3300005872: Bulk soil microbial communities from Harvard Forest, USA - 3Bulk_unsorted metaG

Overview

Basic Information

• IMG/M Taxon OID: 3300005872
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053064 | Gp0104122 | Ga0058710
• Sample Name: Bulk soil microbial communities from Harvard Forest, USA - 3Bulk_unsorted metaG
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 174100691
• Sequencing Scaffolds: 22
• Novel Protein Genes: 25
• Associated Families: 23

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	7
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	5
All Organisms → cellular organisms → Bacteria → Acidobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → unclassified Hyphomicrobiaceae → Hyphomicrobiaceae bacterium	1
Not Available	2
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Sphingobacteriia → Sphingobacteriales → Sphingobacteriaceae → Mucilaginibacter → unclassified Mucilaginibacter → Mucilaginibacter sp. BJC16-A38	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Propionibacteriales → Nocardioidaceae → Nocardioides	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Micromonosporales → Micromonosporaceae → Hamadaea → Hamadaea tsunoensis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → Rhodanobacteraceae → Dyella → Dyella jiangningensis	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Rhizosphere And Bulk Soil Microbial Communities From Harvard Forest, Usa
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Unclassified → Forest Soil → Bulk Soil → Rhizosphere And Bulk Soil Microbial Communities From Harvard Forest, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): forest biome → land → bulk soil
• Earth Microbiome Project Ontology (EMPO): Host-associated → Plant → Plant rhizosphere

Location Information

• Location: Harvard Forest, Massachusetts, USA
• Coordinates
  • Lat. (^o): 42.5502
  • Long. (^o): -72.1737
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001621	Metagenome / Metatranscriptome	662	Y
F002800	Metagenome / Metatranscriptome	529	Y
F004499	Metagenome / Metatranscriptome	435	Y
F004872	Metagenome / Metatranscriptome	420	Y
F005285	Metagenome / Metatranscriptome	406	Y
F006165	Metagenome / Metatranscriptome	380	Y
F019008	Metagenome / Metatranscriptome	232	Y
F021384	Metagenome / Metatranscriptome	219	Y
F024370	Metagenome / Metatranscriptome	206	Y
F027788	Metagenome / Metatranscriptome	193	Y
F031231	Metagenome / Metatranscriptome	183	N
F035930	Metagenome / Metatranscriptome	171	Y
F037600	Metagenome / Metatranscriptome	167	Y
F041374	Metagenome / Metatranscriptome	160	N
F064162	Metagenome	129	Y
F075110	Metagenome	119	N
F086112	Metagenome	111	Y
F087502	Metagenome	110	Y
F088441	Metagenome / Metatranscriptome	109	Y
F095863	Metagenome / Metatranscriptome	105	Y
F097709	Metagenome / Metatranscriptome	104	Y
F097869	Metagenome / Metatranscriptome	104	N
F105481	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0058710_1000557	All Organisms → cellular organisms → Bacteria	975
Ga0058710_1000710	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	925
Ga0058710_1001261	All Organisms → cellular organisms → Bacteria	809
Ga0058710_1001616	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	765
Ga0058710_1001683	All Organisms → cellular organisms → Bacteria	756
Ga0058710_1002112	All Organisms → cellular organisms → Bacteria → Acidobacteria	717
Ga0058710_1003149	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → unclassified Hyphomicrobiaceae → Hyphomicrobiaceae bacterium	653
Ga0058710_1003380	All Organisms → cellular organisms → Bacteria	643
Ga0058710_1003453	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	639
Ga0058710_1003877	Not Available	622
Ga0058710_1004833	All Organisms → cellular organisms → Bacteria	592
Ga0058710_1006795	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Sphingobacteriia → Sphingobacteriales → Sphingobacteriaceae → Mucilaginibacter → unclassified Mucilaginibacter → Mucilaginibacter sp. BJC16-A38	547
Ga0058710_1006961	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Propionibacteriales → Nocardioidaceae → Nocardioides	543
Ga0058710_1007385	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	536
Ga0058710_1007704	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	531
Ga0058710_1007755	All Organisms → cellular organisms → Bacteria	530
Ga0058710_1007947	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Micromonosporales → Micromonosporaceae → Hamadaea → Hamadaea tsunoensis	527
Ga0058710_1009022	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	512
Ga0058710_1009370	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → Rhodanobacteraceae → Dyella → Dyella jiangningensis	508
Ga0058710_1009434	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	507
Ga0058710_1009620	All Organisms → cellular organisms → Bacteria	505
Ga0058710_1009742	Not Available	503

