3300000317: Wetland microbial communities from Twitchell Island in the Sacramento Delta, sample from surface sediment Feb2011 Site L2 Tule

Overview

Basic Information

• IMG/M Taxon OID: 3300000317
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0063443 | Gp0053968 | Ga0026147
• Sample Name: Wetland microbial communities from Twitchell Island in the Sacramento Delta, sample from surface sediment Feb2011 Site L2 Tule
• Sequencing Status: Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: Y
• Use Policy: Open

Dataset Contents

• Total Genome Size: 111737537
• Sequencing Scaffolds: 28
• Novel Protein Genes: 28
• Associated Families: 26

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula boonei	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylocystaceae → Methylocystis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylocystaceae → Methylocystis → Methylocystis heyeri	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	2
Not Available	9
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	1
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → methanotrophic bacterial endosymbiont of Bathymodiolus sp.	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Wetland Microbial Communities From Twitchell Island In The Sacramento Delta
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Marine → Wetlands → Sediment → Wetland → Wetland Microbial Communities From Twitchell Island In The Sacramento Delta

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): marine biome → saline wetland → sediment
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Sediment (saline)

Location Information

• Location: Twitchell Island in the Sacramento/San Joaquin Delta, CA
• Coordinates
  • Lat. (^o): 38.106796
  • Long. (^o): -121.646457
  • Alt. (m): N/A
  • Depth (m): .1

Associated Families

Family	Category	Number of Sequences	3D Structure?
F003605	Metagenome / Metatranscriptome	477	Y
F014882	Metagenome / Metatranscriptome	259	Y
F018557	Metagenome / Metatranscriptome	234	Y
F031889	Metagenome / Metatranscriptome	181	Y
F032246	Metagenome / Metatranscriptome	180	Y
F032706	Metagenome / Metatranscriptome	179	Y
F034230	Metagenome / Metatranscriptome	175	Y
F044612	Metagenome	154	Y
F049730	Metagenome / Metatranscriptome	146	Y
F051235	Metagenome / Metatranscriptome	144	Y
F056936	Metagenome / Metatranscriptome	137	Y
F057346	Metagenome / Metatranscriptome	136	Y
F061187	Metagenome / Metatranscriptome	132	Y
F061489	Metagenome	131	N
F063536	Metagenome / Metatranscriptome	129	Y
F063812	Metagenome	129	N
F065246	Metagenome / Metatranscriptome	128	Y
F067458	Metagenome	125	Y
F069724	Metagenome / Metatranscriptome	123	Y
F073724	Metagenome	120	Y
F080549	Metagenome / Metatranscriptome	115	Y
F086465	Metagenome / Metatranscriptome	110	N
F088780	Metagenome	109	Y
F093113	Metagenome / Metatranscriptome	106	N
F093371	Metagenome	106	Y
F097602	Metagenome / Metatranscriptome	104	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
WSSedL2TaDRAFT_1000081	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula boonei	8229
WSSedL2TaDRAFT_1000326	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes	3888
WSSedL2TaDRAFT_1000759	All Organisms → cellular organisms → Bacteria	2800
WSSedL2TaDRAFT_1000824	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylocystaceae → Methylocystis	2708
WSSedL2TaDRAFT_1004614	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylocystaceae → Methylocystis → Methylocystis heyeri	1351
WSSedL2TaDRAFT_1004621	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1350
WSSedL2TaDRAFT_1008771	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1009
WSSedL2TaDRAFT_1011817	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	879
WSSedL2TaDRAFT_1013685	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	821
WSSedL2TaDRAFT_1015468	Not Available	778
WSSedL2TaDRAFT_1020219	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	692
WSSedL2TaDRAFT_1020516	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	687
WSSedL2TaDRAFT_1020859	Not Available	682
WSSedL2TaDRAFT_1022239	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	665
WSSedL2TaDRAFT_1023059	Not Available	655
WSSedL2TaDRAFT_1023575	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	649
WSSedL2TaDRAFT_1025755	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae	626
WSSedL2TaDRAFT_1028400	Not Available	602
WSSedL2TaDRAFT_1031134	Not Available	579
WSSedL2TaDRAFT_1033058	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae	565
WSSedL2TaDRAFT_1038070	Not Available	533
WSSedL2TaDRAFT_1039812	Not Available	524
WSSedL2TaDRAFT_1039959	All Organisms → cellular organisms → Bacteria	523
WSSedL2TaDRAFT_1040076	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → methanotrophic bacterial endosymbiont of Bathymodiolus sp.	522
WSSedL2TaDRAFT_1041123	Not Available	517
WSSedL2TaDRAFT_1041564	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	515
WSSedL2TaDRAFT_1042659	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	509
WSSedL2TaDRAFT_1043855	Not Available	504

