3300000724: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 29

Overview

Basic Information

• IMG/M Taxon OID: 3300000724
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0075432 | Gp0054448 | Ga0001952
• Sample Name: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 29
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 16827352
• Sequencing Scaffolds: 21
• Novel Protein Genes: 22
• Associated Families: 22

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	1
Not Available	7
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	3
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → unclassified Bryobacterales → Bryobacterales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → unclassified Acidimicrobiia → Acidimicrobiia 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?
F003090	Metagenome / Metatranscriptome	508	Y
F003145	Metagenome / Metatranscriptome	505	Y
F003446	Metagenome / Metatranscriptome	486	Y
F003758	Metagenome / Metatranscriptome	470	Y
F005756	Metagenome / Metatranscriptome	391	Y
F021828	Metagenome / Metatranscriptome	217	Y
F033196	Metagenome	178	Y
F034030	Metagenome / Metatranscriptome	175	Y
F036023	Metagenome / Metatranscriptome	171	Y
F037452	Metagenome / Metatranscriptome	168	Y
F057789	Metagenome	135	N
F060395	Metagenome / Metatranscriptome	133	Y
F061158	Metagenome / Metatranscriptome	132	Y
F065924	Metagenome / Metatranscriptome	127	Y
F066972	Metagenome / Metatranscriptome	126	Y
F083542	Metagenome / Metatranscriptome	112	N
F089460	Metagenome / Metatranscriptome	109	Y
F090955	Metagenome	108	N
F091102	Metagenome	107	N
F094701	Metagenome	105	N
F098285	Metagenome	104	Y
F104209	Metagenome	100	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI12581J11935_100051	All Organisms → cellular organisms → Bacteria	2527
JGI12581J11935_100190	All Organisms → cellular organisms → Bacteria	1802
JGI12581J11935_100243	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1655
JGI12581J11935_100738	All Organisms → cellular organisms → Bacteria	1113
JGI12581J11935_100836	All Organisms → cellular organisms → Bacteria → Acidobacteria	1058
JGI12581J11935_100908	Not Available	1022
JGI12581J11935_101222	Not Available	900
JGI12581J11935_101583	Not Available	810
JGI12581J11935_101666	Not Available	791
JGI12581J11935_102026	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	732
JGI12581J11935_102453	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	678
JGI12581J11935_103177	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → unclassified Bryobacterales → Bryobacterales bacterium	618
JGI12581J11935_103246	Not Available	612
JGI12581J11935_103423	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	600
JGI12581J11935_103961	All Organisms → cellular organisms → Bacteria → Proteobacteria	572
JGI12581J11935_104276	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	555
JGI12581J11935_104280	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	554
JGI12581J11935_104445	Not Available	547
JGI12581J11935_104808	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → unclassified Acidimicrobiia → Acidimicrobiia bacterium	532
JGI12581J11935_105208	All Organisms → cellular organisms → Bacteria → Proteobacteria	517
JGI12581J11935_105686	Not Available	501

