga0208779_1004374	Ga0208779_10043742	F054961	MRRPLHALIAGLTVCLTVAGDASPQAPEHRFAPGSPPIAVRPSALAQIVSELAGSPVNVQRARILWVIDPHAMVIESDSAFDPTWRDRGRVLVVLERRRSLAIPRPPVSIAPVNIIGIARTLLGIQAAHDVPWPQALTRREIERLGVRAAILASSIKTSDGVELTSSTAAPSTAAPSTTTTAP
Ga0208779_1005294	Ga0208779_10052942	F068261	DLRRELNALLELAEREDPFQDRAGSRQLSDRIVIVAAELGEWTLAMDWVERAYLRRPGRLRRVLTDLPYDRGGLAVDPRYARLLRTAGLEDRL
Ga0208779_1005911	Ga0208779_10059111	F018765	RALTGSARGPGCRSPGPLVRSGGMTRMRDGSDGPGPSTSEMARDIVVALVQSGKIHLDPDPKKQGEWLGDLFKALHQKIVVEGALEMLIEDQLKNFDLDDLRQLRELLDAEIAARS
Ga0208779_1006602	Ga0208779_10066022	F001341	MAPKPEGLDPTIRTREISFEADVQSVTPFLKLATVSHNGTAHKTFACDEGPSLGGLGSAPTPLMYFSAALAF
Ga0208779_1007128	Ga0208779_10071282	F001984	MNGVRALPKFAAAVALSLQLAGCAIFTETYGIQEVDNWAARNEPLARSGKMKWSEFYGQYLERVSAAPVISQGPVVETLGIMVTASLFYERGRLGKADFESVQRIVRTYQSIDDAAANVLARDALVKALARAP
Ga0208779_1007157	Ga0208779_10071572	F082716	MISKKDIKIMPFTFIIAPILLVSLTLIVFDAYTDIIQEKEFIASLSCQELKVYTDKQTIDSKLYFGNENYLIYAEERLNTLC
Ga0208779_1007472	Ga0208779_10074722	F019326	MLLSHTRRDGDFALDCWDCSKNPIDELQLQVLPGAGEPKFDAPGGFLFVNWEKSGSR
Ga0208779_1007603	Ga0208779_10076032	F041224	MSGRVLAGGIAAVAAILTLIQLLWMFGMFSPADALGGRNGALYASALAAWFFITLAPLAAAAIILLMTRGDTRPHA
Ga0208779_1007813	Ga0208779_10078132	F001654	MAILRRGQAKQIKKDSKVRRETLDDIGSEIVQERSEPSYRNPNRDQARGDWDRSGRRTDEGRSRDPEKDGDDGLGPASTR
Ga0208779_1008087	Ga0208779_10080871	F005534	PFMGYQRKMSVLRSDSTGGTVPGSFNRSLLRLRTFREYLDDGWALIGTADEVREGLQKYLDATGYQHVLLLMALPGLDTSLALRSMRLFAEQVAPAMAPANGRVATGP
Ga0208779_1008937	Ga0208779_10089372	F044528	MNTVIKLLLAAAIINATARVGMAAARYYQLKDESQELVTFGGNVVPGELQNQIRLKAEELRLPLAFDDILVTRQGVRTTASAVYTDSVELFPSFQYPIRFQFKVEGVNMGAGVSPGANPLRNK
Ga0208779_1008970	Ga0208779_10089701	F086262	MQSSLEAQCQLCGQKINIGDEIVRVASGIWIHDYCKEKSPDEKNNQDNLQQLNQSLLEAKADRLKSLKCIYCGNGTIMKSKLETVPLDDGTIITKKLYPCYTCGHIMEFIENITP
Ga0208779_1009617	Ga0208779_10096171	F013910	MGIERREKGRRAEVVRAVVDHVVHKAEMSVTLEGLQDFLHIPRDAAGRIVSSLVNAGVVREVRAGLWQRIPDLPSTS
Ga0208779_1010321	Ga0208779_10103213	F020028	MGIWDDASTHGIEHELTLRLERASDLSKRAKRANDAVRHEIDRALEIADELRGVSQESEARAGRLRGPQHDR
Ga0208779_1010650	Ga0208779_10106501	F014765	MVACSTVKNTPAQDEAWSRWTACRSQVPGAEIRNVQLDGRISFWANGAFQGRSMLDCLARAGTNGPALPQATYATWPSGR
Ga0208779_1010858	Ga0208779_10108582	F011956	FALAGRHIMTPSVVTLQEVLRHHRTLSRRGREFYESLLAHGDVLAVRLDYLPGAMMWLVTTPGQARLMRKAREGRTTSDVCVMSLSEAQELFTTLGDPMPTGLYEVAAWLLAPAPEDFSTPAGEDSVDLEEPEDPASS
Ga0208779_1012137	Ga0208779_10121372	F034493	SRAGGPPRFRPRLFSDLSYADRAVTHRIHNNGTGLYRAIGVINETQGGDESVTEEAAGFTGKSEMSNRWFRIHRVVLEPGQKTPAHQHKSPVVVLQDSAGKGIASGAMSFEFNEPGQWGFYDSGARHEVTNSGNERLELIEVEIRRK
Ga0208779_1012186	Ga0208779_10121861	F019019	MRFLIAPLALIAVLCLGPLAMPALALAQGQPVQGKIDVDIDTHSGGGGAWWTNPIWIAIGAIALVLLILIIVMAARGSGTTVIKE
Ga0208779_1012537	Ga0208779_10125372	F061025	VSAMRMDWIVKAIGPFELTEYLGLGLIYLALAITAPFAAPRRPVPSAA
