3300031495: Metatranscriptome of soil surface biofilm microbial communities from soil inoculated with nitrogen-fixing consortium DG1, State College, Pennsylvania, United States - MICR_N_R2 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300031495
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0132857 | Gp0330679 | Ga0314817
• Sample Name: Metatranscriptome of soil surface biofilm microbial communities from soil inoculated with nitrogen-fixing consortium DG1, State College, Pennsylvania, United States - MICR_N_R2 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 48180715
• Sequencing Scaffolds: 18
• Novel Protein Genes: 21
• Associated Families: 20

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	8
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei	1
All Organisms → cellular organisms → Eukaryota → Amoebozoa → Discosea → Longamoebia → Centramoebida → Acanthamoebidae → Acanthamoeba → Acanthamoeba castellanii → Acanthamoeba castellanii str. Neff	1
All Organisms → cellular organisms → Eukaryota → Amoebozoa → Amoebozoa incertae sedis → Stereomyxa → Stereomyxa ramosa	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → BOP clade → Pooideae → Triticodae → Triticeae → Hordeinae → Hordeum → Hordeum vulgare → Hordeum vulgare subsp. vulgare	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → malvids → Brassicales → Brassicaceae → Coluteocarpeae → Noccaea → Noccaea caerulescens	1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae → Phycisphaerales → unclassified Phycisphaerales → Phycisphaerales bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	1
All Organisms → cellular organisms → Eukaryota → Haptista → Haptophyta → Prymnesiophyceae → Coccolithales → Coccolithaceae → Coccolithus → Coccolithus braarudii	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Soil Surface Biofilm Microbial Communities From Soil Inoculated With Nitrogen-fixing Consortium Dg1, State College, Pennsylvania, United States
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Freshwater → Groundwater → Unclassified → Soil → Soil Surface Biofilm Microbial Communities From Soil Inoculated With Nitrogen-fixing Consortium Dg1, State College, Pennsylvania, United States

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): terrestrial biome → land → biofilm material
• Earth Microbiome Project Ontology (EMPO): Unclassified

Location Information

• Location: USA: Pennsylvania
• Coordinates
  • Lat. (^o): 40.7997
  • Long. (^o): -77.8629
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000240	Metagenome / Metatranscriptome	1481	Y
F000344	Metagenome / Metatranscriptome	1257	Y
F001633	Metagenome / Metatranscriptome	660	Y
F005444	Metagenome / Metatranscriptome	400	Y
F005592	Metagenome / Metatranscriptome	395	Y
F006377	Metagenome / Metatranscriptome	374	Y
F007020	Metagenome / Metatranscriptome	359	Y
F011252	Metagenome / Metatranscriptome	293	Y
F017262	Metagenome / Metatranscriptome	241	Y
F035212	Metagenome / Metatranscriptome	172	Y
F039900	Metagenome / Metatranscriptome	162	Y
F040485	Metagenome / Metatranscriptome	161	Y
F043177	Metagenome / Metatranscriptome	156	Y
F050966	Metagenome / Metatranscriptome	144	Y
F067854	Metagenome / Metatranscriptome	125	Y
F069732	Metagenome / Metatranscriptome	123	Y
F085198	Metagenome / Metatranscriptome	111	N
F087976	Metagenome / Metatranscriptome	109	Y
F100115	Metagenome / Metatranscriptome	102	Y
F105419	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0314817_102820	Not Available	1586
Ga0314817_105582	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium	1106
Ga0314817_112411	Not Available	734
Ga0314817_112815	Not Available	724
Ga0314817_113892	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia	698
Ga0314817_114088	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei	693
Ga0314817_114548	All Organisms → cellular organisms → Eukaryota → Amoebozoa → Discosea → Longamoebia → Centramoebida → Acanthamoebidae → Acanthamoeba → Acanthamoeba castellanii → Acanthamoeba castellanii str. Neff	683
Ga0314817_115521	All Organisms → cellular organisms → Eukaryota → Amoebozoa → Amoebozoa incertae sedis → Stereomyxa → Stereomyxa ramosa	664
Ga0314817_116730	Not Available	642
Ga0314817_117483	Not Available	629
Ga0314817_117756	Not Available	625
Ga0314817_119569	Not Available	597
Ga0314817_119601	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → BOP clade → Pooideae → Triticodae → Triticeae → Hordeinae → Hordeum → Hordeum vulgare → Hordeum vulgare subsp. vulgare	597
Ga0314817_120692	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → malvids → Brassicales → Brassicaceae → Coluteocarpeae → Noccaea → Noccaea caerulescens	583
Ga0314817_122114	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae → Phycisphaerales → unclassified Phycisphaerales → Phycisphaerales bacterium	566
Ga0314817_122845	All Organisms → cellular organisms → Bacteria → Acidobacteria	557
Ga0314817_124082	Not Available	544
Ga0314817_125357	All Organisms → cellular organisms → Eukaryota → Haptista → Haptophyta → Prymnesiophyceae → Coccolithales → Coccolithaceae → Coccolithus → Coccolithus braarudii	532