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0058710_1000192	Ga0058710_10001922	F105481	AQQNWILKVQDDTVWGLVCGPCTPAVVAMVDEGRVDGDTVRFHINHIDTPPNAARRGIQRNVMTGTLPTPGNGNVMKFRWVAEQSPTQTGEIVMIGPIR*
Ga0058710_1000557	Ga0058710_10005572	F086112	VLLSQAIGIMGGRNAPVLPPYGRWFSRLGLKMLAGVDMPSHLADFLAHGSVVDCSRLGAEFGWKPAFSSRQAMDALARGRQMEQIEPPSPPQEYELQVYLQQRRRRARFLN*
Ga0058710_1000710	Ga0058710_10007101	F027788	MTTVGSSAADALLGAVAVTLLVVMYGQWLYRSRRLRRCQERLRVVRELIADGERTKTAYADASDASAAHGGFLQRCDSSLRDQFGDSFARRIAAYSEFEWIQPASLISNEQVFAWYDTERRLAGLRELLYEALLDLGEASLDLGSLVE*
Ga0058710_1001261	Ga0058710_10012611	F064162	MHGRKDQKNANESGNTVSGESDEQALTRDLKRFVEESDLGIPKIASKMGVFSATLSMWIAGTTKPSRTELLAIKSFLERRG*
Ga0058710_1001344	Ga0058710_10013442	F087502	MLMPDSVLAAIIAGSATLSASLLQLRSALLREAAARSSSSASRRKSRV
Ga0058710_1001616	Ga0058710_10016161	F006165	QGWCAFVGIVHGPSATMERAMKTLIADRAVSAERALNTAIVNADITRGFEEYLALVDQYYAEDVEVSTDTSPDPLVGKDQLKSLLLRFLVPLHMMAEIGGLWVSVHEASIPGDSLDEQHSEWSLELIGVTGRRVTAAWCARRTWKQSRVVSEYHYAHRQDGEPLSFDDLRIAAPPDPDTVTPS*
Ga0058710_1001683	Ga0058710_10016831	F088441	YFACSDQTGLARVAMPQGTYGLDVLKTGYEALSRVLDVNGDVTVEVEVAVTSPENPDAYWLFDPTA*
Ga0058710_1001683	Ga0058710_10016832	F004499	MMSTFKTVVAAVAVGLLLIAAVAWAASDEKTITGVISGVNPTTRIATLTPAGGPPIVVQFAFNVGGPCNTCLGSGRSGPTFAETVTEGSTWTLTYTSSVPAGAAAWFPGGTVNTVLRAVPVK*
Ga0058710_1002112	Ga0058710_10021121	F004872	VPLARLWQLPDGTSCLLLKDDRAGNWQLRVIRGGDTLRSEHFGSPIVAMDQAKQWRTLYDDSVEPTS*
Ga0058710_1003149	Ga0058710_10031491	F037600	THADERVLGGMSGSPIVATSGRAIGVVCTITSPRDGGPNARLSHNLPGWLLRDTL*
Ga0058710_1003380	Ga0058710_10033802	F005285	KAGVHRVGGDRMVGSWSDMNQGSRSGEGAAFMVSRRPEEPRPEGDRASIVAWKRGNARGAKGGRKVEA*
Ga0058710_1003453	Ga0058710_10034532	F019008	MGKEALGFALLGVVALGIFAHSFLPRYEWREVRETSAISIIVYDRWTGRIQRAVYDDKGGLNVMGVYTPF*
