3300017648: Enriched Miracle-Growth compost microbial communities from Emeryville, California, USA - eDNA 3rd pass 37_C BE-Lig MG (version 2)

Overview

Basic Information

• IMG/M Taxon OID: 3300017648
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0127392 | Gp0191726 | Ga0180216
• Sample Name: Enriched Miracle-Growth compost microbial communities from Emeryville, California, USA - eDNA 3rd pass 37_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: 539597735
• Sequencing Scaffolds: 17
• Novel Protein Genes: 17
• Associated Families: 14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	5
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Acidothermales → Acidothermaceae → Acidothermus → Acidothermus cellulolyticus	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Boseaceae → Bosea → unclassified Bosea → Bosea sp. 32-68-6	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. 200	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
Not Available	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?
F002119	Metagenome / Metatranscriptome	591	Y
F007999	Metagenome	341	Y
F011188	Metagenome / Metatranscriptome	294	Y
F014051	Metagenome	266	Y
F036417	Metagenome / Metatranscriptome	170	Y
F036582	Metagenome / Metatranscriptome	169	Y
F037930	Metagenome / Metatranscriptome	167	Y
F054147	Metagenome / Metatranscriptome	140	Y
F060456	Metagenome / Metatranscriptome	133	Y
F068021	Metagenome / Metatranscriptome	125	Y
F081030	Metagenome	114	Y
F090842	Metagenome / Metatranscriptome	108	Y
F092498	Metagenome / Metatranscriptome	107	Y
F098955	Metagenome / Metatranscriptome	103	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0180216_1000859	All Organisms → cellular organisms → Bacteria	29015
Ga0180216_1002270	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	16264
Ga0180216_1003753	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	11842
Ga0180216_1017828	All Organisms → cellular organisms → Bacteria	3847
Ga0180216_1029627	All Organisms → cellular organisms → Bacteria	2599
Ga0180216_1040617	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Acidothermales → Acidothermaceae → Acidothermus → Acidothermus cellulolyticus	2054
Ga0180216_1057316	All Organisms → cellular organisms → Bacteria	1587
Ga0180216_1075820	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1285
Ga0180216_1076649	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1275
Ga0180216_1078554	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1251
Ga0180216_1096497	All Organisms → cellular organisms → Bacteria	1069
Ga0180216_1099027	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1049
Ga0180216_1124594	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Boseaceae → Bosea → unclassified Bosea → Bosea sp. 32-68-6	879
Ga0180216_1156328	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	736
Ga0180216_1165819	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. 200	704
Ga0180216_1185698	All Organisms → cellular organisms → Bacteria → Proteobacteria	645
Ga0180216_1197114	Not Available	616

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0180216_1000859	Ga0180216_100085927	F098955	MDPSAIPVFLAGPFPVIHSARIRPVEEEIELDVGLIIGGLPSILAATVFPLDDSWERVNAALASGDARLGVAGMLHEQESPTGEFEVFPSAYVGLECANGERLILAHIRSPDPDQEPEAFAREVIAALLNGQTPADLGELIDD
Ga0180216_1002270	Ga0180216_10022709	F011188	MMDTYNLYMDEIPADDGDDAETVDVEFRVVPASEDTSDDDNTPVVAGLDLVDLINLRDALSQEIDNYALTALEAEATAALGAEE
Ga0180216_1003753	Ga0180216_100375312	F092498	AGPAAAREDAVAFARSLTQGAVMPGFDWSGWLVSITDEHGRQVDEVPIDAVG
Ga0180216_1017828	Ga0180216_10178281	F014051	ATKDDGLPQKKIEAVAALMKKIGAIKEDKQPVKFSDFVDQSIWKDANAKVK
Ga0180216_1029627	Ga0180216_10296273	F037930	MTTFTKSGKPKRSIASMQIERRYRNVLTLFLSGQLPNFNHQRHVHVANILKHIPYGRELMHLGLQTMTYRQFVVGKYSAEITDFYWDQLDGTLPDPSLFEDLPGGADGTKGAAPAACGQPGAEA
Ga0180216_1040617	Ga0180216_10406171	F014051	TVTGHSKEICKEALKEFLAIDFWATKDDGLPQKKIDAVAALMKKVGAIKEDKQPVKYADFVDQSVWKDANAKVK
Ga0180216_1057316	Ga0180216_10573162	F007999	LETPSARGAKARENLVAALKECGELADAVATFQGKELLEVLDYLDSLRFVMAESGQLLQGVTRGEI
Ga0180216_1075820	Ga0180216_10758202	F054147	MAKRDPDHDKDQELDPAGERGGDTGPSSYKDDGPQAEKGDLRRDTPVHSGPTRSGAKRHSRSGSDSNES
Ga0180216_1076649	Ga0180216_10766492	F090842	VPRIFDVILRREREYPPVPKCPDHKRDMILRGKMGRPTRFEDQSEELYTLIYYCPVEGCNQTATIDRVNTQIPVPGAAPARPPYARRNY
Ga0180216_1078554	Ga0180216_10785542	F090842	MPTLLDRIFRQNLEEPEIPICPDHKVEMRLRGKLGKPTRFFEQTESEYTLIYFCPVEECNETANRIATRTQIPVPGDTPDRPSYSRKGEIESL
Ga0180216_1096497	Ga0180216_10964972	F036417	STVPYRTRIPTVVVRLATDEGEITFRARWSRAAIELQRRILYRLRQGKPLWFEDEWGHAMCFKPEAVWGAVVDGRPSS
Ga0180216_1099027	Ga0180216_10990272	F036582	VSNPRFQASFAEFCEVTAAWRRRKADEYDRDERNLRTAAALDDLAAHVRALPADDARLVELHRLAASGDDFQPDQRVLYELGRFRFHHPETGLDAFLDTLVELAIADRGEMGRFGGRLPEGDDPWG
Ga0180216_1124594	Ga0180216_11245942	F060456	MPPSLTKEALDYLVASAGLDLDEAQKADLASIHEDLQVMKALVRQPRGHMAELAHTYGFTEEDLA
Ga0180216_1156328	Ga0180216_11563281	F002119	VGVSAKEAVLNVFASLVKPLMRVAFEYGITASEIAGVVRRTYIQSLEKRLLEQKRPTTDARLAIVGGLSRSEVVALREALRAGAPHSMRGGVSLDQITSLLTVWHTHPNFSGAYGLAMDLDLVPIPDSPRRHFRELVEIACPNVDRDALLDELVAAGSVEVIDSS
Ga0180216_1165819	Ga0180216_11658192	F081030	VVALLATGLLAAWTARACLQAQQRDSPPSDVLVWSALAAVFVGYSQLKLVRGLGWLTGFGGWLRSLARQHGLYADRRAFQIIATVAVALGVIVLFVYGLMWIWHYIKRYRLAIGFASLAVGFGLIRFISLHEVDAWTAANPWARPLIELVACAGASTLALVRLHQLGELPRLFQRFRA
Ga0180216_1185698	Ga0180216_11856981	F068021	MICSGCGIGINIDTNRLANLADELQKATAKVPPEITVKFYR
Ga0180216_1197114	Ga0180216_11971141	F014051	VTGHSKEICKEALKEFLAIDFWATKDDGLPQKKIDAVAALMKKVGAIKADKEPVKYADFVDQSVWKDANAKVK