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0314817_102820	Ga0314817_1028202	F039900	MDSSLAPSDRDLSDYVLSDYRTFSEMETEADIPVPDRLLPRSECRRLVEALKLSQKIGLLLWLNRAELITLGGRERLLYLQAKASFEALEAGLRFARRLTEEGKLRSDFKHQLRELNRRPQSKHFRQAEARRIGVGYRDKGMLPDSSLRARRQAHEESWIRADLVPLLLLNSLKLIHPAILSEDGEWVDLSMVPGSFGTQRDIGVRSYLLPPL
Ga0314817_104751	Ga0314817_1047512	F000240	RMRAVAVVLLFAAAVYAAGDAWPYTAGIGGYVPTSTPFDNPKTLTERTPTIPNSPDCSVRPQTVVEIQRMRESASRIAQMIEAEVQIMNKRKSFFEQMTTYLNDRIRELNKVKSELAEETRWIEVSTNRIQELAEREKLVKMQDILACLNGDKKTLADESSAQASTIEALKSQSEAVSKRIAEIKAKIEAAAEGKDAGGSGDKGGDE
Ga0314817_105582	Ga0314817_1055822	F105419	MRKFIALSALLVAAAASNGCISTTMYGCEITETLAPGASEGEVVMKHGAPDNIVYLGGQYFNPQTGERGEVDKYLYEYRIGGGTTLLGKVFASDEFHNIAYLIEGGRVMGGGYVGEGKGSIILGMGGILSTPLGVIDLRMGGFLHPKARAGYGGDGNPMGEADTVSEDN
Ga0314817_111677	Ga0314817_1116771	F000240	LETKGQAMRAVVLVVLFAASALAAQDAWPFSAGVPGYVPTATPFDNPKTLTERTPTIPASPDCSVRPQTVVEIQRMRESASRIAQMIEAEVQIMNKRKTFVEQMTTYLNDRIRELNKVKSELAEETRWIEVSTNRIQELAEREKLVKMQDILACLNNDKSTLSQESTAQASTIEALKSQSEAVQKRISEIKAKIEAANEGKEAKGGSGGDS
Ga0314817_112411	Ga0314817_1124111	F040485	PLMRCLIAIAIFAFIAVAFGANPAAPSWPNAFAASVWAQDNQGRPPRFFRWYYDATKMKERFDGVVPWNDEQYFAEQIRDFTTDKQYDVFYQQEYASCYTHPINGTVPHPNFAQFSYIGQALVQYEPVYHWGYFDRTNNMTFNYFDSQDAREPKRFDLADLNRGWEETWVFMGFDAQPQDAEVFVVPSTLLPLCNQVTVPPQKY
Ga0314817_112815	Ga0314817_1128152	F035212	MEPIEGRNALEQGLHVLEQYNDPELVEAYRAYMQRLEELVGREYLDTYALVYQRERRQLYGQAAGATISPAEQVVRDTVAADPQVHALYDQYIALAKSHGIADPEFDSADQQ
Ga0314817_113892	Ga0314817_1138921	F000344	MRPKHPHAVESGVGKHNTRESERVQACAAGKERVTNA
Ga0314817_114088	Ga0314817_1140881	F001633	TVLTVAGRELSSEASAPGSDAPCRERRAGRGVDTPATFIFRVGTFYRGVGISLWLIVGPALRV
Ga0314817_114548	Ga0314817_1145481	F005592	QHNMGAGSVKGLLLMETIFPSGDNSTVFDDPKMKQKLMAEIKKGKIKPQTASDEIDVDEDQDSKIDAQAQEIWSYYDPKGLGTINKKQVQQFFKDCFTLHCLRKHQKEKEALGMGISMKVALDTATKMLDPSGQGVVSKQTFIDFLNEVDLVELLGPFTGQTGPRSINSRLPQNMMFDPSTLPKDAGGKVNLGEVKYRDYNQTLE
