3300000894: Wetland microbial communities from Twitchell Island in the Sacramento Delta, sample from surface sediment Feb2011 Site L1 Bulk

Overview

Basic Information

• IMG/M Taxon OID: 3300000894
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0063443 | Gp0053965 | Ga0026047
• Sample Name: Wetland microbial communities from Twitchell Island in the Sacramento Delta, sample from surface sediment Feb2011 Site L1 Bulk
• Sequencing Status: Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: Y
• Use Policy: Open

Dataset Contents

• Total Genome Size: 70007605
• Sequencing Scaffolds: 38
• Novel Protein Genes: 38
• Associated Families: 36

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	16
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → Syntrophus → Syntrophus aciditrophicus	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Dehalococcoidia → unclassified Dehalococcoidia → Dehalococcoidia bacterium	1
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Archaea → Candidatus Thermoplasmatota → Thermoplasmata → unclassified Thermoplasmata → Thermoplasmata archaeon	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula formicica	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	4
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia	2
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales → unclassified Bacteroidales → Bacteroidales bacterium	1
All Organisms → cellular organisms → Archaea	1
All Organisms → cellular organisms → Archaea → Candidatus Thermoplasmatota → Thermoplasmata	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Bacillales → Paenibacillaceae → Saccharibacillus → Saccharibacillus sacchari	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): 0 to .12

Associated Families

Family	Category	Number of Sequences	3D Structure?
F014730	Metagenome / Metatranscriptome	260	Y
F016394	Metagenome	247	Y
F017269	Metagenome	241	Y
F018557	Metagenome / Metatranscriptome	234	Y
F020727	Metagenome / Metatranscriptome	222	Y
F025314	Metagenome	202	Y
F032323	Metagenome	180	Y
F033858	Metagenome / Metatranscriptome	176	N
F035352	Metagenome / Metatranscriptome	172	Y
F036300	Metagenome	170	Y
F036769	Metagenome / Metatranscriptome	169	Y
F042655	Metagenome	158	Y
F042955	Metagenome / Metatranscriptome	157	Y
F047754	Metagenome / Metatranscriptome	149	Y
F054975	Metagenome / Metatranscriptome	139	N
F055830	Metagenome / Metatranscriptome	138	Y
F058719	Metagenome	134	Y
F060094	Metagenome	133	Y
F060461	Metagenome	133	Y
F061489	Metagenome	131	N
F063812	Metagenome	129	N
F067458	Metagenome	125	Y
F067886	Metagenome	125	Y
F071750	Metagenome	122	Y
F071802	Metagenome / Metatranscriptome	122	N
F072483	Metagenome	121	Y
F081505	Metagenome	114	Y
F084418	Metagenome	112	Y
F085861	Metagenome / Metatranscriptome	111	Y
F088780	Metagenome	109	Y
F092121	Metagenome / Metatranscriptome	107	N
F093371	Metagenome	106	Y
F094060	Metagenome	106	Y
F098776	Metagenome / Metatranscriptome	103	Y
