3300017658: Enriched Miracle-Growth compost microbial communities from Emeryville, California, USA - eDNA 5th pass 30_C BE-Lig MG (version 2)

Overview

Basic Information

• IMG/M Taxon OID: 3300017658
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0127392 | Gp0191744 | Ga0182738
• Sample Name: Enriched Miracle-Growth compost microbial communities from Emeryville, California, USA - eDNA 5th pass 30_C BE-Lig MG (version 2)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 880230362
• Sequencing Scaffolds: 35
• Novel Protein Genes: 35
• Associated Families: 31

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	1
All Organisms → cellular organisms → Bacteria	7
Not Available	4
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea → Hymenostomatida	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	7
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae	2
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Chloroflexia → unclassified Chloroflexia → Chloroflexia bacterium	1
All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Spiralia → Gnathifera → Rotifera → Eurotatoria → Bdelloidea → Rotaria	1
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea → Peniculida → Parameciidae → Paramecium → Paramecium tetraurelia	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae → unclassified Phycisphaerae → Phycisphaerae bacterium	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Lignin-Adapted Enriched Soil Microbial Communities From Emeryville, California, Usa
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Unclassified → Unclassified → Compost → Lignin-Adapted Enriched Soil Microbial Communities From Emeryville, California, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): terrestrial biome → anthropogenic environment → compost
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Soil (non-saline)

Location Information

• Location: USA: Emeryville, California
• Coordinates
  • Lat. (^o): 37.83
  • Long. (^o): -122.29
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000911	Metagenome / Metatranscriptome	840	Y
F001784	Metagenome / Metatranscriptome	635	Y
F001868	Metagenome / Metatranscriptome	624	Y
F005470	Metagenome / Metatranscriptome	399	Y
F007999	Metagenome	341	Y
F011188	Metagenome / Metatranscriptome	294	Y
F011929	Metagenome / Metatranscriptome	285	Y
F015351	Metagenome / Metatranscriptome	255	N
F016560	Metagenome / Metatranscriptome	246	Y
F021587	Metagenome / Metatranscriptome	218	Y
F022330	Metagenome / Metatranscriptome	214	Y
F023152	Metagenome / Metatranscriptome	211	Y
F025080	Metagenome	203	Y
F028371	Metagenome / Metatranscriptome	191	Y
F029053	Metagenome / Metatranscriptome	189	Y
F030705	Metagenome / Metatranscriptome	184	Y
F032316	Metagenome / Metatranscriptome	180	Y
F035602	Metagenome / Metatranscriptome	171	Y
F035663	Metagenome / Metatranscriptome	171	Y
F035899	Metagenome / Metatranscriptome	171	Y
F040613	Metagenome / Metatranscriptome	161	Y
F041209	Metagenome / Metatranscriptome	160	Y
F042653	Metagenome	158	Y
F044406	Metagenome / Metatranscriptome	154	Y
F047414	Metagenome / Metatranscriptome	149	Y
F047589	Metagenome / Metatranscriptome	149	Y
F049152	Metagenome / Metatranscriptome	147	Y
F054879	Metagenome / Metatranscriptome	139	Y
F057460	Metagenome / Metatranscriptome	136	Y
F070358	Metagenome / Metatranscriptome	123	Y
F097539	Metagenome / Metatranscriptome	104	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0182738_1001252	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea	32348
Ga0182738_1002409	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	22218
Ga0182738_1002853	All Organisms → cellular organisms → Bacteria	20219
Ga0182738_1006119	Not Available	12594
Ga0182738_1008173	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea → Hymenostomatida	10444
Ga0182738_1022942	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea	4831
Ga0182738_1034465	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	3434
Ga0182738_1034509	Not Available	3430
Ga0182738_1035532	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae	3344
Ga0182738_1036705	Not Available	3258
Ga0182738_1038438	All Organisms → cellular organisms → Bacteria	3134
Ga0182738_1046225	All Organisms → cellular organisms → Bacteria → Proteobacteria	2682
Ga0182738_1054376	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	2347
Ga0182738_1056996	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	2260
Ga0182738_1059787	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	2173
Ga0182738_1064437	All Organisms → cellular organisms → Bacteria	2047
Ga0182738_1066997	All Organisms → cellular organisms → Bacteria	1984
Ga0182738_1072163	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Chloroflexia → unclassified Chloroflexia → Chloroflexia bacterium	1871
Ga0182738_1075812	All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Spiralia → Gnathifera → Rotifera → Eurotatoria → Bdelloidea → Rotaria	1800
Ga0182738_1091401	Not Available	1558
Ga0182738_1092479	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1545
Ga0182738_1103811	All Organisms → cellular organisms → Bacteria	1415
Ga0182738_1110465	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae	1350
Ga0182738_1138801	All Organisms → cellular organisms → Bacteria	1134
Ga0182738_1155926	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea → Peniculida → Parameciidae → Paramecium → Paramecium tetraurelia	1039
Ga0182738_1156962	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1034
Ga0182738_1165535	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	993
Ga0182738_1177897	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	941
Ga0182738_1200666	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	859
Ga0182738_1274197	All Organisms → cellular organisms → Bacteria	679
Ga0182738_1296030	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	641
Ga0182738_1297044	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	639
Ga0182738_1347135	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	570
Ga0182738_1378855	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	535
Ga0182738_1382009	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae → unclassified Phycisphaerae → Phycisphaerae bacterium	532

