3300000094: Wetland microbial communities from Twitchell Island in the Sacramento Delta, sample from surface sediment Feb2011 Site A1 Tule

Overview

Basic Information

• IMG/M Taxon OID: 3300000094
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0063443 | Gp0053966 | Ga0026102
• Sample Name: Wetland microbial communities from Twitchell Island in the Sacramento Delta, sample from surface sediment Feb2011 Site A1 Tule
• Sequencing Status: Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: Y
• Use Policy: Open

Dataset Contents

• Total Genome Size: 129333279
• Sequencing Scaffolds: 30
• Novel Protein Genes: 31
• Associated Families: 29

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	8
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium	2
All Organisms → cellular organisms → Archaea → Euryarchaeota	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales	1
Not Available	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → unclassified Syntrophobacterales → Syntrophobacterales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaU1.Bin231	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → Desulfatibacillum → Desulfatibacillum alkenivorans	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): 38.107057
  • Long. (^o): -121.647578
  • Alt. (m): N/A
  • Depth (m): 0 to .12

Associated Families

Family	Category	Number of Sequences	3D Structure?
F007558	Metagenome / Metatranscriptome	349	Y
F019578	Metagenome	229	Y
F019677	Metagenome / Metatranscriptome	228	Y
F031503	Metagenome / Metatranscriptome	182	Y
F031716	Metagenome	182	Y
F040940	Metagenome	161	Y
F047753	Metagenome / Metatranscriptome	149	N
F049734	Metagenome	146	Y
F054975	Metagenome / Metatranscriptome	139	N
F056185	Metagenome	138	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
WSSedA1TDRAFT_c000119	All Organisms → cellular organisms → Bacteria	11372
WSSedA1TDRAFT_c003026	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2793
WSSedA1TDRAFT_c004912	All Organisms → cellular organisms → Bacteria → Proteobacteria	2112
WSSedA1TDRAFT_c006389	All Organisms → cellular organisms → Bacteria	1802
WSSedA1TDRAFT_c006484	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1784
WSSedA1TDRAFT_c012213	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium	1161
WSSedA1TDRAFT_c012870	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1118
WSSedA1TDRAFT_c013542	All Organisms → cellular organisms → Archaea → Euryarchaeota	1074
WSSedA1TDRAFT_c014016	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales	1049
WSSedA1TDRAFT_c014336	Not Available	1033