Sequences

Scaffold ID	Protein ID	Family	Sequence
WSSedL2TaDRAFT_1000081	WSSedL2TaDRAFT_10000812	F067458	MKRLVFAGLIFLVLLQGIWFAAADDSPDYAKIVVVHLTINKSSITEKSVEMRYGHPPNIEARNGDFKGTLKTADGSTIREFNLWDPRYQLGDVLEKNNESSGYLSGYLTYSDNADLVLILPYYENQMTFELYDKKTGTLLKKVNMSQAITKFQSNYPKDPGSISVSPIQFDKSVLYVITGVVISILIIGMILSMVRKK*
WSSedL2TaDRAFT_1000326	WSSedL2TaDRAFT_10003263	F003605	MAIGDAAQAAGFPLVPDTGEEGRVRYGAREINRTRDEVAGVLSSIPASKAAYRTAAGISAGTGDPSGGSDGDIYFKLLS*
WSSedL2TaDRAFT_1000759	WSSedL2TaDRAFT_10007591	F061489	MVNIGLMIAGILGVIVGIVLIAPSGALGTALGAMFL
WSSedL2TaDRAFT_1000824	WSSedL2TaDRAFT_10008242	F086465	MNNRKIVEFPMRTDPPRRIWCGILQVLFPVIYGHRIAQPQRDSAGSEPLETRLEIATEFSFSPEWRGAGRSIFCQPISKLADGDDHVLIVRHHWTRALMEEHQAGRSTIDCIEAQRVPWNPGSEVVFVDATEQADFAEFAELEAEELSDEYFTLEKYQVDPGPRENSIFFMGVDYDEDDHCSILPVEASVGRDRVLKRTTFFDPGALDAGLFKIKRIK*
WSSedL2TaDRAFT_1004614	WSSedL2TaDRAFT_10046143	F086465	VGRFGGIAAMINRKIIEFPVRTDPPRRIWCGILQVLFPVIYGHRIAQPQRDSVGSEPFENPPEIVTEFSFSPEWRGAGRSIFCQPISKLADGDDRVLIVRHHWTRALMEEHQVGRLTIDCIEAQKVPWNPGSEVVFVDAIEQAEFAEFMELDAEELSDEYFTLEKYQVDPALRENRLFFMGVDYDEDDHCSILPVEASVGRDRVLKRTTFFDPGALDVGLFRVKRIK*
WSSedL2TaDRAFT_1004621	WSSedL2TaDRAFT_10046212	F014882	MRRASGLTDEELAEIRRRRPGVRASLACEGMHLTAEEEALFEQMDAERLTPDERAARITAYSRERRRLKARASA*
WSSedL2TaDRAFT_1008771	WSSedL2TaDRAFT_10087711	F069724	MALLSFRGIDTPSLQAQGEQRLPPIFNIQRDIPRA
WSSedL2TaDRAFT_1011817	WSSedL2TaDRAFT_10118172	F051235	VVAIYARRLSRQILGLITILLRGPLLALLTLCRFFKFNCIFTVYPGSQKDIDGYLPHGFKWVKHLASGKPFVAGVITTGNGLGRGLILAVPNTVDQFKTDRKLVGDIMKRLKNTKTLTGAKTIAVAGQGPRFFKSHFPYEQPFVYGLKGRVFSVVETVERVSEKHGMAKDANTVAILGVGEIGEAI
WSSedL2TaDRAFT_1013685	WSSedL2TaDRAFT_10136851	F057346	LYRLRVATKRPTGNWTPEGKAESAALRRDYLELTPAQRMEQVFELSRFMSRVAEAGRRQRSG*
WSSedL2TaDRAFT_1015468	WSSedL2TaDRAFT_10154681	F073724	LVGDLELRMFDAMILKREMGKSCNVDVKILETMKDGLILRITENIINNNSLALITDFVNKHKLNILFDNGVYFISNQIIAPSEPAFVSE*
WSSedL2TaDRAFT_1020219	WSSedL2TaDRAFT_10202192	F056936	NIYQLAAILGLSVLAGFAFRSKMALKYRTKIQELEREILNNYEHILELERETLNMESRMQDIKSPVITMKAPGKEVEVPSKKVPDISLRKQLLSKKNIEQQSASGL*
WSSedL2TaDRAFT_1020516	WSSedL2TaDRAFT_10205161	F061187	TTFVSRGRLNGVLRQRPSGGGPAEGSATQPGREQNSVDELDTQTFEALYYRARLILGEPLPRPGRFQNRGH*
WSSedL2TaDRAFT_1020859	WSSedL2TaDRAFT_10208591	F093371	MTKFNRERRWTVACVLVIALSAFALAGCFAAVGNHMNWQPVDMARVLASDAGDQKWNTYRFQTVGPFATQRIAYVMFNDDITMDMWYTPYVNLGKMSVREVLQNHDAYLQQCMWIGTALVFEEYQRDGKLIGYKANEFQMEVDLW
WSSedL2TaDRAFT_1022239	WSSedL2TaDRAFT_10222392	F034230	EAGPENDKLKVKVGPFFIQESEKKINLEGTASHVVRKGKRINVTVTVENYGKEKSEPVRLKYVETGKKAGEPRFYRIQAIEPGKKWERTFMARFDESGRKSVTATLLTLENQPLADEKGKSRPDTSHTGSVNLTVKEM*