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0182738_1001252	Ga0182738_100125251	F047414	MKKESAAGLTLDTRMSPFFGKDLSPRMHHRDSLMLSPLFSSNNHNGGFFSGFTPRYFSNVPHMQDNNKTFGPDDFLLRPSPTHMEIDVNSRFEKAVENMKMELRNNPNQHHMGDHGMDQQGLNLDIDLIDDSYLHAPLTKSPHLQFVGSQPTSKCSFKKFGEWTLSPNASFLPRKKF
Ga0182738_1002409	Ga0182738_100240916	F097539	MTQRPWTHLVDQPAARHLVAVRHAPKAADEPAALLTTLIEGLCPNGDFALLTRCEEEGALTLCAFATPRDAEQLASAVGAEETEDYPEWASQRCFTLDEPTAQAITDAIEASGIALGVLQHHAPSGVQYANH
Ga0182738_1002853	Ga0182738_10028535	F035663	LRLSQTWVQSGRVNTQELTEIHQALAAVHDAVGTLTFPGCDRDDMFELMDRVEAELDAAHPNTQVIGTFLNSIARSLRNQPEAREACLRIEDVMERTGLPSTWQTGL
Ga0182738_1006119	Ga0182738_10061191	F005470	MSVKLRKEGQVITEFPSEMVPRSRLLTKLVEEFSSTEVDLEPAPGKDFSPATINKVKEFLEKFDKGLNKMPKKPLLIFVTYNDWLDNNFDEKTREWLEEFLKPKSFYDLVELFNAAFYLQIDDLREICAARIAHSIILERKAPEDFLRDFGVVTQYQDFFTPEEEVKFIEKEFINKNDFEGVAAEDDEELNKE
Ga0182738_1008173	Ga0182738_100817311	F035602	MSLSNDIKAWLETYPRLNWRLTFDFLLAPENAKAVEFSDYGVACFVKGFQREFIDRDYHEALNWYETGAMQYDSLCLFRLHEIYIGDTHFKVPYDERQAICHLVYSALLSQFEIFDAKVSFWQKFEAFWKKESSKTAYIQELLLSPSADYFVATGGLFSKLFTFYGTKNNFPDILPELRNLSADILKTKFFSIINAMFDFLAYTYNSGFSKVDLQKYVDTILDMLTNDILFDNFFQNYITHIKLLRAKKKFAHVFQRRLETDCFWVWSFSFLVSMKNYYLGILQTYEDTFCDGTLVLKWKNTASWVNNFVGFCNEKGIGTSKSTDKAMEAYERDMNEMPRVLFSRFRHILLRKRGQLQGQQPFQEDIDPQLEEEITSLKSMIEGRFEDQNRMDCYLYYVYGKVYEKIDEDIDTAIQWYQKGVDSDTDSCLKNHLLCNEGWRMKCDKRLQKLKMKKGLQTLIINKNQED
Ga0182738_1022942	Ga0182738_10229425	F005470	MTSINLRKEGQVITEFPPNLIKRSRLLTKLVEEFSSTEVDLEPAPGKDFSPATINKLKEFIVRFESGLPKLPKKPLLIFVTYNDWLDNNFPEDTREWLEEFFKPKSFYDLVELFNAAFYLQIDDLREICAARIAHSIILERKAPEDFLRDFGIVTQYQDFFTPEEEAKFIEKEFINKNDYEGVAAEDDEELNKE
Ga0182738_1034465	Ga0182738_10344654	F030705	VTEAGSGLTVEQFLTEAAQLHQTWIRRFDVQHRRRPRPPEVEAERLRLVRRLQLIQRLQSEGTPHAEFSARLETFISAPREARLVDGDNPFLEALLQTWNNAQLPQAATLAAGAQPPQPSATVEFRW
Ga0182738_1034509	Ga0182738_10345091	F049152	MSDDGDLDAMPGPIRPDGGLLQQAADQIQEMLGVHRQLDKLLYQSATQIGGVEFASIFTPVPPERLSAKPRLDALDHDQTFLRSSPLCTADTERSLGLLEILHGPHAQANVDVFVRFCEREKFFERLADGQSFVFVGSHL