Sequences

Scaffold ID	Protein ID	Family	Sequence
WSSedA1TDRAFT_c000119	WSSedA1TDRAFT_00011910	F040940	MGTLNNIFSLVFGINLIVVGLVAFIVGIVSLLKRDDSVKKLISIAYIIAGIAAVYFGVVLSRSAYXM*
WSSedA1TDRAFT_c003026	WSSedA1TDRAFT_0030264	F092937	LLFLLVLMLGCVYTEPYRVAVTVEPMVRNCTCLGYISEISDMGAPQINPKFTYDAQERVLRKADMMNATHLVWIGDYPFAATAMIYRCSN*
WSSedA1TDRAFT_c004912	WSSedA1TDRAFT_0049122	F072484	MRNTLNNRKGWLVFLVTLFGLMWSTSLHAANFLFFWSASTDPSATGYGIYQRTGGSSYVKIDEVSVQDLDNPATPSYLVTGLTDGNTYWFAATSISAFGTESDLSNQTCITVNGQIVECTDNDDNGTTVFISCFISAAGL*
WSSedA1TDRAFT_c006389	WSSedA1TDRAFT_0063893	F096267	LKNKHHAVSQGARRFGKRSPPAADEHLQKPCNAGSRREALFFNNLFMHSFT*
WSSedA1TDRAFT_c006484	WSSedA1TDRAFT_0064843	F007558	MQAIADLKALLLEILESAFQNGDVHATQQMGVNMSNAVKREGVVIIQNQNVEVLARIMPSMVKTLKLCDAMESSWRSQAAIELETQQKQLPPPVDDDDTDPIEACCSWLYENHINWQNMQDLMRARYLEY
WSSedA1TDRAFT_c012213	WSSedA1TDRAFT_0122131	F019677	MITYSTLEASRILGIEKSRVRNWIVKGYIIPSWHKAMARGDKHLLTYDNLCYIYLFQQFRSKGLHRTAIAFIISEIEKTGLSKNLESGFRYVIWNTKNPKEGGIVAISSEIPTAIIDALIVDDRRAAPRGSSQMLVIDLLEVKNEVDRKREKRGG*
WSSedA1TDRAFT_c012870	WSSedA1TDRAFT_0128701	F047753	MMKKIIRILEGLKVDDTWLRVAPFALAGCRKESYGKLTRLCRRKETLMAVVVAGVIGLYSAKKHVELCKKAVKAGRNASGDSDRELNKYLDAIWRVYLLDTSIDKQRLIEKAIGYVSGKLDQELSHSLTEAKKEYRAIIQQIMGAVQAGTGHSENAVHGYLSAFLNSI
WSSedA1TDRAFT_c013542	WSSedA1TDRAFT_0135422	F054975	LTKQLFSIFDNKKKFFLISEDELKKFQHYVFDGLSVFDHPDARNLFHDVGSRQAQNDVRSWQLVCKYCPMNLRCEVLIEDTSKCAIFNKLTIRNYTLHAMEEIQFQRQRLHEILAGLKNGGTCDNHCELCILCDNVGHCVAEEAMRLLRESKIEDPSGTVCVA*
WSSedA1TDRAFT_c014016	WSSedA1TDRAFT_0140161	F063812	PILMLISDYFVSLTMSTKHHDSKKHDDAKPAPDCHFCKEKYVYPEHPTPSGICHKCQTKIGVIILIIFVITGGIVFFGLI*
WSSedA1TDRAFT_c014336	WSSedA1TDRAFT_0143362	F031503	MDMNEIKELFKATAAISTPEGIAAYKEFAAALTTPILQAIEQQSIMRQLFAVERLGPGAQASYPVAEDFEIPVWVLPGLGYVAQNFIEGIGEEVYVPTFSIDASGDWKLTYARDSRVDIAARAAEKAAKGIADYEEECGWRIILPAATSRFFGKGLLGARPAPIYEVDPASTGAGYLSKELINKMIVGFKRIGRTLTDLYISPEDAADIREWTDTD
WSSedA1TDRAFT_c018605	WSSedA1TDRAFT_0186052	F060457	MNKNITDPKSSSSDLGIFLSTIFHIASIACVPFLVHATVNGNLYACGLLMAWTIYYSIRLFRSRKLLGLAFFVMTLSAVVFGIYNFGLMSQYKNSKIYLEEEKTFCRETTYETLKLKYETEKSMISTNFRICLDKQHVPPETCITEVNQATSLNEVMLGNRLL
WSSedA1TDRAFT_c020625	WSSedA1TDRAFT_0206251	F102133	MEQPGQPPDRGGSKLKILDSLKTAALFLIAAGLFVMSFVIYDVMGKHGRYVPVSDDDEKVVVMDTHTGEVWSVNYESKETASLKIFNPIAGEPQIFPKKLIARVSN*
WSSedA1TDRAFT_c023764	WSSedA1TDRAFT_0237642	F100426	MRNRIIYGSQSVWCNGEILYRVQTLGSTTTFTSEDIFELGHLDIIDVVDDVPAVAVTLNSNDWGDVRTMAILAQVKPAKLAM
WSSedA1TDRAFT_c024037	WSSedA1TDRAFT_0240372	F056714	DMKQSVILLMILTIAVPLSAFAATLQNTDSQTYNLQIQESGRPYSSQYQVIENAQVDICFNGCEMTLLSTGQTVRVNPNDAVVIDNGVMNVTSGN*
WSSedA1TDRAFT_c024779	WSSedA1TDRAFT_0247792	F087857	MKRNFIVVPLLVIAFVAFQIVPPAHAEPITLTIMAIAGITTVMTAAFTDMAVHGEAITQANSQQEKPAEVYAKDRSADSSKKQDGEATTVR*