F099351	Metagenome / Metatranscriptome	103	N
F101440	Metagenome	102	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
WSSedL1B2DRAFT_1000015	Not Available	41564
WSSedL1B2DRAFT_1000507	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → Syntrophus → Syntrophus aciditrophicus	4879
WSSedL1B2DRAFT_1000519	All Organisms → cellular organisms → Bacteria → Proteobacteria	4837
WSSedL1B2DRAFT_1000900	All Organisms → cellular organisms → Bacteria	3579
WSSedL1B2DRAFT_1000953	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Dehalococcoidia → unclassified Dehalococcoidia → Dehalococcoidia bacterium	3467
WSSedL1B2DRAFT_1001175	All Organisms → cellular organisms → Bacteria	3061
WSSedL1B2DRAFT_1001885	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	2255
WSSedL1B2DRAFT_1002523	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1878
WSSedL1B2DRAFT_1002618	All Organisms → cellular organisms → Archaea → Candidatus Thermoplasmatota → Thermoplasmata → unclassified Thermoplasmata → Thermoplasmata archaeon	1834
WSSedL1B2DRAFT_1002734	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula formicica	1784
WSSedL1B2DRAFT_1003142	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	1628
WSSedL1B2DRAFT_1003991	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	1403
WSSedL1B2DRAFT_1004123	Not Available	1376
WSSedL1B2DRAFT_1004194	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia	1362
WSSedL1B2DRAFT_1005176	Not Available	1209
WSSedL1B2DRAFT_1005277	All Organisms → cellular organisms → Bacteria	1195
WSSedL1B2DRAFT_1006753	Not Available	1033
WSSedL1B2DRAFT_1007578	Not Available	968
WSSedL1B2DRAFT_1009516	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia	846
WSSedL1B2DRAFT_1010203	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales → unclassified Bacteroidales → Bacteroidales bacterium	816
WSSedL1B2DRAFT_1010359	Not Available	810
WSSedL1B2DRAFT_1010638	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	799
WSSedL1B2DRAFT_1010700	All Organisms → cellular organisms → Archaea	797
WSSedL1B2DRAFT_1011505	Not Available	767
WSSedL1B2DRAFT_1012537	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	732
WSSedL1B2DRAFT_1013368	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	708
WSSedL1B2DRAFT_1014137	Not Available	687
WSSedL1B2DRAFT_1014346	All Organisms → cellular organisms → Archaea → Candidatus Thermoplasmatota → Thermoplasmata	682
WSSedL1B2DRAFT_1014374	Not Available	682
WSSedL1B2DRAFT_1015327	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	661
WSSedL1B2DRAFT_1017618	Not Available	616
WSSedL1B2DRAFT_1017875	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Bacillales → Paenibacillaceae → Saccharibacillus → Saccharibacillus sacchari	612
WSSedL1B2DRAFT_1018355	Not Available	605
WSSedL1B2DRAFT_1019148	Not Available	592
WSSedL1B2DRAFT_1021229	Not Available	564
WSSedL1B2DRAFT_1025222	Not Available	521
WSSedL1B2DRAFT_1025242	Not Available	521
WSSedL1B2DRAFT_1025427	Not Available	519