Ga0182738_1035532	Ga0182738_10355322	F044406	MPPLELMLPLAAAGWAFLVWLCGGGLGLAILVFIVLKVLGH
Ga0182738_1036705	Ga0182738_10367053	F028371	VGVDESVFISASNDGFNVSGLLDLFTFDGLLLAEFNTVVSDVPLSEGSGVDLDDAALDQSVGSDEFVVGGVVDDHDDLGLSGDLFRSPGEVTSIESEGLEFVVSSSHSVSSDGLFADLGEGGRTTRFVLLLLLVDGHTTTGKSSLVSRVSGDTHYV
Ga0182738_1038438	Ga0182738_10384384	F029053	MDDETPEMERLSMQMRAVMAAWTADPNNEALKRQYRDLQGRYQRLFGDYKQRQRSNGAVH
Ga0182738_1046225	Ga0182738_10462254	F001784	MGEVIHASFGTEREWEQTHEKTVDGLLTIGNLFGDDEALMRAKAECVYHILREIVEDIPSVQITTRMPDNLTDEQMTMLTESIRQAALKGIEVAMTHSVQVLMSSIYDLCTSKLKVRPC
Ga0182738_1054376	Ga0182738_10543762	F015351	MPVQIRKLTSEESAKLFPKRGQMDLTEYVVALGSLQPGDAGEVGLGGLSTRALKRRLGQAAKQLNYSLRWAREQSNSAVRFQVREARVPKPRGTGRRGRPRKNPV
Ga0182738_1056996	Ga0182738_10569962	F040613	FEFALGPPDAAKLIFERGALLHQLLGLLRVVPEIRVLGEVVQFGETRSCGIDVKDASSAARLTA
Ga0182738_1059787	Ga0182738_10597872	F035899	MVYPRACPHCGVTEPSPEQLYSTRSAFDGGTPSPWKSEIPGRVLDLRCGACWVLFRWDYFGSRLIQVLSEGKPGETTGTGSS
Ga0182738_1064437	Ga0182738_10644372	F007999	MRDDITERSHARAHQARRNLVNALRECGELADAVEHFEGRELLEVLDYLDSLRFVMAESGQLLQGVLRGSANYTKSV
Ga0182738_1066997	Ga0182738_10669972	F032316	MRIPLKLSAIDQEHLQELYDSAGVARDELPYSEKFEEIWQGFQDRTFKNAERDQLYGALLKYVRSSSCSATELPPSTLNEEQLKQLKHLLPRHARGSKLLPYSDEFDAAHKEFMKLAGVELSAQDFWRAAVRAQGAKRLPPRRARVTAPADEDDSDVE
Ga0182738_1072163	Ga0182738_10721632	F007999	MENIDRRMAARAAQARTNLVNALRECAELADAVEHFEGQDLLDTLDYLDSLRFVMAESGQLLAGVVRGQQS
Ga0182738_1075812	Ga0182738_10758121	F041209	MSCGLTLAAVSADLCEQIANLRRKLQRIGPARTLFLDETALRLNAAPNHTLALPGQQPLVLATDTSAYAARYDMIAVCSFVETLLPMVFTPAERRGADVRGINGAMLQQFIDNTLAQAVEGLDRYPLTLVLDRAPIHLNTQQLLQSFHDRSSESIKEILLLPPNAAKRMSPLDNALFHDWKERCRKRCPVTNHTIEGVMSDAWNQLPAALIHQHYKHCGLVRGQDPYFDCPDP
Ga0182738_1091401	Ga0182738_10914013	F042653	MNEWILYIMTWASNLSGYPYPDTLPQVQFQSESWFSHRVCKDHVPCPVFGLYEDGEIVYLREDLTEAAKDHVAVHEFVHYLQRESGRFDLNSCLDSDKREQEAFRVQTRFVAEVQNGFARFGMNHLACGPA
Ga0182738_1092479	Ga0182738_10924793	F023152	VKLTDRGARVQRIKWVELSCMLCGEWAATLEGGSVLRPRAAGTAKISGQRIVCGRCGGALTPTDQGERVSFV
