3300000698: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 57

Overview

Basic Information

• IMG/M Taxon OID: 3300000698
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0075432 | Gp0054325 | Ga0001980
• Sample Name: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 57
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 9377701
• Sequencing Scaffolds: 10
• Novel Protein Genes: 11
• Associated Families: 11

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
Not Available	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Eubacteriales → Eubacteriaceae → Acetobacterium → Acetobacterium dehalogenans	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi 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?
F000209	Metagenome / Metatranscriptome	1592	Y
F001022	Metagenome / Metatranscriptome	804	Y
F010721	Metagenome / Metatranscriptome	300	Y
F011811	Metagenome / Metatranscriptome	287	Y
F012657	Metagenome	278	Y
F040358	Metagenome / Metatranscriptome	162	N
F046517	Metagenome / Metatranscriptome	151	N
F062933	Metagenome / Metatranscriptome	130	Y
F075781	Metagenome / Metatranscriptome	118	Y
F079486	Metagenome / Metatranscriptome	115	Y
F091102	Metagenome	107	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI12489J11917_100142	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	2017
JGI12489J11917_101389	All Organisms → cellular organisms → Bacteria	891
JGI12489J11917_101421	All Organisms → cellular organisms → Bacteria → Proteobacteria	878
JGI12489J11917_101637	Not Available	821
JGI12489J11917_101745	Not Available	796
JGI12489J11917_101839	All Organisms → cellular organisms → Bacteria	772
JGI12489J11917_101916	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Eubacteriales → Eubacteriaceae → Acetobacterium → Acetobacterium dehalogenans	757
JGI12489J11917_102125	Not Available	716
JGI12489J11917_102234	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	699
JGI12489J11917_102575	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	651

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI12489J11917_100142	JGI12489J11917_1001423	F001022	MKILEIVPRDRTRLYGALVAKEAAIRKSGRGTYSRVGRRSLGSARWKHKMYKGSVQLAHDPSEIVTAKVRAATPEDERKLLSSFLGFVDRHCGDYVDTITIQYRQIR*
JGI12489J11917_101389	JGI12489J11917_1013891	F040358	MRIAIFALAVLAGGGAAEAGQIEVISASPRHIEIAAWCWTAGSNCQQEASDVAQGYCHGSDYPHYPRRALYVRSGILERDFFSERVIFVYGAIGDLL
JGI12489J11917_101421	JGI12489J11917_1014213	F075781	LRVDNQTKCSFSSKEPAMTAGAVIKKAFPVVMVSVLDSKDGSVEVIK*
JGI12489J11917_101637	JGI12489J11917_1016372	F062933	KIELIPMRHIAARHVFALLVALIVGVTVFYRLPEPLPELTRAEFMAEVRAGHVRRIEIEDQEVIIAESSTRGEFRTGFDRKVDVNLPAELRALGVEVYFSKSPLGLI*
JGI12489J11917_101745	JGI12489J11917_1017454	F046517	ESIRRDLDAVKVAFGDTWQQSHLPEGYSALMTAYSVHHFFVSESSTTK*
JGI12489J11917_101839	JGI12489J11917_1018392	F010721	PKGRLSAGFTVPGMADAADVAMQLRERGWAPYKLRLDLEQHAWIAVVIDWKRAA*
JGI12489J11917_101916	JGI12489J11917_1019161	F011811	MLTADQINDLHHLYWAERWPIRKIEQHLCMSWRTIKKYLEAPAQKPATRSRLSKLDPFKTTIAELLEK
JGI12489J11917_102125	JGI12489J11917_1021251	F012657	SLLWKSGHNRSFVSQKGRDLLVCSRDFEAKAAASRIIAMAWLKIIEKKRLLSASPVMIAASLHQMAEKYDPQVAPTTLHLPEAVHADFREKVFLYREANVLLALVDRVNPSSDGRDSLFEPVFWEYERIIFRESSDHFGELSDHPILRAARRESVAAALQDLNFRMHPPRVNKWDFAVDWSRNWFAGIGHNELNPARLERFSEFWSREYTAVQQALDATVTTGR*
JGI12489J11917_102234	JGI12489J11917_1022341	F091102	PSWAIEXRFLEIPGPHDSIVTFDLDTVQIIQPGRFTVVSTEIDNPEVMQFRLNVLEHLRTHCAHAEGKYPAPPELFTLGRPDIAVGDIEVAHVSGSKFVRWFYPYRLLSPTLENYEILFCDGESNYFEMRTLIANGSRHKDVYDCTRGLYGTMHDENDPTSALLXVVPEGSYLFDYYVAVCRAXTHEEPYLPQKH*
JGI12489J11917_102575	JGI12489J11917_1025752	F079486	VNADAIPASQLACLLYDAAEGICADVAAVMLIDRHGHFLHDPAFRRIIAAGSSITTGQPLAVIRWTAAIHALE
JGI12489J11917_102888	JGI12489J11917_1028881	F000209	MAFVKNISNHRSSELRPVDRLTLGLVGMAVIFASLGLGEAVYRLLFFDFDGATDRLPIEMMFGLAFAWVVMRLAKRIYQQQQLTSAKINQVWDRNYRIRNAVEAIPPVPYPAHQQAIRVIRDEVDRIEWVLADIQPR*GRGRALEAAEELASATVSYE