Ga0058710_1003877	Ga0058710_10038771	F021384	MSTQNQPPEYGLLRPAEGSRANPQFVHDPYPRVIDWGMPEDVHAGDFTFAVLEAALAAGASEIQLTPIEEFGEVSVHFKIDAAYIRQESLTQIQFGLIAILLAHIATPRRYDLESPPLIRSFRTKDGIEYYVRYSKIRVADNNTAILIRLLIKENGTQTAA
Ga0058710_1004833	Ga0058710_10048331	F041374	QHSEWSLELIGVTGRRVTAAWCARRLWKQSRVVSEYHYAHSQDGGPLSFDDLRIAAPREPDTVKPS*
Ga0058710_1006795	Ga0058710_10067951	F097869	MAADASWADILVMRNPDGSPDTFRQEETVALLSDEQIDAIRPFAEELELPADQLVLREGQTELDFLVVLRGGIEFSATDSFGKKNIPVVRLPERSFTGDLSCFTNTPLVGDGRTTGATRI
Ga0058710_1006961	Ga0058710_10069611	F024370	HPHFTPDINLGHLVQAVVVVTTVGGGILAGYLSLRGDVDLQRAEFRATLAGHEARLTVAEHQLQERHAEDRQFQAETRAALDRLLEAIGGLRTELVQKQNRK*
Ga0058710_1007385	Ga0058710_10073851	F041374	EVSTETSPEPVVGRDRLKSILFGFLGPFHMIAEIGGLWVTLRGTSIPSDSIDEQHSDWTLELIGVTGRRLTSTWCARRIWKQSRVVSEYHYAHSQDGEALSFDDLWIAAPRDPDTVMPS*
Ga0058710_1007704	Ga0058710_10077042	F097709	SALLWALARMREGADPGSLIAEAARHGIDIAALPAFAARLR*
Ga0058710_1007755	Ga0058710_10077552	F035930	MEDRIRLITHKGKAILLVDASHCSATELLKLSRMVPLYVKPEPRGSV
Ga0058710_1007947	Ga0058710_10079471	F031231	DKACASSLAGAQTRGDHLTIAEALKCRARIERERGAFHESIATLRIGIFEAEGLEDRLLQAEMLREFGQTSRELGNSADARLAWREAAESFEDVGAQHEAAEINALLASLPS*
Ga0058710_1009022	Ga0058710_10090222	F001621	VNAPVPKYVAQGRAAVLLGIPEEELSRISNESGFGHRERAGNEEETFYTYEELRKICQLAVYQVH*
Ga0058710_1009370	Ga0058710_10093701	F002800	DGTAVVTLAHTSEAGLFRNGAFTAITAVGQTADCWTTRVGKYVFTANTGSKTISRLIGTGNNVFVDSSVAASIATGGAPADIDTDAGVLGVIDHGAGQSHLSLFTYNEFGELVASGAPITLGVANANGVAIMSPPDVDER*
Ga0058710_1009434	Ga0058710_10094341	F075110	MTVYVLVREDQSEHGFVDASIVGLFRTQDEATVVLKSSVAEAREQGLRVCGDPGTEPEWEVSWNIEPHPLR*
Ga0058710_1009620	Ga0058710_10096201	F041374	DSLDEQHSEWSLELIGVTGRRVTVAWCARRTWKQSRVVSEYHYAHTQDGEPLSFDDLRIAAPRDPDTVTPS*
Ga0058710_1009742	Ga0058710_10097421	F095863	TAEPKSLPSYIPFQTTQASVTEINKERLKFERVATRFSVIMGVIPALAFLFSGVTALPGFAVPCILVGAWIFGAFLAYVSSLFVLNRFCPWKKLVLTAVFDGILPKVTREKARAAKDHFDGLYLVVDQQQRWKSSLLPDPRPRALDPLLIGELKQGRCRKFFLIHQF