3300031477: Metatranscriptome of soil surface biofilm microbial communities from soil inoculated with nitrogen-fixing consortium DG1, State College, Pennsylvania, United States - STER_R3 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300031477
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0132857 | Gp0330674 | Ga0314812
• Sample Name: Metatranscriptome of soil surface biofilm microbial communities from soil inoculated with nitrogen-fixing consortium DG1, State College, Pennsylvania, United States - STER_R3 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 19788102
• Sequencing Scaffolds: 8
• Novel Protein Genes: 8
• Associated Families: 8

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas → Sphingomonas jaspsi	2
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas → unclassified Sphingomonas → Sphingomonas sp. URHD0057	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas → unclassified Sphingomonas → Sphingomonas sp. SE220	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	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?
F022207	Metagenome / Metatranscriptome	215	Y
F042676	Metagenome / Metatranscriptome	157	N
F051771	Metagenome / Metatranscriptome	143	Y
F057344	Metagenome / Metatranscriptome	136	N
F061570	Metagenome / Metatranscriptome	131	Y
F062141	Metagenome / Metatranscriptome	131	Y
F077752	Metagenome / Metatranscriptome	117	Y
F089547	Metagenome / Metatranscriptome	109	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0314812_100697	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas	3993
Ga0314812_101152	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas → Sphingomonas jaspsi	2531
Ga0314812_102968	All Organisms → cellular organisms → Bacteria	1227
Ga0314812_102998	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas → Sphingomonas jaspsi	1216
Ga0314812_103077	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas → unclassified Sphingomonas → Sphingomonas sp. URHD0057	1196
Ga0314812_104465	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas → unclassified Sphingomonas → Sphingomonas sp. SE220	914
Ga0314812_107801	All Organisms → cellular organisms → Eukaryota → Amoebozoa → Discosea → Longamoebia → Centramoebida → Acanthamoebidae → Acanthamoeba → Acanthamoeba castellanii → Acanthamoeba castellanii str. Neff	608
Ga0314812_108653	All Organisms → cellular organisms → Eukaryota → Amoebozoa	563

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0314812_100697	Ga0314812_1006974	F051771	MQGNMTDGPSHLEPVDDQAVPKPGRRWTWDRLGPHASRVALELFIVFVGVSAAFAVENYRDARQQDLRRLAVYRALDRELTQMAETHGPVFQRQMTEQLTVWDQAVAKGEHPLPPTFRMPRAERPPTGVWDAAVATGSIELIDPELFFELARLYNRAESAGDLYQRYATSAQADVWARLDEGPGAFWQPDGKLRPEIKAHVQRLRDFQDLQGQRVNEAREIRAKLRQAAAN
Ga0314812_101152	Ga0314812_1011521	F062141	VTMPRGLIFLILVILLLVAGVYFLSQSADEVPVQTIESDITANAATN
Ga0314812_102968	Ga0314812_1029681	F022207	TTFEGRTALGGIALQPVRLVLLLLVGPREGENDFLEFPSVEEAVAYARELYGERRFQLEGIEDRSGRSVVSYDVLHDRCRAPDRIQERRFG
Ga0314812_102998	Ga0314812_1029984	F077752	FEKGRFEMTFSFVDSRQIATSLAAALITSLLFVSAATSLPIA
Ga0314812_103077	Ga0314812_1030772	F089547	ERVEIALTALSVALTSSIHVSTYVCLDDTVFALSTSDQMAIVRFKDREYRLPRRQSSIAIKYATEEATLYLDGDFAAFVAEDRWPPGCQRLESGESRSP
Ga0314812_104465	Ga0314812_1044652	F057344	MTSKRAHFFTACGPLFLAIAACQPASENMEDSEAELLMSNAGKGGAPGFTPQGWGWKPGSSVEISLFNEPDSQGKPNPSWKKILDEKVDTSTMFGFSADAPFYPVRRTLCGNPAPRQFMLAMAKDTKTGRTRMRPLPVDLYFTFQPCPHSGAPIPQAAPPPQQPMQ
Ga0314812_107801	Ga0314812_1078011	F042676	THKTHHKMAQQEYSIGGMITFPQLTASYGLISGVIGAASLINPHLCYDLVGQPSRWVPMLESSSGLYTLRLFGLQTVALAAVSLHAAVNVKEPAKRQQLSNVLAALNIGNGLIAAWMYKEGILNPLGVSIHSGLSMALGLGFLVYGLREDRRTGAGEPARD
Ga0314812_108653	Ga0314812_1086531	F061570	LAALLLVAIVVADAHKAQNLQKVGFCSATIRGSTYDLTAASHNGTTDWTYTGYDGKKYFLNVCNNLVSTNPCGNDSPAYEFDPSTGDCTRLGLLEAEWWGNSYFDTQGQGDGVVVMYNEGDSCSGSARAKVSMLFHCNHTVSATTLTSVVGIGMYCHWVAHFESPLGCQLSL