Sequences

Scaffold ID	Protein ID	Family	Sequence
WSSedL1B2DRAFT_1000015	WSSedL1B2DRAFT_100001521	F081505	MKPKTILTYGLSLLFLLGLLYIFSQVFQDVSAPITSSESXSQALWGTWGATIXIVSFVLFAGGAGILVLLGGGWRWE*
WSSedL1B2DRAFT_1000507	WSSedL1B2DRAFT_10005074	F033858	VEKIESLRKIRLSATMLEVGFKSENLSEMIQCQIELEELAARLQAEQGDLVTPQQCEAAKKSLDAFVALVDQAIEKAALNQGITPGSPKPKPTTLE*
WSSedL1B2DRAFT_1000519	WSSedL1B2DRAFT_10005194	F085861	MSIRQGASKNIGTMCCGPWTHQRNPARKMKVGTLLVTIGLIWLGARLGLLDFSWLQAVHFWPAVFILLGVWMVYRGFRQGKPSTIDNKTKEV*
WSSedL1B2DRAFT_1000900	WSSedL1B2DRAFT_10009004	F084418	MIITVISLTIFMTSMIVYSICRIPSRAYANVCHKSLIFDNLAEARRLEDLLADGDTESVHRILKELQQRGDIDIFESENEIYVSGRRGVSIDQRRTITRDLLVSDYDPVEDFRNLSVMSRFNTDAQTMNANEGVCVIKYEAVSATNHEESKDDLFVSEYDIIELLESLNIRSGCNLTVQTPS*
WSSedL1B2DRAFT_1000953	WSSedL1B2DRAFT_10009533	F072483	MKGYVSVHRIADGQILANIRKFRIYARLNGFISEGIFNNGQSALDATFALMASLNPPRIDYILDMRFSDPWPSDILKLWKKKALGIFSKYPQVYAVGVTGEDSPFWSQIYDIKVLFQKHGDRILGIFETPEKAEAFLDKLRNFELP*
WSSedL1B2DRAFT_1001175	WSSedL1B2DRAFT_10011752	F101440	MGSFMSTLAEISGXPFILCLILGAAKHFAMSFSEREWSTHLPDFIELMVMWAVYVWLSNLFSSRIFHIDESDAINLLAIFLVCLSVALFRGKDDQAFYP*
WSSedL1B2DRAFT_1001885	WSSedL1B2DRAFT_10018852	F014730	MVFKREIGTTCSLDIEMLDTINDGIVLSIDKNLVNSNNLSFITDFVGQHNLSLLLDSERYFISSKALAPYAKSSWESW*
WSSedL1B2DRAFT_1002523	WSSedL1B2DRAFT_10025232	F092121	MPKHFYTLLIIPHKKKDSVKKFLATPIHFRVVTAVSVVLFCFFGYCAVDYLTIKLEQMELANLRQLTSTQQEQIDTLQEKISFFDRKLADLKQVDEKIRNMASDLTGKSRKPSRKEEAKSREQVLGIGGPMPADEA
WSSedL1B2DRAFT_1002618	WSSedL1B2DRAFT_10026181	F071802	MGVKASKPNYASVITKILIVLVILNIAGDVLAAAFFLWDPSLGELSVYGGLIASFAGQNGAVMITSAILLGYAVVYAVCVFGLLGKLKWAPPLVIAVSVVNRALAFGVIFEPNFAWLFWSACKLVIIALAFYLWRKT*
WSSedL1B2DRAFT_1002734	WSSedL1B2DRAFT_10027341	F067458	MKRFVFAGIIFLVLLQGIWSAAADDSPDYSKIVVVHLNIDKSTITEKSVEMRYGHPPNIEGRSGDFKGTLKSADGSTIREFNLWDPRYQLGDVLEKDNESPGYLSGYLTYSDNADLVLILPYYENQMTFELSDKKTGIVLKKVNMSQAITKFQSNYPKDPGSISVSPIQFDKSVI
WSSedL1B2DRAFT_1003142	WSSedL1B2DRAFT_10031422	F099351	MKVLVELLFVVSVIMICLGSAFGKVDEFVGHPILALVIFCGAVFLWYRFQET*
WSSedL1B2DRAFT_1003991	WSSedL1B2DRAFT_10039912	F035352	VPNYSKKPVLTNSDEEYLMLIEVSEEFERQKIDKTAREKSGNPAEIVLRNRLIRRNLNLSLIPDVTIQGSKIKNDLLLLKSGVDPNQKTYLSNQVKMVIEVKNNSVGGKTLENGKQEDPSKVMRVKFNELEATTNVRNFAVVVLSEMLLPPRTLYRWRFKEDVIGKENCKVFTLVARQTYPPGGLYIKSNIDDMLQKGQMKKTGELLALINYLKCL*