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI12581J11935_100051	JGI12581J11935_1000512	F104209	QERRNGHGGAGTHAHSTLSAETTHVQVFYRFHPLYSSTLQILRRPKRGDGAVCVSDPMGRRLKIPMWMLLPNSAEMKIAEQAYLSKEALLSLVLLVSTPREIENRVHANLLQAVVDTCKGGQRATTTTPGAGDRKSGGHGADRRRDTNRTDRSHGPHSGGGLSNGRRKSR*
JGI12581J11935_100190	JGI12581J11935_1001906	F057789	MSETALQFTGTDLRGLLDVLLEALKVIRRTGRRPTITVNGKLYASHDLRKVAALLPDEDLQRHHQALVNVMFAKKQRGYRKTAYNLADRVNSWRTEEQKLAARQAAKTSALAVAEPAPFRNRGFSERTIRALMDCSIDEPERLLFMQPANLKKIPGVGKASFDEIMRYRAKFIRS
JGI12581J11935_100243	JGI12581J11935_1002431	F066972	MCGASQKGRPVVRSAILIFLAILVSATTPARAQGTWLETRMTRAICSSEATPVANTDRLARRLNLTEPQKAALKDLTDASASAHASA
JGI12581J11935_100738	JGI12581J11935_1007381	F065924	ESAVLDMTSIAAVHESACGPSVWTGRALQAESDDLEVIGLAHLYPACNGTFVPGQYGYPRALDLIRVSAPKAIRAT*
JGI12581J11935_100836	JGI12581J11935_1008362	F083542	MKKRIGAVLSRREFARRAALLSATSVVSPAAMLDLPSAGGGDYQVDAGGPKLSPEGQAEASARYQQVLSLYGERLNDEQKTRVKKMCAELQPALDHIRSYELENGNAPALYLKPLYEREKRQQSTSANGKP*
JGI12581J11935_100908	JGI12581J11935_1009082	F091102	RRQPVAGLKSLFPKAAKNFHSVETFFPRPGPAPRSSLESKADSDFNSVVNYTVRHLGENRMKQWKLLPLICGAWVVTWYPSWAIEKRFLEIPGPHDSIVTFDLDTVQIIQPGRFTVVSTEIDNPEVMQFRLNVLEHLRTHCAHAEGKYPAPPELFTLGRPDIAVGDIEVAHVSGSKFVRWFYPYRLLSPTLENYEILFCDGESNYFEMRTLIANGSRHKDVYDCRRGLYGMMHDENDPTSALLIVVPEGSYLFDYYVAVCRALTHEEPYLPQKH*
JGI12581J11935_101222	JGI12581J11935_1012222	F037452	MVLVSLMESSFLIEVDNTSILRTGALHCYHYTLNRLPAPRLLLPRSGLERSDFV
JGI12581J11935_101583	JGI12581J11935_1015831	F090955	MLSVVLLFLGLGTASRPLPVADEGPPTLVVQVVDPVWIPLPDSEVTVKPAGGKGASRSAHADENGYARFWVETGVEYTIEAKTHGFNKKTLKHVFIAKPKPSLPTAHVQIKLQPSGPFTYSK*
JGI12581J11935_101666	JGI12581J11935_1016662	F098285	MKLRLIAAILVITAVPVCAQAQKPDAAKVTNADAQKVLKIISGDKAKTQTYCDILNLGVQIEEADQSKDAKKADELIQKIDELTKKLGPEYLALVDGLQDVDMESEDGQQ
JGI12581J11935_102026	JGI12581J11935_1020261	F061158	VERGGNWLTRSFGAGYPDLDSVVDQIEKYRVIDAAR*
JGI12581J11935_102453	JGI12581J11935_1024532	F005756	VSHVRRKLIWYSILGGVFITLLAVVLRSVGIYGPVPYLTYAGAYLMETFFQRFLEWIPWRYADNLISEVVLFLLLNILSYAFVIFLLLRIFFPDRSSDLPPLTGKK*
JGI12581J11935_102724	JGI12581J11935_1027241	F089460	LAKILERTWDKAEDYGGDTALSKTNHALFEEIDKAMDQFGNMLIDHPNSAPDQAKLKAAYTYYLEKLKLGD*
JGI12581J11935_103177	JGI12581J11935_1031771	F060395	MIAHNPLHGSGQAALPHPALALGNDAHAAQRIGMTDGRQRQPASDEAPHTVPKDAAILAAPRQRAVPEASHLEPEKRQRRLVPGHSVIVDVSTHHRLQPFTQFRNGRMQASLKLGFHLVQLRLQPFADRLPQYRIHSVAPLLYADVRKAEKVERLRFPFSTSLPVQDRERSEFQQSRFLGMQ
JGI12581J11935_103246	JGI12581J11935_1032462	F036023	MTRVSLRFAVLALSLMLAITAFAKPRSENITLYHDATVNGTNLPAGEYTVKYDVDGSNAQVRFMQGNKQVATATGQVKTLSKKTGSSQVVLDTEGNMRSISEIDFGGKDEALTFGSNGTAVGK*
JGI12581J11935_103423	JGI12581J11935_1034231	F003090	VEELLRLEMLIGKMTVIDYKGYRIEVGPVGKGWRASIFSPGSIRPWPNSPANLEKSSAEELVAEAKRIIDVRLGPRRL*
JGI12581J11935_103961	JGI12581J11935_1039611	F003758	AIRNIKFDPRVSANVIRAFENAEDEVLVNTLPGAARLNVPKLFRPEFMEAVMKEHPEYFADLPKL*
JGI12581J11935_104276	JGI12581J11935_1042761	F003446	KATERFVSRLREQVAPVMEEARADFQKLVASQAVFKEESRTIYRQVTDQLESDANARLLQTHRQLETNSTSVVNECNEKMLDLSQAFEKLARDSAQNMIASATNEGNKNLEERAAEISGHFADQLEGHVRSYLEFIGESIKEFPKKPPAA*
JGI12581J11935_104280	JGI12581J11935_1042801	F003145	MLLKEACLDRVVGEVEDLAARVALLKGRFAKQKVSVKLEHYWELEYVRTRFAEFKRRVRDLEDADDLEIDRIQEAVEVAWNDLIHAVETLLAALP*
JGI12581J11935_104445	JGI12581J11935_1044452	F094701	MNPKRLTLAKPLTVALLLVVLSAASPLAFAQRPAAIHIDWTIVLAGPAYDGMAPIGNSDYEVQNTYRRFEADCDQVNVPDGTLLDVHVNGKYAGSFRSLDQGGALVLTGKRAPNVTKGTKVSISVHNGPTIVSGHY*
JGI12581J11935_104808	JGI12581J11935_1048081	F021828	MKYVVISRLAPGIDNARKALEVFQKAGLPPGTEATWAASDGKTFVNIVDADTPDMTASSTYAPFFEETTTIPVVPLDDAWMKAIQAAQDNWG*
JGI12581J11935_105208	JGI12581J11935_1052081	F033196	VKSVRFDRLVASTALGLILMLSSHAGMAQQSDVQITAAVPMPDTTLPS
JGI12581J11935_105686	JGI12581J11935_1056861	F034030	RRREFILLGAYVIAGCVAAVTSADLALAQAKNSTSMEDRLSAKIRCQDFQKNSDGKWTSSSKAKIGKIDFSNHTFGVDEVDIGGADLATFLNRKCAAH*