3300000711: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 26

Overview

Basic Information

• IMG/M Taxon OID: 3300000711
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0075432 | Gp0054452 | Ga0001949
• Sample Name: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 26
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 11770306
• Sequencing Scaffolds: 12
• Novel Protein Genes: 12
• Associated Families: 12

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. 139	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Acidisarcina → Acidisarcina polymorpha	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	3
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Candidatus Acidoferrales → Candidatus Acidoferrum → Candidatus Acidoferrum panamensis	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	1
Not Available	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Tropical Forest Soil Microbial Communities From Luquillo Experimental Forest, Puerto Rico
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Loam → Forest Soil → Tropical Forest Soil → Tropical Forest Soil Microbial Communities From Luquillo Experimental Forest, Puerto Rico

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): forest biome → tropical forest → forest soil
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Soil (non-saline)

Location Information

• Location: Luquillo Experimental Forest Soil, Puerto Rico
• Coordinates
  • Lat. (^o): 18.0
  • Long. (^o): -65.0
  • Alt. (m): N/A
  • Depth (m): .1

Associated Families

Family	Category	Number of Sequences	3D Structure?
F002450	Metagenome / Metatranscriptome	558	Y
F003758	Metagenome / Metatranscriptome	470	Y
F007624	Metagenome / Metatranscriptome	348	N
F018438	Metagenome / Metatranscriptome	235	Y
F054652	Metagenome / Metatranscriptome	139	Y
F057789	Metagenome	135	N
F066611	Metagenome / Metatranscriptome	126	Y
F069413	Metagenome / Metatranscriptome	124	Y
F070751	Metagenome	122	Y
F071877	Metagenome / Metatranscriptome	121	Y
F076736	Metagenome	117	Y
F078037	Metagenome	116	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI12585J11927_100034	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	3292
JGI12585J11927_100548	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. 139	1456
JGI12585J11927_101374	All Organisms → cellular organisms → Bacteria → Proteobacteria	982
JGI12585J11927_101419	All Organisms → cellular organisms → Bacteria	967
JGI12585J11927_103441	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Acidisarcina → Acidisarcina polymorpha	600
JGI12585J11927_103549	All Organisms → cellular organisms → Bacteria	592
JGI12585J11927_104022	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	556
JGI12585J11927_104059	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	554
JGI12585J11927_104283	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Candidatus Acidoferrales → Candidatus Acidoferrum → Candidatus Acidoferrum panamensis	538
JGI12585J11927_104573	All Organisms → cellular organisms → Bacteria → Acidobacteria	520
JGI12585J11927_104846	Not Available	507
JGI12585J11927_104931	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	502

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI12585J11927_100034	JGI12585J11927_1000341	F007624	VGGAVSGRCRLLFEPMQLREGSFHGPRPTCPKHPKQRVHRHGFYVRFENCDSQRRLRIERFVCPRCGRTLSVLPKNRLPYVAVNTTILESDFDARASGTDPPSCSEKERGCLGRAFERFADRVAPLCALLGQMIRPIKPSVSECWRALRQLDNLEGILLLLGTKFNTSLLADYRCLQPGF
JGI12585J11927_100548	JGI12585J11927_1005481	F069413	MQSSLPAGWLAFTGRESNPLDHYKRFQITLSSPSSGFILAQRTAGFS
JGI12585J11927_101374	JGI12585J11927_1013742	F078037	MDVKLITAILVTAAMASAALAQGPSTEKLKADAQEVVKIISSDSAKAQAYCETIKLGDQMDQAEQNNDSDKAEGLSNKIDELNQKLGPEYLKLGQDLQDIDPNSPDGLELGRTLAALDK
JGI12585J11927_101419	JGI12585J11927_1014192	F057789	LKVIRRTGRRPTITVNGKLYASHDLRKVAALLPDEDLQRHHQALVNVMFAKKQRGYRKTAYNLADRVNSWRTEEQKLAARQAAKTSALAVAEPAPFRNRGFSERTIRALMDCSIDEPERLLFMQPANLKKIPGVGKASVDEIMRYRAKFIRSSVMKKNP*
JGI12585J11927_103441	JGI12585J11927_1034412	F018438	MGIDDKSSHPELCLEVAGGVTRTIVGLFREPDAGNPPVRFDEREQETELCQTGLRRRCKNFVNSHRETNATAPVLDSTHWQLG
JGI12585J11927_103549	JGI12585J11927_1035491	F076736	MVQGVDNIGICTTDVERSVAFYQRLGFSEAYRNNRGVLV
JGI12585J11927_104022	JGI12585J11927_1040222	F071877	MQHSLLFSILDYLHGDGLTILPEMELLLFALGILIFDFLLEKKEKHWNAMLALFGIAASAFGLFMQSRRYNAIRLDPTSPGDLTGFHSTVVVDGFFLVFASIFLAATALVV
JGI12585J11927_104059	JGI12585J11927_1040592	F054652	MSNSTKVHWGRVLLGGLLAELLVFAIVFPMRHFFGQRAFLASILIASATMPFVLALWVARRIESHFVLHGALIGLVAALIYMGLARGQPQPLLYKVAHGFKIVGGAAGGLVASRRKATE
JGI12585J11927_104283	JGI12585J11927_1042832	F070751	EDAQKEGNELFLDVCESFRYGVISYASEQAIPREVLMQHEIQKITSNTQKYMRYLELTARQANSITFTIPRRRWFH*
JGI12585J11927_104573	JGI12585J11927_1045731	F066611	MAKPTIRAIIFDIGRVLVRVDIRKAKMGLADGLSLSPEELWSAIENDPRWSDWQ
JGI12585J11927_104846	JGI12585J11927_1048462	F003758	IRNIKYDPRLSPNVLRAFENAEDEVLINTLPGAPRLDVPNLFRPQFMTDVQKEHPEYFADLPSLK*
JGI12585J11927_104931	JGI12585J11927_1049311	F002450	EQTERRATSRIDAHLPLFIYGSLLGGDPFYEETFTISINGTGGLILMASTVQPGQRIMVTNQGNDQTQECVVVSVTAQPAGSYVAFKFPTPMPQFWHGLEIGKGTLRSWLEYFIEALILQIRGDHTPETPVPDKFYKRGSQESFVLPSPRE*