Ga0208779_1013460	Ga0208779_10134601	F045819	LQVRSLADSVRARATLFRDPALPRSLVVSGSPQAKRLDGLTHGDSPAEPQRVAMVFAIAGEELVTLTIRSWPRDDVDREVEQILDSFNIIAT
Ga0208779_1014217	Ga0208779_10142171	F058268	YDVSIYSHAAARLPHTESPVLLQVELLHKGGIAGGAPAAHADGVTKSVLEYVDQFSTRIHNAGK
Ga0208779_1014955	Ga0208779_10149552	F018339	MEMTFNLPDGTRAGILPTRHLRNLTIRELGAECFVPAEKVSVVFHVANRQALDRVRERFGLGR
Ga0208779_1015208	Ga0208779_10152081	F101108	ASVVVGPCKPGETPGTKKACSEESAVHIAVCVRVPESAKVKEVLLYVRSEDSEQSWADARVQAGQDSGQARFADKFIERPDSDSTKQVCQGFVNWSRDKSRLARILVRYTL
Ga0208779_1017189	Ga0208779_10171892	F015265	IQITKKPVLMEKNAIDNLNNVGLPVFLNPINDIMPIASPTKNPTKFSIFSRRNSNDV
Ga0208779_1017482	Ga0208779_10174821	F011445	ELDYKISQLQRKAKDMTPRSVVRRVMPERTLDYALGGVLTLVGAKLAWGRYRAHRNRRERLRASLDTSHSW
Ga0208779_1018211	Ga0208779_10182112	F103989	LSVRESQKNQEYEKEINATDIFMRDLRRSYPEFAKALEEFMKTELERLEEEN
Ga0208779_1019413	Ga0208779_10194132	F036876	SAPADYDFLIGTWRFTFQARLRDGSFTPPFTGHWVFTRKQTGGEGVLIEDHWRPDDASSTWDAGTWTYRAYNPERKLWEMQGINTHLGAWQPGLMWSAGDDRLLAEWYGPMLVRFRYFAIEPDKFLWRADATFDRGKTWIRDYWTMEVHRISR
Ga0208779_1020400	Ga0208779_10204001	F074939	EGRRITRQQRDMAEAAANLLDAWVRSVLGRQQQPDRRTTSRTFEEVLDRFAGQAIERGSAVSIVVFLMADAASYPGLTQQWIARIRGVMRAVDIVGMLGEGEVALLLHDTPFDRAEAVAKRIVKMLETIGDHHPSPVVATGVASRLPSSGGGAGLAAEARNAAMFRATASRIDKEPPRS
Ga0208779_1024234	Ga0208779_10242341	F078463	MNLSDPVVAALIIASGTVLTALVQLRISWRKELRERERGQPITKKTRRGPVLFIFALFIAAGVGGFALSQYFVSL
Ga0208779_1025389	Ga0208779_10253891	F102738	VTIDVASDAMPGNRTIVAVNTNGRTAPRPITVYAHVPAISTPKIVSAAVNQPDVQFQFAMTETPNEIGTTPYVWFFLGCGGEPESGVVKGKFANGVVTAAIPNPRTQLKPFAPPPNNRCDLELRASDSKMADSNTLKTTVDFK
Ga0208779_1026745	Ga0208779_10267452	F062080	LVYAAVNGGVSYFETSQLVDQAVFEAGRRPRAAAVVGQAPVSTLQEFAVDTREAILVAARRSNAPVDASKLTVAPDGAGIRVSLHWSYVVLEIAGETVLAVPLWLDRTFELKP
Ga0208779_1026815	Ga0208779_10268152	F008142	MVQALLSLSGTNDRGTIPMKRYVLTLAWILWAHETAQVGEQIIDRGYTAIDSFETRQLCHVAMTDYAALKLVRQGRIRVEFSCLPEQANPKAPRSAVG
Ga0208779_1027061	Ga0208779_10270611	F008920	AHAQPERGTARLDHAGVQGLLATLGYQPRAARNESGAEYEIILRPSGGLAVTTRVTLSKDGTLIWLVAWLKKVPPDRTISGNAILSMLAENDAIGPTHFSYNESRRWFFLNKPVPNQGLTAERLQAELQQLGATVARTEALWDFDRWK
Ga0208779_1028127	Ga0208779_10281271	F026115	MSDVNTFIETIGKDVNATVVPKVGTLAETVSKQTFTEYGPRISVFANQLVKDIIDEQSETVRDFVTGIVEELFHRYKPELTGEL
Ga0208779_1028714	Ga0208779_10287141	F031556	VRDSSMTVNYETRYSLPHTCPAEATKCEGGTLADRGKGRELRHAFVGGVMAVAVALVVSSAVIAQAPPQARQVKSPWVYYPLDTISGNGGPAPKRDLSGTWAGPGSTDAIPRGAAAERPSLTPLGQQVLSQRKPIGRYGPAGTNDPTARFCDPLGFPLNFIYQNRAMSVSTMPNRVVF
Ga0208779_1029934	Ga0208779_10299342	F032230	SHDKHRVAMKRLTFDELVNQNRVLVGSAEEMRDKVAYVRERLYLTDLAGNFALGGLSDAQVRASMRRFMDHVAPNVG

Bioinformatics & Integrated Biology Lab
Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026016: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Browns_TuleA_D1 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences