2046860005: Sediment microbial communities from Lake Washington, Seattle, for Methane and Nitrogen Cycles, sample from SIP 13C-methane aerobic no nitrate additional fraction

Overview

Basic Information

• IMG/M Taxon OID: 2046860005
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0060820 | Gp0051622 | Ga0026414
• Sample Name: Sediment microbial communities from Lake Washington, Seattle, for Methane and Nitrogen Cycles, sample from SIP 13C-methane aerobic no nitrate additional fraction
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: Y
• Use Policy: Open

Dataset Contents

• Total Genome Size: 58805457
• Sequencing Scaffolds: 29
• Novel Protein Genes: 33
• Associated Families: 33

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira oceanica	1
All Organisms → cellular organisms → Bacteria → Spirochaetes → unclassified Spirochaetota → Spirochaetota bacterium	1
Not Available	17
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Skeletonemataceae → Skeletonema → Skeletonema marinoi-dohrnii complex → Skeletonema marinoi	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Chitinophagia → Chitinophagales → Chitinophagaceae → Lacibacter → unclassified Lacibacter → Lacibacter sp. S13-6-22	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	1
All Organisms → cellular organisms → Archaea → unclassified Archaea → archaeon	2

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Freshwater Sediment Microbial Communities From Lake Washington, Seattle, Usa, For Methane And Nitrogen Cycles
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Freshwater → Lentic → Sediment → Freshwater Sediment → Freshwater Sediment Microbial Communities From Lake Washington, Seattle, Usa, For Methane And Nitrogen Cycles

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): freshwater lake biome → freshwater lake → lake sediment
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Sediment (non-saline)

Location Information

• Location: Lake Washington, Seattle
• Coordinates
  • Lat. (^o): 47.07
  • Long. (^o): -122.27889
  • Alt. (m): N/A
  • Depth (m): 62

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001057	Metagenome / Metatranscriptome	791	Y
F002371	Metagenome / Metatranscriptome	566	Y
F003066	Metagenome / Metatranscriptome	509	Y
F008613	Metagenome / Metatranscriptome	330	Y
F009825	Metagenome	312	Y
F012202	Metagenome	282	Y
F013524	Metagenome / Metatranscriptome	270	Y
F014521	Metagenome / Metatranscriptome	262	Y
F015655	Metagenome / Metatranscriptome	253	Y
F017630	Metagenome / Metatranscriptome	239	Y
F018862	Metagenome / Metatranscriptome	232	Y
F026169	Metagenome	199	Y
F027172	Metagenome / Metatranscriptome	195	Y
F036694	Metagenome	169	N
F044499	Metagenome / Metatranscriptome	154	Y
F044785	Metagenome	154	Y
F044910	Metagenome	153	Y
F050936	Metagenome / Metatranscriptome	144	Y
F057116	Metagenome / Metatranscriptome	136	Y
F057911	Metagenome	135	Y
F058141	Metagenome / Metatranscriptome	135	N
F059900	Metagenome / Metatranscriptome	133	Y
F062755	Metagenome	130	N
F065433	Metagenome	127	Y
F070168	Metagenome / Metatranscriptome	123	Y
F074886	Metagenome / Metatranscriptome	119	N
F076869	Metagenome / Metatranscriptome	117	N
F082695	Metagenome / Metatranscriptome	113	N
F088308	Metagenome	109	N
F088340	Metagenome	109	N
F092033	Metagenome / Metatranscriptome	107	N
F096912	Metagenome / Metatranscriptome	104	Y
F099288	Metagenome	103	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
LWAeNNiAF_contig00008	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	1756
LWAeNNiAF_contig00019	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira oceanica	3138
LWAeNNiAF_GBUVFP102F6RNE	All Organisms → cellular organisms → Bacteria → Spirochaetes → unclassified Spirochaetota → Spirochaetota bacterium	505
LWAeNNiAF_GBUVFP102FO7CY	Not Available	502
LWAeNNiAF_GBUVFP102FQKSZ	Not Available	530
LWAeNNiAF_GBUVFP102FRCNF	Not Available	520
LWAeNNiAF_GBUVFP102FRJDG	Not Available	506
LWAeNNiAF_GBUVFP102FSKNZ	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Skeletonemataceae → Skeletonema → Skeletonema marinoi-dohrnii complex → Skeletonema marinoi	522
LWAeNNiAF_GBUVFP102G015D	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	537
LWAeNNiAF_GBUVFP102G0Z4A	Not Available	559
LWAeNNiAF_GBUVFP102G2CTZ	Not Available	505
LWAeNNiAF_GBUVFP102GA2HO	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	527
LWAeNNiAF_GBUVFP102GBZZ0	Not Available	601
LWAeNNiAF_GBUVFP102GDSVX	Not Available	531
LWAeNNiAF_GBUVFP102GK1IL	Not Available	501
LWAeNNiAF_GBUVFP102GSYKD	All Organisms → cellular organisms → Bacteria	507
LWAeNNiAF_GBUVFP102H08HT	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Chitinophagia → Chitinophagales → Chitinophagaceae → Lacibacter → unclassified Lacibacter → Lacibacter sp. S13-6-22	580
LWAeNNiAF_GBUVFP102H6MDV	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	533
LWAeNNiAF_GBUVFP102HPFGU	Not Available	543
LWAeNNiAF_GBUVFP102HQXNO	Not Available	548
LWAeNNiAF_GBUVFP102HWFL2	All Organisms → cellular organisms → Archaea → unclassified Archaea → archaeon	532
LWAeNNiAF_GBUVFP102IGMX4	Not Available	509
LWAeNNiAF_GBUVFP102II5TG	Not Available	537
LWAeNNiAF_GBUVFP102IPJ1E	All Organisms → cellular organisms → Bacteria	519
LWAeNNiAF_GBUVFP102J2S3F	Not Available	501
LWAeNNiAF_GBUVFP102JD5AH	Not Available	510
LWAeNNiAF_GBUVFP102JGVBF	Not Available	520
LWAeNNiAF_GBUVFP102JPAZT	All Organisms → cellular organisms → Archaea → unclassified Archaea → archaeon	527
LWAeNNiAF_GBUVFP102JQIO1	Not Available	515