WSSedA1TDRAFT_c025747	WSSedA1TDRAFT_0257471	F068995	MKAEKKTEFVKAIHPSQPEWEYYLPKEDKALIKKLSKKPIFPKLCERPCTSVITLFPKDTVEGNTGKGYHMINIDGYRMINAYVISDPLNSTNQRGFTLELSFSLNNFVYGVGVIGETSYFFNFDSYFEPGTVSHKLQRCETNDLTTTGGLPLIGGVDLTHILRIPVMGPYVRAS
WSSedA1TDRAFT_c026067	WSSedA1TDRAFT_0260671	F062885	MNLSTLREVPQANLGTSSACEVEVGPLRFKVWHKSPTYLCLLAGQDPSTLPEFREGETLTMAFHDSGSVLPAEHLKTAVRKIKRNEEGKLKGQYLVDLEILKSYH*
WSSedA1TDRAFT_c027250	WSSedA1TDRAFT_0272501	F098776	MSVKYFDFTTPKFFLFRNQSKRLSIPQYHILILAWCALVILYGEPGPSPTFGHSEK*
WSSedA1TDRAFT_c030562	WSSedA1TDRAFT_0305622	F060458	GIGLVCRYSGIQMRLEAVVRKIASLQEFIAKSCSDATVATAACRKKSGPQCVFDIIHESEKGVDPLFIKQVTGFKEQKIAKILYKLFKYGEIRIEPGGLYVAVAGR*
WSSedA1TDRAFT_c032976	WSSedA1TDRAFT_0329761	F049734	MSESKNYGFQTQFTIVKKYHRHVLWLILGLLFALDIFTTSMSLHLGNFEKNPLMIPFAGNPALHGIVKLLAYIFLFFVIERAVIFIQERKPEKTPFWIKLNFQTLYGLIIFVLIYLIWLYLYVVAS
WSSedA1TDRAFT_c035211	WSSedA1TDRAFT_0352111	F031716	MSRFSSGPWHVEEENGSYGVFSNDALLAVTLSDDLKDKDAAKANAHLMASAPRLLEVIKEIKEHLDNNMIVTGEGLKINDSHLRESIID
WSSedA1TDRAFT_c035371	WSSedA1TDRAFT_0353711	F057781	MSKPDLRLLTQWLDPALVSRLEDRRHLKNEWRRHRKLATLETLWLMLAVSLD
WSSedA1TDRAFT_c036916	WSSedA1TDRAFT_0369161	F057771	EFPIYGQLKLGGSQSEINFREGPGVNSKVLSTVSNSNLLVILPGEPKNGYVEVFDIESSSFGFVYEPLVKVTDTLHFQKQHFFEKSGENDTEDVEIELINRTDHSLFVWINKNVYNLAPHEKKELIFSDEDVIYFSSAPGLYPVFGREILKKGTSYKLDFSL*
WSSedA1TDRAFT_c039044	WSSedA1TDRAFT_0390441	F056185	LPKEKELRANWKNYHTYCLGSYAMLFQLKGDQIIQRDDPWREVTSDEMASGCASFLIDSSPVMQLLGENEKIFGYVIYNFDDQIWASIIDPKTIRLFYHVHPKGP*
WSSedA1TDRAFT_c042394	WSSedA1TDRAFT_0423941	F007558	PQLPPPGDESDADPIEACCTWLYENHTMGVNMSNAVKREGVVIIQNQNVEVLARIMPSMVKTLKLCDAMESSWRSQAEITINPQHPQLPPPGDESATDPIEACCLWLYENHTKWQDMQDLMKARYLEYVISRFKTKTEAAKWLGVGSTYLCKLSKTTMNN*
WSSedA1TDRAFT_c042600	WSSedA1TDRAFT_0426001	F103514	KKISFNLKQNKKFIEIEVPGDEILQTVEADSLEFEKLVKQKVIEYIQSL*
WSSedA1TDRAFT_c042717	WSSedA1TDRAFT_0427171	F085853	MIEGAHRFYADHHFEEIGRRMEESLTARQAEVEQLNQKKDQIQKSKEGLNNALKNIKTRFGKLGLEVEDAILLAPLALSALFFVAALQLCQNIQLRKSFHRLFQASDPQKVAITDAEIALAMPLWVDPLAAPIQRKIKLAALMIPAIASVLTLLVVFYCWTIPDAFSGLTGIDYMKY
WSSedA1TDRAFT_c044021	WSSedA1TDRAFT_0440212	F060102	MSKKSAKNTDTQPPPAREEKESFFTMFSKIDSRQKHRILAYLFWLLGIFIILF
WSSedA1TDRAFT_c045750	WSSedA1TDRAFT_0457502	F019578	NPCMEKSANGSLQVKKKDEAVGIFGADSSVVAVLPKKKTGDDTRVAEAYLFAAAPQLFEVCRTIHSILENSLIVTPEGFKINCSDIKISLRDAILRAKGYRKSPDEP*
WSSedA1TDRAFT_c047715	WSSedA1TDRAFT_0477152	F069004	FTLDVGIDDEELIMSLLAGLALYVRKGNSIKVRQSYVTFSGSQEIVTKFISKTEQVGDWSKETKQILSALKKKR*
WSSedA1TDRAFT_c047922	WSSedA1TDRAFT_0479221	F019677	ASFGNSVRSYMITYSTLEASRILGIEKSRVRNWIVKGYIIPSWHKAMARGDKHLLTYDNLCYIYLFQQFSSKGFHRTASAFIISEIEKTGLSKNLEFSFRYVIWNTKNPKEGGIVSISSEIPTAIIDALIVDDRRAAPRGSSQMLVIDLLEVKNEVDRKREKRGG*