Ga0182738_1103811	Ga0182738_11038112	F001868	MPQVVDFNFTPELRLRDGRIIRNLEDAAAFVREHEVRPGVDIRDEVLHRIERAHSQEEALAAAYLFTRWLEELEIVE
Ga0182738_1110465	Ga0182738_11104652	F000911	MSISMEFFASEGHFATYDPFEGSRSRVGIFQLQCRCCGYEPEDAVVPPRVCPKCHSEAWERFAKPGSILENANRY
Ga0182738_1138801	Ga0182738_11388013	F011929	VDEIEIIYLRFPVHPNITVIQTGPGIEKIIREGASYWIYGTPDGPLAGKKVEIPSDNVAALQWKTGDETTQA
Ga0182738_1155926	Ga0182738_11559261	F022330	LHFVVENQDEGSTHTSEDVGEGTLEEGLTTFILVDLGEAVEGTVVHDGLTTRLHHESSSDGIEGIRDQTRSSSDELGNNELEEDRGLAIREQDSLQGIVTTEVAGSVGDDTED
Ga0182738_1156962	Ga0182738_11569622	F011188	LDTYNIYMDELPAGEEIDGEEMIEVEFRVVPGSDDENDPENNAVIAGLDLVDLINLRDALQQEIDNYALSALEAEANRLAGDMG
Ga0182738_1165535	Ga0182738_11655352	F011188	MLVARSGVITPGGEHVETYNIYMDELPTGEEYDGDEMVEVEFRVVPASDDDDDPENNAVIAGLDLVDLINMRDALQQEIDNYALTALEAEASMADS
Ga0182738_1177897	Ga0182738_11778971	F016560	MLASQYAVDRLTRVSDRDEVQVARWTAIKGPVGLRLREIRQDRVQVRSQARLAGDLEELGYHVTQSMVSRYEQGLVDAPLTLERIVGWALCCEALSSDAFKETLLLAGYYLPWQEAELASFDDLLHSYRRLS
Ga0182738_1200666	Ga0182738_12006662	F021587	MSETTQPLDTQTQDPMLAKIVEALEEIRSEEFDYEILRAASAVTGDNAFETWKPSLNYLPPEKIGDEYHVTVYAKGACESCPVKRMHVDSIEPKVRHLVGSDNVFVHDYFDMYDFGQAYMSPE
Ga0182738_1274197	Ga0182738_12741972	F054879	SFRSAQVSEMSPADTRVFLFHSPNAAADASGAMDKVNAWLGKDRTNSAYPNLKITDITVTSDGSGGVYTLVVCNLGASKPREDF
Ga0182738_1296030	Ga0182738_12960302	F070358	YLDHRARIADIEINPLVLRPDGEGACAVDVRVIWR
Ga0182738_1297044	Ga0182738_12970441	F025080	LSCRLEPDTMISFATDFRALWIALMTMLAGATSVAAQSAPTGCPPPRTIYTFTDSSSIQALPGAPAPFCRFANVNGGQQVDLFLGAFSAASPIVQANIDVLTTLLPLQVGKAVHLVRAGTGDKGWQANVSVEKYESVEVPVGRLNCFVLLWTEPSGQGRWERRWWYCPSLEYAAKYSARFEIVSPGGRTLSSSPTSWELAGIRVP
Ga0182738_1347135	Ga0182738_13471351	F011188	KTARHIWPVVTEDNIIHAQGGGELDTYNIYMDELPAGEEIDGEEMIEVEFRVVPGSDDENDPENNAVIAGLDLVDLINLRDALQQEIDNYALSALEAEANRLAEDMG
Ga0182738_1378855	Ga0182738_13788551	F047589	RLCGETGFTASSEHSLGGRLIDWRREHAKVCKEWPRYAEQKGLNLDCNGALLYANEDGPYEPRVRPRYEDEEVDDQPAERILPRFDLMSVPAHELAQTALF
Ga0182738_1382009	Ga0182738_13820092	F057460	GQPPQIQHTVLVQTPKGKAVSYCPDEISVEGKLTVREKKEDGFIISIFELEAGSVKPVAP