Sequences

Scaffold ID	Protein ID	Family	Sequence
LWAeNNiAF_contig00008	LWAeNNiAF_2527910	F074886	MPKIPRNFIQEFPYGVSIEDSLNKGMKYLNADPNYITNWKDIIFTPIENFIHHQVFIFSEGKDMLIGFLVSQQATFLPDFISATIQLFGGVYTIDDTTNSIFIQEFIYYSILFLIGLGSARLAISMWLIINPYTMPWFLLLTATEWFMDSFAGIFPAVFGIEMTGSIVLGLLGSLAVYVKNLVLTMPYLPSEAIKQTIGIHEVYTFGGIPILWKIFSVPDKLREEWYKSTPYLIENLIKYYGDEGVEFVPSRILKEFYNNTPVADYTYYFAFVFSEFKSTFYQLEIHNNLLAFVFNPNIFESFNSHQFYNIFNIL
LWAeNNiAF_contig00019	LWAeNNiAF_3614230	F082695	LFVQFTFFSYESETGDETDVAKWAHKLMNRSVANRTITKQEAMCELGGLPMVICSESIETISITGSTKCATDTNTSTILSQYRNRPDAQQHLSLHQFYHIKKNKKLASTPSYREFIPHYVGGKGQPVYPITRSYARSELLKHLPWGRKNPMPNDCDLITMFKQFLENPKCPVGVRLGFERAKLRKELKEKGIQEAFQPDIEHSSNTDDVDDDEVGEVIALTESLGYTEDELEKLENNGFFLGKDYDWGKRIYTVSNPTIHRTRFGIILNY
LWAeNNiAF_contig00105	LWAeNNiAF_750860	F092033	PQYCGPHWMASEKTWVPIPVVEMNCSRWCCQLQYIPLTLAYAKTCHTFQGQTVGKNHPISCIIVQPGTRDFEGKCPGLFYVFLSRATDIGSPGDRSTSAIFFEGPDMTNDRITDLTHSLTTKREYVKVTKRRIWTNHLQNNLINIEISKQQKSNLIRWCERTKISERDVQRVIQDPRWRKSDMLNH
LWAeNNiAF_GBUVFP102F6K1J	LWAeNNiAF_3638580	F017630	MTKPLHVINWQGKEYRIPFDVNLNLDAKDKLIEVPNRF
LWAeNNiAF_GBUVFP102F6RNE	LWAeNNiAF_1374680	F026169	MANKSKGGSLTGLNASNKRDKGIDPKGAWTKVQKKTLAGAKGKAKLTADKQLGATKMKKK
LWAeNNiAF_GBUVFP102FO7CY	LWAeNNiAF_1775310	F002371	MEIKRGGKRKNAGAKPKYLEQTKTVSFRCPLSKVDELKLVVKSKLSEWSVK
LWAeNNiAF_GBUVFP102FQKSZ	LWAeNNiAF_2823710	F057911	FKTYPFLSSRAEIHMPFNRAKSTFSTGSLWLWPKFDKRPVGYLIFMEGFAPCIWYSERQEGMTFRWILPPHFSQKTTVCLANILAGESVLQIEDILINNGKDVWSTTIFSERWKLLNDFWNNLPPDQPLLAFKPQIVKPIALSDWHLHYNAAIYWIIQPDHAKQPRWYWRDTVERV
LWAeNNiAF_GBUVFP102FRCNF	LWAeNNiAF_593710	F062755	MKVEKKEVVCIRLPESIKKKVDAEAKKMYLAPSKLVSIIVQMYYEKL
LWAeNNiAF_GBUVFP102FRJDG	LWAeNNiAF_3247510	F044785	MKKKEQKWNVVLNQYLREKQFYCYYELKQNETESFPFSKIEKVQWEGLQATEKHGLVWKLSDEESRPKPCDGFSTPPLPSYLIIKFKDEFCLIRFEKILELRNEGV
