3300012886: Microbial communities from bioreactor (seeded with sewage sludge) at Lawrence Berkeley National Lab, California, USA - Biofuel Metagenome 8 (Illumina Assembly)

Overview

Basic Information

• IMG/M Taxon OID: 3300012886
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0046201 | Gp0191377 | Ga0160425
• Sample Name: Microbial communities from bioreactor (seeded with sewage sludge) at Lawrence Berkeley National Lab, California, USA - Biofuel Metagenome 8 (Illumina Assembly)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: Y
• Use Policy: Open

Dataset Contents

• Total Genome Size: 407855438
• Sequencing Scaffolds: 18
• Novel Protein Genes: 21
• Associated Families: 16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia	1
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula boonei	2
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → unclassified Methanoregula → Methanoregula sp. PtaU1.Bin051	1
All Organisms → cellular organisms → Bacteria → PVC group	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula	2
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Candidatus Koribacter → Candidatus Koribacter versatilis	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes	1
Not Available	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Microbial Communities From Bioreactor (Seeded With Sewage Sludge) At Lbnl, California, Usa
• Type: Engineered
• Taxonomy: Engineered → Bioreactor → Anaerobic → Unclassified → Unclassified → Bioreactor → Microbial Communities From Bioreactor (Seeded With Sewage Sludge) At Lbnl, California, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Water (non-saline)

Location Information

• Location: USA: Berkeley, California
• Coordinates
  • Lat. (^o): 37.82
  • Long. (^o): -122.29
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F004177	Metagenome / Metatranscriptome	449	Y
F010231	Metagenome	306	Y
F011098	Metagenome / Metatranscriptome	295	Y
F025048	Metagenome	203	Y
F030458	Metagenome	185	Y
F031889	Metagenome / Metatranscriptome	181	Y
F032286	Metagenome / Metatranscriptome	180	Y
F041367	Metagenome / Metatranscriptome	160	Y
F051629	Metagenome / Metatranscriptome	143	Y
F063257	Metagenome / Metatranscriptome	129	Y
F067178	Metagenome	126	Y
F083634	Metagenome	112	Y
F084897	Metagenome / Metatranscriptome	112	Y
F089576	Metagenome	109	Y
F089856	Metagenome	108	Y
F106182	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0160425_1000052	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia	193616
Ga0160425_1000088	All Organisms → cellular organisms → Bacteria	155069
Ga0160425_1004141	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula boonei	10030
Ga0160425_1006593	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula boonei	6812
Ga0160425_1007579	All Organisms → cellular organisms → Bacteria	6070
Ga0160425_1010511	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	4578
Ga0160425_1012328	All Organisms → cellular organisms → Bacteria → Proteobacteria	4007
Ga0160425_1013558	All Organisms → cellular organisms → Bacteria	3717
Ga0160425_1017055	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → unclassified Methanoregula → Methanoregula sp. PtaU1.Bin051	3068
Ga0160425_1018929	All Organisms → cellular organisms → Bacteria → PVC group	2815
Ga0160425_1018996	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula	2806
Ga0160425_1022492	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Candidatus Koribacter → Candidatus Koribacter versatilis	2441
Ga0160425_1032018	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1809
Ga0160425_1045806	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1345
Ga0160425_1055696	All Organisms → cellular organisms → Bacteria	1143
Ga0160425_1099320	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes	706
Ga0160425_1101940	Not Available	690
Ga0160425_1114880	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula	625

