3300000692: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 25

Overview

Basic Information

• IMG/M Taxon OID: 3300000692
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0075432 | Gp0054565 | Ga0001948
• Sample Name: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 25
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 7426224
• Sequencing Scaffolds: 9
• Novel Protein Genes: 9
• Associated Families: 9

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → Pseudolabrys taiwanensis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
Not Available	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	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?
F000466	Metagenome / Metatranscriptome	1105	Y
F003090	Metagenome / Metatranscriptome	508	Y
F007624	Metagenome / Metatranscriptome	348	N
F016190	Metagenome / Metatranscriptome	249	Y
F031318	Metagenome	182	Y
F035932	Metagenome	171	Y
F040358	Metagenome / Metatranscriptome	162	N
F058548	Metagenome / Metatranscriptome	135	Y
F078037	Metagenome	116	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI12380J11932_100142	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1670
JGI12380J11932_100194	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1540
JGI12380J11932_100429	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → Pseudolabrys taiwanensis	1175
JGI12380J11932_100465	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1146
JGI12380J11932_101482	All Organisms → cellular organisms → Bacteria → Proteobacteria	694
JGI12380J11932_101508	Not Available	689
JGI12380J11932_101681	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	652
JGI12380J11932_101834	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	629
JGI12380J11932_102893	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	514

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI12380J11932_100142	JGI12380J11932_1001423	F058548	AAKNAPFDGAETGGAEAHIAEQSRSWRAASGERAVMRGS*
JGI12380J11932_100194	JGI12380J11932_1001942	F000466	VKRDWVPTGRIDFATRFYGNLEDSDQPSEFKLIVEERRIVESITGNENLEIQWRLATLNEAKVVVAQYHKYLSENSLIKSVFDEPASLPPPKRIQKIQESTAA*
JGI12380J11932_100429	JGI12380J11932_1004291	F078037	MDVKLITAILVTAAMASAALAQGPSTEKLKADAQEVVKIISSDSAKAQAYCETIKLGDQMDQAEQNNDSDKAEGLSKKMDELNQKLGPEYLKLGQDLQDIDPNSPDGLELGRTLAALDKLCK*
JGI12380J11932_100465	JGI12380J11932_1004651	F031318	MRTTTIATVAVVVLALLIVAKSRTVGLTEATGNPQQNTVSTYDLSVGHPNMK
JGI12380J11932_101482	JGI12380J11932_1014823	F035932	MVIPVGLPGAQQLVVAEKDLSGRVTTKEIMPVLFSVLEESDXPXFRASXSX*
JGI12380J11932_101508	JGI12380J11932_1015081	F016190	VVFPGSTAGDNTLRFRVISELPGVEGTLAESVLKRLSEPVGTRSSNVWEAEADGRHYFVAVGQVSNIDWPWQVVVTVPRTGLLQAASKSTVILIGAMGLAALIALAIGYATSRTIGAPMTRLLSNAQLARHGNIELMEDVNTGLREIDETGKILKELATQQRGRERR*
JGI12380J11932_101681	JGI12380J11932_1016811	F007624	QLREGSFHGPRPTCPKHPKQRVHRHGFYVRFENCDSQRRLRIERFVCPRCGRTLSVLPKNRLPYVAVNTTILESDFDARASGTDPPSCSEKERGCLGRAFERFADRVAPLCALLGQMIRGIKPSVSECWRALRQLDNLEGILLLLGTKFNTSLLADYRCLQPGF*
JGI12380J11932_101834	JGI12380J11932_1018342	F040358	MRIAIFALAVLAGGGAAEAGQIEVISASPRHIEIAAWCWTAGSNCQQEASDVAQGYCHGSDYPHYPRRALYVRSGILERDFFSERVIFVYRCNRRSIICEAGSC*
JGI12380J11932_102893	JGI12380J11932_1028932	F003090	LEKMTVIDYKGYRIEVGPVGKGWRASIFSPGSIRPWPNSPANLEKSSAEELVAEAKRIIDVRLGPRRL*