WSSedL1B2DRAFT_1004123	WSSedL1B2DRAFT_10041231	F061489	MIAGILGVICGVVVILPAGYMGTLLGAMFLCMGVGVFIMGLLRGRLN*
WSSedL1B2DRAFT_1004194	WSSedL1B2DRAFT_10041942	F036300	MDDMVAQGFGAIVIIYGGLIVITLGIVLFITKFWDALVSGDTGFILLWCAVILVLVSLYAGGGLLLRKYNII*
WSSedL1B2DRAFT_1005176	WSSedL1B2DRAFT_10051761	F020727	MKYQVLIKTISGKGGEFWGAFQKMPIEPMKGVIIESSWSLYGYWDFVLFFKADSNENSLHFVGEILRAMPGIADTSTSPMTVLKEHKM*
WSSedL1B2DRAFT_1005277	WSSedL1B2DRAFT_10052771	F093371	MVIIKRERKWRAAGVLAVALSAFLFAGCFATVGSHMNGQPVDMARAMAGDAGSQKWNTYRFETVGPLAEQRIAYVLFGDDVAMDMWHTPFVNLGKMSLREVLGNHDAYLKERMWIGTPITFQEYRWGGKVIAYTANESQMEVDLWEMAAAGSKVDIRMIYIDRRSFSGGGGPLA
WSSedL1B2DRAFT_1006753	WSSedL1B2DRAFT_10067533	F063812	MSTKHHDSKKHDDAKPAPDCHFCKEKYVYPEHPTPSGICHKCQTKIGVIILIIFVITGGIVFFGLI*
WSSedL1B2DRAFT_1007578	WSSedL1B2DRAFT_10075782	F042655	MKVFELIIPKDDMDHINKEIKKPKRQNTELLELWLERELKIENEGLYGNLPIDESHVTVQLLPNGNYKVLISDACFNMIASHVQPEPHSHKINNEDIFHFWLDMKTNKLHAKEHIDVKEITSN*
WSSedL1B2DRAFT_1009516	WSSedL1B2DRAFT_10095162	F036300	MDDMVAQGFGAIVLIYGGLIVIALGILFFITEFWDALVSGDTGFILFWCAVILVSISLYTGCGLLLRKYGII*
WSSedL1B2DRAFT_1010203	WSSedL1B2DRAFT_10102031	F071750	QLLSNPSLTVEDFEIALTNTSHLIRILEKHNFIYSTVGETKVITPGTMPNPLVPDLRASNSKKWEPKKQGEQPIVEVDMYEWEPNYAPHSEVIKTIRVLIRRDSTYADKTDKFLEEMKSKYPNRRKRYFRNSDQFKAYGEAYNVFTNNSKIEVRTETEKPIFDRFYILDFDLIK*
WSSedL1B2DRAFT_1010359	WSSedL1B2DRAFT_10103592	F058719	YIGGIKMKFYSVVLKKSIEIPNNKIKYVVKNKRKFAVGTYTAKGKTYAAYRIIGMNKNKK
WSSedL1B2DRAFT_1010638	WSSedL1B2DRAFT_10106382	F042955	TLQAAEETSMSRFIRFTLVAGAAAMLAWLWFAAWPELFRDGMPSITEDADFALLVRLTGFVVILATALYFAVKNLMKK*
WSSedL1B2DRAFT_1010700	WSSedL1B2DRAFT_10107002	F088780	EKYFMNLLRKIERGLTVLALAPLSGLEKKERDRRLDERLRRLEQKHNRN*
WSSedL1B2DRAFT_1011505	WSSedL1B2DRAFT_10115051	F047754	MKIIYCVLVVISLIFLCGACSLIGISNPATTGTVSSNYPDTVTYKIELSDETYLCSSFNVISTDALIALRLNDVYVLSSDGKITWIGKEKEISAVKIEKILK*
WSSedL1B2DRAFT_1012537	WSSedL1B2DRAFT_10125372	F055830	KIMEMTKWKDTAGHKPGCPYKGVPVSGTAAEMAKYHSGYCPGCNIPVKWEEEKREKENAALQS*