WSSedL2TaDRAFT_1023059	WSSedL2TaDRAFT_10230591	F093113	MIEVHKVPIVAPEFQSVGPQPNFKGSYLSNQKLFCSTEQTGTGSAQNIAHGLGKTPAKVFVSCTDNSGSSGTFTVAEGSHTATNVVVTVTAGAKYKVLAWL*
WSSedL2TaDRAFT_1023575	WSSedL2TaDRAFT_10235751	F018557	MTELKNGRPIFFPENLVLFGNLALFLWIVLDSVAFMLYNFTTGIVFFILTLILIYGVLHLLGCLRPCYNCIKCTHGMGRLAALYFGRRIFKDYKYNYKLPTAIFFTLYIGGFPAAFALYSTIVDFSAIKAAVFVALLVFTTYG
WSSedL2TaDRAFT_1025755	WSSedL2TaDRAFT_10257551	F032706	IGQTRARVAEVMVTEPIPGRIFVPAGGVATRVRKVPERIVNYEKRGPVGIITARVQNIGEAYDEIDALLDRIEQDKEVQVVAIYTLNGLFASLPIRCGNASTA*
WSSedL2TaDRAFT_1028400	WSSedL2TaDRAFT_10284002	F080549	SRIPLNVQPVGHYGINGRLWLLRIRFSGVFTGFTFFAYIYMNLKFLPVAQKSKSKVAKAEAPRPEAIKSTDKNVPVKRKLSSRISVAKIFHEKEIPMAQIDKTNVDHHMAKKYLTKYLDRVPTEADIDKATIIKKSDSISYLKYGGKFLGTMTKTIYQTAEQKKAGKGIGVKMEFKPK*
WSSedL2TaDRAFT_1031134	WSSedL2TaDRAFT_10311341	F031889	ARVRLPTNDEMLGRLAQQKSIRRSIGRRKSQTEYVPNPKADLALFNQLRLDKDGPEFDEFEASNALSKLTYCEVTDCERVGDEYRITLKTPFGDTIHMMRIPTQRDVTLYRRTVVSATDLPHGQEELRYRTEPAIDLYNSVVTKAEGYADGLKIEDVPPHHKSAVVVELVQTIDDLDPQIDPNS*
WSSedL2TaDRAFT_1033058	WSSedL2TaDRAFT_10330582	F032706	MKAPKKTASIFQWVADSAATCLGPTRARVAEVRVSDPIPGRVCVPAAGHAARARQEVSRLVLYERKGDIGFITAKVNNVGEVYDEIDALLDEIERDKNIRTVAIFTLDGLFAALPIR*
WSSedL2TaDRAFT_1038070	WSSedL2TaDRAFT_10380702	F088780	LNALKKIERGLTALALAPLSGLEKKERNRRIEERLKRSEQKYRHN*
WSSedL2TaDRAFT_1039812	WSSedL2TaDRAFT_10398121	F032246	MDKVTIEVDSRWVTIARSPLCWVVAALQGPSVTFAPLFLYWSGKGKMFPDYEWLIVPLCFATILLVGLFYMILGAKFIGELRKRPISA*
WSSedL2TaDRAFT_1039959	WSSedL2TaDRAFT_10399592	F044612	LNAINLMPRGFRLLVIHIHASSSGQPSLCPIHDRHHHLQIAQEFGARPGRSLLLLLPLCFEKQLGIIQNALAD
WSSedL2TaDRAFT_1040076	WSSedL2TaDRAFT_10400761	F097602	GLGRCNCDTLSPKRSSNVDVMNRGSTDEAVVIVKFGADEFMVTWRRVKHRISDRMLEVKGGTRKRLWPLIKDRRTEISLIGAVDYSRRKQ*
WSSedL2TaDRAFT_1041123	WSSedL2TaDRAFT_10411231	F063812	STIIFYVVPMSSKHHDSKKHDDAKSVHACHLCKERFVFPEHPTPSGICHKCQTKIGVVLLIIFIVLAGMVFVGLL*
WSSedL2TaDRAFT_1041564	WSSedL2TaDRAFT_10415641	F049730	PAEIMQSRRELRGKRKPSMLILGSFEKLKQDLIPALFRIATDHEIGDIDIIPSSEAVDLKRLMGYTLIFVAFEIYRDNESFFRMLPESIQDRVTILSRPAEFPSVAPEIRCACFCTELKALLPREEAQLFDHHTAPAKPR*
WSSedL2TaDRAFT_1042659	WSSedL2TaDRAFT_10426591	F063536	KLRRAGVWDEFLGGAGMMEGILYGRTQGAAVNPGQTVTVTRQQINTGIKFLPKAYATWYPLDDWEMDDGSGTGGVINSGPSKIVDEYQLYMEAMVMTMNTMQEMDSFRHGQSSAATISDNRIKTINGLDEALNNGIDPSVYGNIYTNYGGQARNGNIGTALNSTPLYLG
WSSedL2TaDRAFT_1043855	WSSedL2TaDRAFT_10438551	F065246	TPVVQESSGRGGGHQGCNSDIHVPRNANVRILAQSGVWSDVDIDEDGNADGQVRTSDLTSNLATMPPWGPSS*