Ga0314817_115521	Ga0314817_1155211	F005444	FATTKSKKMKLIVVLLLCVAVCALAQTPQKPIWPNGWSATVRVHRSDERHPSFFRWFWDRSQNKDRIDGVAKWKDEFYLAERIFDHNAGKAYDIFYQEDAVNCFDRKINQTDLPKPTFSQFQYIGKALVNYQPAYHWVYEDKLRGFLFALYDRQDNREILRIDIDDITRRRAESWIFLEYDIGPQGKEIFEIPQIILDQCNDF
Ga0314817_116730	Ga0314817_1167302	F069732	CDVKDKQKCCKCGAKGAKRAIAAAPRFEEVHSDAEMMPSFMEVVASFKHAAENGVEECCPCKAK
Ga0314817_117483	Ga0314817_1174831	F087976	DAQLKSEAEAFKWKRELARVKREQADRLREERKKCAGKCDREFPILVGPKNVPAKETRSVVVIGDRAANKKRWSKVSTHKRLFWHPKGLKKSAKHIGRAARTIARVAAKRKRISEAPLVEKF
Ga0314817_117756	Ga0314817_1177561	F017262	VAPKANCAPLCEETSCSWSCAKPTTCPRPKCELQCSKPACDVKDKQKCCKCGAKGAKRAIAAAPRFEEVHSDAEMMPSFMEVVASFKHAAENGVEECCPCKRK
Ga0314817_119569	Ga0314817_1195691	F006377	VSGGLVGKTEFTEVLSDHIELDFDIGIFLSGVDTNDRADHFRKNDGVSELSLNWSGLLSWLKVLLVLSELLDESLVLMLKTSVESSSLSGSEEFDELFVLQGSKVFQGESSESVLSDGSVSSLFTHGFIFL
Ga0314817_119601	Ga0314817_1196011	F043177	VKGNAEVVKKDFHHLDWFPWSWKMWEAMRKCDVMYEPLWALHIVFEDIYPWSSIWRAYDEIRGKSDNAFYTFEQRLLKGLEEEGGESKDPKALVEKTKGTVMTDFRADASKATLKYYAAVLKIIVMPPFEKLVFPACKTIIDPIADLVPEPLKQFIDPNAMFEELINGIIDESIDTVLSADQ
Ga0314817_120692	Ga0314817_1206921	F085198	QRQSVDSFPVCPSGWTILCVFGTTTVETTVLLANRGETSEFTVFVDGVHNPVDFGVTTDGFVGGVDQDDFIVFVGRILHNPVRAQDTQVTSTTANSLLSNRLVGSLEFELVNTSAGGFTIVDTLGQRLLASSSTNTDTVDHVALLGFVAQATSLVRSSWVGNSVNGREVSVFPASKPEQSPQNVRLLLLVKLFM
Ga0314817_122114	Ga0314817_1221142	F067854	MVASQAETLRKAIENLIDAKLHDALSRPGGLERLTAHRLTGVASFDI
Ga0314817_122845	Ga0314817_1228451	F011252	YIETERELWALFPETDGRRVNFVQIGLTAMIYAEVPETGAELSFEETYILMPCSDYAMRPIRMRACRRLTLSEYRMGHLTAIKLVGKVNEAGEVMREIGCQILGEEVLSEAQARLTKNDQ
Ga0314817_124082	Ga0314817_1240821	F050966	MRENRTSGSRWQGVETGHGRDIEALSEETERNWSVCPKPW
Ga0314817_124353	Ga0314817_1243531	F100115	MAAKVAEYVGKLQVPQERLVRFGPGKYYIQPFSPLEWRGKTVTEVLQHAALDYPRIKAQRRNGKYAIFTHKKRGGFLSKLLRQDVPFFWRWRAHAQRFYGWGVPAALLAGWMVYPALPAKWQRVFLSPVPNFLVPGGKPKDEVA
Ga0314817_125357	Ga0314817_1253571	F007020	AMAKAALVCALLVLAVAMVNAAGFKAKLDARHRAKVYNHLLQSRPGHTSFADFAQKTGVDASEDHLSQIRADLDAMDWSDMEETSAEEENAEDLSLVQVGTGVKKVQSFCEICILVMQMKERGQPHLCAGLNDQYYITCVEVLISLLRADKALVYWLKNGCMHMDSTGPEIVRPCP