WSSedL1B2DRAFT_1013368	WSSedL1B2DRAFT_10133681	F036769	PDPADVQAAAPQDVMAGYWVLTFEDGRVGWANLVSDDYAKTSFSSKGKVEVPGFKPVDITSGVIPEFYKVGQVILYNAQATQKPFHFVRFVIEGNQFMTGYVATFDNKQYKFKAHRR*
WSSedL1B2DRAFT_1014137	WSSedL1B2DRAFT_10141372	F054975	MTKQLFSIFDNKKKFFLISEDELKKFQHYVFDGLSVFDHPDARNLFHDVGSRQAQNDVRSWQLVCKYCPMNLRCEVLIEDTSKCAIFNKLTIRNYTLHAMEEIQFQRQRLHEILAGLKNGGTCDNHCELCILCDNAGHCVAE
WSSedL1B2DRAFT_1014346	WSSedL1B2DRAFT_10143462	F025314	MGLLNRKFPAFSLEFVGEEIRSMINPELAQDMDVLCDVIVYMEYSLHSMQKIVEINHAAEKLAKCREDIQNADWWKEKQNQVNGATTVDEVWPFLKKTMK*
WSSedL1B2DRAFT_1014374	WSSedL1B2DRAFT_10143741	F093371	MVQIKGERKRVAACILTVALIALVLAGCYTAVGNLMNWQQVDTARALSGDAGNQKWNTYRFQTVGPFEEQRIAYVLFSDDVTMNMRRTPYVDLGKMTLREVQEDHAALLRQRMWIGTALVFREFRRGGNVIACTANEFQMDVDLWEISAEGPKVEIRLNFIDRRSRSGSGGSLSNP
WSSedL1B2DRAFT_1015327	WSSedL1B2DRAFT_10153272	F018557	MTEXKNGRPIFFPENLVLFGNXALFLWIVLDSVAFMLYNFTTGIVFFILTLILIYGVLHLLGCLRPCYNCIKCTHGMGRLAALYFGRRIFKDYKYNYKLPTAIFFTLYIGGFPAAFALYSTIVDFSAIKAAVFVALLVFTTYGALTWRPRKPKNPKEEV*
WSSedL1B2DRAFT_1017618	WSSedL1B2DRAFT_10176181	F060461	MNAKQFFRIEVSISWGHLITERKTLTKDEEKVREARRAYRDGVKEAWDIYTQGNMVVKEAKKALDLAIDEAYKLCLPEHGEKMAQTEYEHATKLYFKTLYKVHRKFADTIGQIWAVFMKDMETSLSPTKKNI*
WSSedL1B2DRAFT_1017875	WSSedL1B2DRAFT_10178751	F067886	RMRYFDPESYAQALSAVRKILVIVADTLVPPGEKTYRDKKGHERSIAPDQYFNRIFSYIEQNSGNDPGVSMIESEMAYIFAKAEHPHEKTRVLHERVSKDDVELAIIHMYLVIAEIAKIRKIETIYLKTAPSGNYDASPKLSPPGLE*
WSSedL1B2DRAFT_1018355	WSSedL1B2DRAFT_10183553	F098776	MSVKYFDFTTPKFFLFRNQSKRLSIPQYHILILAWCALVI
WSSedL1B2DRAFT_1019148	WSSedL1B2DRAFT_10191481	F094060	GYKPYTSSGTISPGQNVVINAALTKTAQPTPTQSPLSLVPIVGALCVVVLLSVVLLKKR*
WSSedL1B2DRAFT_1021229	WSSedL1B2DRAFT_10212291	F016394	MQTEDLVRLAKRVRNSLPNLEVFPLSTIYTFIKEQEETDMNLPDFKELIYHLTGWDISLQVIRRQLEINQIVR*
WSSedL1B2DRAFT_1025222	WSSedL1B2DRAFT_10252221	F060094	QWLVVHRLDIGGKENPIGTESPRILSLFTMEVLSGLKEKALANGIELFVNVETSDESLIESINVQAARGSIAIEESDVAPACAETEKRLTALYGQPVKMSACKVFQIRRLPSIYLEYGVEKPALAHAQYLIQLKPDHYIVMTLTCRPASLPRLRQELDAIVASFRPT*
WSSedL1B2DRAFT_1025242	WSSedL1B2DRAFT_10252421	F017269	TEKGNFTIMQRKRKGEIFEEGKKQVNVPTDVSQEEKKALDQTGEDATSGW*
WSSedL1B2DRAFT_1025427	WSSedL1B2DRAFT_10254271	F032323	KGGISMSYFVFRMKNDSELKSRVLYAILSQNPSYSVKEYKEEPDPADSNYDIISLTAYEKGPYRHIRKILAEFIKNNEIVCLNGPSSDLI*