LWAeNNiAF_GBUVFP102FSKNZ	LWAeNNiAF_3019490	F018862	EEMRLQSQNDRKDCNGEDMTNVIDCAKKEAKQFLHRTRDPANPHKHRATVCIICDSFIIGTETIHKLTKEEIGVHSERLGVKSYEEYYQTTLKAEVKRQYQVQGLIDMLLSPQLRKYPDGYATFSVCYTGMQPKMASKKTPPKFAIANGFVIGSFPREIKFFNKEGQRVTRKV
LWAeNNiAF_GBUVFP102G015D	LWAeNNiAF_2861430	F014521	LPDVSKALADPQHIYPVSKVVSVTIAKDSSPAGVLSEGDLLKLEPGQEAVLKNLAENSLLKMRVMTSKGEDGEVPAGTVVNVAVKDLQDFDNEFRAKLDLALTEAAKNKDAFKQGAVKK
LWAeNNiAF_GBUVFP102G0Z4A	LWAeNNiAF_1417720	F050936	MELSNDEVSFLNENIVLKDYFYDLLLNIKNSNETKIILCKNSYERRFVHILAISLGLYHSRYGDWSDWFKKYRDYQETVDKIDGQDHYKIVGVKVSTKPLLLSRKDKIHQECK
LWAeNNiAF_GBUVFP102G2CTZ	LWAeNNiAF_2108370	F044499	MKSTKLMLAVIATLLTTWIVMGTIGWCLSDLSFRDCITHGGTLMLMLIFGWIPAIIVGDDVNDHLKS
LWAeNNiAF_GBUVFP102GA2HO	LWAeNNiAF_229740	F027172	MAEKTILVCDTCGKPAAETVTIKTERGNFVKDLCSSHVNELTAGARKPRRGRPRAVVAWAAPRKATTAKKTAGTAPKRRGRPRKKPA
LWAeNNiAF_GBUVFP102GBZZ0	LWAeNNiAF_2731540	F058141	LYFVYEQFQKIKKHTNMKIRIENIECRFSQNQYEFVKWYPNKYFGTKAQLIAEGYELIVSQDDDFSLVKHNHHVHGSCFQNPEGCYTIATIVYDKNEHCTEIKSVGSRLLGLTKKERNNFFEVYQYADKQIKKLNK
LWAeNNiAF_GBUVFP102GDSVX	LWAeNNiAF_1970340	F059900	MAVAKKKVKVADIAKLAKKIRKPNEKWTDAIKRAAAQLK
LWAeNNiAF_GBUVFP102GK1IL	LWAeNNiAF_1047860	F008613	DMLQNVDKWQDKEGVCLYSKNGQTIHKIKAAKYLLLHHLKSELSSTEKIMDVWLDQGMPDYQTFYNYIVTTFDFELAEQAKGTISRIVDGKKEVNKIVDGMNNFVNNRLRSLPSRKEQAQLVISSYGETNRAAFVFKILDNRPLGKEVYKKLLFQVLK
LWAeNNiAF_GBUVFP102GSYKD	LWAeNNiAF_1464780	F009825	VKPRLLADENTSHRLVAACRQIEANFPLVHISDWQEGAYLSVKDPALLMTLRESGIILVGFDRASIPMHAGELTREGLGHAGVILFRRSVSAVAYGKQAR
LWAeNNiAF_GBUVFP102H08HT	LWAeNNiAF_2129490	F012202	MEQAYIIARLKEITMPELLDAIAEAHAGKPIDIYEHLPPDLIDKTTDTIWEFIEAVKKY
LWAeNNiAF_GBUVFP102H6MDV	LWAeNNiAF_2280350	F003066	MAKKEPVAWLYEEFDVRSGDLKKSYLWSFHPNQLSYLNDLKNTTHHIKITPLVPGEAVEEYKGLSKYDSKR
LWAeNNiAF_GBUVFP102HPFGU	LWAeNNiAF_1297060	F076869	NNITFSQEYIDALYDLPINVIVELRESYSAEKLVSA
