3300000666: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 17

Overview

Basic Information

• IMG/M Taxon OID: 3300000666
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0075432 | Gp0054605 | Ga0001940
• Sample Name: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 17
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 3206642
• Sequencing Scaffolds: 5
• Novel Protein Genes: 6
• Associated Families: 6

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. AC87j1	1
Not Available	2

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?
F012657	Metagenome	278	Y
F013041	Metagenome / Metatranscriptome	275	Y
F014124	Metagenome / Metatranscriptome	265	Y
F029309	Metagenome	188	Y
F057789	Metagenome	135	N
F104209	Metagenome	100	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI12382J11879_100021	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1902
JGI12382J11879_100194	All Organisms → cellular organisms → Bacteria	1017
JGI12382J11879_100323	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. AC87j1	803
JGI12382J11879_100741	Not Available	560
JGI12382J11879_100907	Not Available	520

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI12382J11879_100021	JGI12382J11879_1000211	F013041	LLALASLDLACRDHCPDVSATLATTAFDRSSSRWLGISDLIAEPEGPAFISRTVTRSRMDRLRS*
JGI12382J11879_100194	JGI12382J11879_1001942	F104209	HVQVFYRFHPLYSSTLQILRRPKRGDGAVCVSDPMGRRLKIPMWMLLPNSAEMKIAEQAYLSKEALLSLVLLVSTPREIENRVHANLLQAVVDTCKGGQRATTTTPGAGDRKSGGHGADRRRDTNRTDRSHGPHSGGGLSNGRRKSR*
JGI12382J11879_100323	JGI12382J11879_1003231	F057789	MSETALQFTGTDLRGLLDVLLEALKVIRRTGRRPTITVNGKLYASHDLRKVAALLPDEDLQRHHQALVNVMFAKKQRGYRKTAYNLADRVNSWRTEEQKLAARQAAKTSALAVAEPAPFRNRGFSERTIRALMDCSIDEPERLLFMQPANL
JGI12382J11879_100643	JGI12382J11879_1006431	F014124	MNTPIERLQSALETLGLKAVEARLENLLEQASKKEPSYADFLDELLSCEVEARRTRY
JGI12382J11879_100741	JGI12382J11879_1007412	F029309	MIYKVRTKKKYPFKRMGLGETFKLNDLDVRDAQKAAYYYRSLCKRPIRIVITKQDDGYYCRRVA*
JGI12382J11879_100907	JGI12382J11879_1009071	F012657	ETKAAASRIIAMAWLKIIEKKRLLSASPVMIAASLHQMAEKYDPQVAPTTLHLPEAVHADFREKVFLYREANVLLALVDRVNPSSDGRDSLFEPVFWEYERIIFRESSDHFGELSDHPILRAARRESVAAALQDLNFRMHPPRVNKWDFAVDWSRNWFAGIGHNELNPARLER