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0160425_1000052	Ga0160425_1000052102	F011098	VRRASLGRAIAESVVPGLTCLVLAAAVITALGWWFHAHYALSWQSPVAVHFQLPFVLAERTVSEGALQAQADQQGRGLTAWQQYACRKFGPDCRVALAIQRAENAAGKCEIYHYNTDGTLDWGYFQINTVHLKRPGLNLRDLLDCKANIDFAYQLFREKGGFTPWSTYKDGRYLRYMGVNR*
Ga0160425_1000088	Ga0160425_100008824	F025048	MLNPTLITDAIASVLLSIPELYAAMGGRITAFHYRLGQEHRLAEAIYKMPAPSMLIVWEGTKGGSFDGQTIWKHRWGVYYRMGNAAGVAEPVGYEDLWWITCNCPPGGSGPNIRYLQLYPGLDIMDTPSIDHELDEDLIDRFKGLFIIPEIGDN*
Ga0160425_1000088	Ga0160425_100008827	F031889	MYGDIPAAGITIRVPNPPKTAQLRLPTNEEMLERLDQQRSIRRTIGRRKSQTEFVPNLKADLDLFSKIRLDEDGAEFDEFEAGNAISKLSFCEVTDCQRAGDEYRVTLRTPFGETVHMVKIPTQRDITVYRRTVVSSTDLPHGQEELRYRIEPAVDLYDSVVTKIEGYAASIKPADVPPHHKSAVVVELVQAIDDLDPALDPNS*
Ga0160425_1000088	Ga0160425_100008828	F041367	VHAADLCDGGADGPRGCPDANDVTCGKCGLARTVDDTNAPGACPQCGGWQFTVNRCAHCKLDDLDYARTHSHAGRLFERVLELEFDAAHFSIPWSDVTAEEVRGLQILKEERERYQREQMQKRTGGSPLCA*
Ga0160425_1000088	Ga0160425_100008829	F030458	MPFQARITRARFVLGPFTAEDMQTLGGVLVDSISTRIRKALNVNDAPAKALKPGRNGRRGYPDYKASHGLMPVRDWVWTGRTLRSLKVKSVNENQAVIGFVNPNADRIAHANNLREKQFGVSPKDRSALNAAVLALLRQARAIRVKRAA*
Ga0160425_1004141	Ga0160425_10041413	F089576	MFGLPDITILVFGGVTLVAFVALLYWGLTFKGHD*
Ga0160425_1006593	Ga0160425_10065932	F089576	MFGLPDITILVFGGVTLVAIVALLYWGLTFKGHD*
Ga0160425_1007579	Ga0160425_10075793	F089856	MTAIRFLAPLFAAATLTGCINVMNNRPTGVSSIPCTYRFKALSRPEDQSRVEAAIHSVAVGSVVKAGTVSYPEYRFRVARMADLDRLHPQLLFNNPQAFIPSTLRQSLNLRGGGVDMTFDSTDVSASATLTLTFAVKPGSRLYYKNPGGYESDITARVDKKGRVVLPVTVKEGQRYLYARAMKDNVVRYIRINIFTNHVEDIPKHQY*
Ga0160425_1010511	Ga0160425_10105111	F010231	RLCAMAADVQFGGFAPAFTLSFYDSECSRNPPNAHSLGR*
Ga0160425_1012328	Ga0160425_10123283	F004177	LIDRSAHARIKSIRQRAGCPRPPRKIVANPAMSLTWDLPMVINPGDVWIIEEPMWENSADSTSISNASALATATMSLPTNNYVTTGMLAAGFTVDTNGNESPDGDAPIREDWVFGADGLSKVAGLVFQMQGTLGIESNAAQRLYLNRPVTVGDVKGYVQAAPTGSGLTFTIYVGGTVWLTLTIPAGQTAVVATPSQISTLTQIPANTAVSIGISAVGTTFPGASLSVFIYS*
Ga0160425_1013558	Ga0160425_10135581	F010231	TRLWALAGDVHSGGFAPAFTLSFHDSECSRKPPNAHSLGR*
Ga0160425_1017055	Ga0160425_10170556	F083634	MDGGANPQINLDHIRIGGRICHLARKLIVTVEYEDDRLTFSNEEFGLVVSAETLEEGIAGLSGELAVLWEVYVGADPANLTADALRLRNNLTTLVPAGVSP*
Ga0160425_1018929	Ga0160425_10189292	F084897	MAKSDAFAETSKARFEVATAQEVNLGVGGSFKAAEIGVLGTSGGGLKD*
Ga0160425_1018996	Ga0160425_10189962	F089576	MFGLPDITILVYGGVTLVAIVALLYWGLTFKGHD*
Ga0160425_1022492	Ga0160425_10224922	F063257	MAIMKPHPGKRPDLIAFLREFYTMMCTKQYSRDLLLQDLKHPDDLVHIRYWLSDEARDAAMNDPDVHHYWKDLGAFGNITTIYEELEPIFSTREGIPGDDIIQAATKSDSA*
Ga0160425_1032018	Ga0160425_10320182	F051629	ETTKEQKQFLFAALAKANNVREISVRRAPIERLVNWTAATLTLPDQIANNLLQDYLLHDHRAMIVSYVESLGIPHSDGIIEEGFDLASLPKERVQDAARTLLASPDRQAAELYLKYLVVQGGPWSVIEEVLPTGDA*
Ga0160425_1045806	Ga0160425_10458061	F067178	MVASEVGITVSVELLVRHAHLSLATILVYRSLLALALLALIVRPARNQWLPRSPRLALLRVVTGGLTFIGWFGAIGLLSGRVTQSVLLLDSLILAYVRGDHRSYERRTLFVLTTALILFAAQAVREPGTILNAGRGIVFLTIALASRAATYKVWERAQRKDEHLFWLIAPALLGGALGGVFLGVASQSGIQRLSPLMWCAMLLVAMVGLTGYFYMNTVMSLLGAFYTRVVELWQVPMLWAIHLLTDYAGIDWLQGALGTLVACASAYAYLQHRRGQIPKIQPR*
Ga0160425_1055696	Ga0160425_10556962	F106182	MKWMDRLFAWMLVALGGAHLLALWIPKLGLLRGPWTGGAAVAIISAGLMNAVRSRRKSDRFLRWCTALATLLTAAMCLITLYRFSGNVLHQPAALAISVLAVVEL
Ga0160425_1099320	Ga0160425_10993201	F032286	MVKWVCQIVTHIRHRALIFDTRLFDGNAADDTLVTGGTFRFCRLMCLCVKRRNIMLNDKRRSLLNSALFRADNRTGQKTFSPFSLALIFTFVFAALSERRSCPEDRSRRFVPVGTLTLSRSWRLLRWGTYPVRTVMQFSRFRCDCKTILAKNIALSRISKRSENAPKNANFHAY
Ga0160425_1101940	Ga0160425_11019401	F083634	MYIMLKMADQTISLDRIKINGRVCRLARKLIVTVEHENDRLTLSNKEFGLVVSAETLEEGITGLSEELASLWEVYVDADPANLTADALRLRSNLTSLVPA*
Ga0160425_1114880	Ga0160425_11148802	F089576	MFGLPDITILVFGGVTIVAIVALLYWGLTFTGHD*