LWAeNNiAF_GBUVFP102HQXNO	LWAeNNiAF_3253080	F015655	DMKKDAHENYTDKLIIDIIDDIKAKKAKYDDYLLYKKYYDKVMKTPENKLETLYEKEPDIFNLLEKYNYQNPKEVEHESPELNIVILDDLLGSDAFSKKTKSVLTNAMIKNRHIGVVFMVLVQSIRAVPKNIRLNCSVFQLATFKNKKIILEDIYEEISNVIDIDGFEELYDHATAKPYGSL
LWAeNNiAF_GBUVFP102HTDNQ	LWAeNNiAF_495160	F065433	VYSPKNLIMEICTSMCLLNNEFLDNILDRGLKAKYTENSQAFLTDIKNLLLTKNRLDLGQFVNNRCQSDDETAKINGIFESVEFNIEKDWEKLINSRLTARNIIDKLLPSEKLSSDRIAKIYWLGPNKNEEFKEDIVVEMVDGQQYSLFLNKNLSLQKSASFNTFADDIIP
LWAeNNiAF_GBUVFP102HWFL2	LWAeNNiAF_1184670	F088308	MKALLIALLLWGFNDKVVIEKAGDVEGRKTYHVKVGKKTYEYMYAEEIAHALTTGDWVYNEDLKLNK
LWAeNNiAF_GBUVFP102IGMX4	LWAeNNiAF_1932950	F096912	MFTVKLIKQDGKLVYPNDKSKLNYQIFLDKLTEGQEVEVYMGLTSSDKSVAQLAKVHACIRA
LWAeNNiAF_GBUVFP102II5TG	LWAeNNiAF_449630	F036694	EDMLHELYFKLLAEKPESIDKYNKDGKLYILGLYRLRDLFRNRTRTLQHIDGNTSSLHEMANYEIRDFADEPMELLPIDEITIERIKNCIFDGLLNQDHDIEVFVMAQIEPLYRMEQRTKINRSSLKKAYENARIKLKQSI
LWAeNNiAF_GBUVFP102IPJ1E	LWAeNNiAF_3292040	F001057	MVPAMQTTIQLDASNRIVLSRELRRAAGIPRKQKLRVSATPGRIVLEMESNPSGRIIKRGKLKVWTGAVPATPIDEAVQQARHYTR
LWAeNNiAF_GBUVFP102J2S3F	LWAeNNiAF_1858450	F088340	MIPLKKIDARDLCVGKQYLIEYAGSHVVSNPRIKGTFIGNILPECEYQCTLSKFTDVLQTGNVSIPDLKLQDCFYNYYEADALTRAYTRH
LWAeNNiAF_GBUVFP102JD5AH	LWAeNNiAF_1752040	F057116	MKINPKMVPFFSPLTPGEGKHCMAAYIAPINHNRVDSRMVASIMSTMKGNYCRDESLDNTHLQDMGLDAAVLIGYYKESVSIL
LWAeNNiAF_GBUVFP102JGVBF	LWAeNNiAF_2649950	F099288	MVEYRYNTYEEAQTALDTVNAYFELPSGGTLTWTEIQEGDGYWFLQADRLDEVLG
LWAeNNiAF_GBUVFP102JP6QL	LWAeNNiAF_722310	F044910	MLQDAHTKKESIPVVTTTSGDNIVIAAQTDAWIYIHELMGDLDADDTLKVYAGSRLLAQFDLSSGQGITEQDEPGEDNRPRFECRPGEAFILNITGSAVFKGTCHYSLRY
LWAeNNiAF_GBUVFP102JPAZT	LWAeNNiAF_615610	F013524	MKTNKEVVNRLREFTQNNCNTTLDPKLCEDIRYLCDEVERFGVQMLLMNEYGDEDYITIQKYKSKLEKCQS
LWAeNNiAF_GBUVFP102JQIO1	LWAeNNiAF_1797350	F070168	GTLFADAAALSTCDSFGLARDRVFTDVGYSLRILHDAFGVYQQLFSIDVAVPLNRREGLATCLGHTVTPIVRPAFSVLLSFLPSF