Sample 3300000721

Overview

Basic Information
IMG/M Taxon OID	3300000721 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0075432 \| Gp0054651 \| Ga0001964
Sample Name	Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 41
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	15696697
Sequencing Scaffolds	18
Novel Protein Genes	18
Associated Families	18

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. AC87j1	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
Not Available	7
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Acidobacteria	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	2
All Organisms → cellular organisms → Bacteria → environmental samples → uncultured 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
Location on Map

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Family	Category	Number of Sequences	3D Structure?
F001022	Metagenome / Metatranscriptome	804	Y
F014529	Metagenome / Metatranscriptome	262	Y
F015758	Metagenome / Metatranscriptome	252	Y
F016554	Metagenome / Metatranscriptome	246	Y
F027877	Metagenome	193	Y
F029309	Metagenome	188	Y
F040312	Metagenome / Metatranscriptome	162	Y
F048198	Metagenome / Metatranscriptome	148	Y
F054391	Metagenome	140	Y
F057789	Metagenome	135	N
F066972	Metagenome / Metatranscriptome	126	Y
F070356	Metagenome	123	Y
F073875	Metagenome / Metatranscriptome	120	Y
F073892	Metagenome / Metatranscriptome	120	Y
F083637	Metagenome / Metatranscriptome	112	N
F092928	Metagenome / Metatranscriptome	107	Y
F094225	Metagenome	106	Y
F104209	Metagenome	100	N

Family

Category

Number of Sequences

3D Structure?

F001022

Metagenome / Metatranscriptome

804

F014529

Metagenome / Metatranscriptome

262

F015758

Metagenome / Metatranscriptome

252

F016554

Metagenome / Metatranscriptome

246

F027877

Metagenome

193

F029309

Metagenome

188

F040312

Metagenome / Metatranscriptome

162

F048198

Metagenome / Metatranscriptome

148

F054391

Metagenome

140

F057789

Metagenome

135

F066972

Metagenome / Metatranscriptome

126

F070356

Metagenome

123

F073875

Metagenome / Metatranscriptome

120

F073892

Metagenome / Metatranscriptome

120

F083637

Metagenome / Metatranscriptome

112

F092928

Metagenome / Metatranscriptome

107

F094225

Metagenome

106

F104209

Metagenome

100

Scaffold	Taxonomy	Length	IMG/M Link
JGI12410J11868_100400	All Organisms → cellular organisms → Bacteria	1432	Open in IMG/M
JGI12410J11868_100720	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. AC87j1	1147	Open in IMG/M
JGI12410J11868_101393	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	864	Open in IMG/M
JGI12410J11868_102264	Not Available	701	Open in IMG/M
JGI12410J11868_102790	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	645	Open in IMG/M
JGI12410J11868_102844	All Organisms → cellular organisms → Bacteria	640	Open in IMG/M
JGI12410J11868_103111	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	620	Open in IMG/M
JGI12410J11868_103169	Not Available	615	Open in IMG/M
JGI12410J11868_103475	All Organisms → cellular organisms → Bacteria → Acidobacteria	594	Open in IMG/M
JGI12410J11868_103627	Not Available	585	Open in IMG/M
JGI12410J11868_104252	Not Available	551	Open in IMG/M
JGI12410J11868_104291	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	549	Open in IMG/M
JGI12410J11868_104371	Not Available	545	Open in IMG/M
JGI12410J11868_104493	Not Available	539	Open in IMG/M
JGI12410J11868_105001	All Organisms → cellular organisms → Bacteria	517	Open in IMG/M
JGI12410J11868_105222	Not Available	510	Open in IMG/M
JGI12410J11868_105231	All Organisms → cellular organisms → Bacteria → environmental samples → uncultured bacterium	509	Open in IMG/M
JGI12410J11868_105382	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	504	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

JGI12410J11868_100400

All Organisms → cellular organisms → Bacteria

1432

Open in IMG/M

JGI12410J11868_100720

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. AC87j1

1147

Open in IMG/M

JGI12410J11868_101393

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium

864

Open in IMG/M

JGI12410J11868_102264

Not Available

701

Open in IMG/M

JGI12410J11868_102790

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria

645

Open in IMG/M

JGI12410J11868_102844

All Organisms → cellular organisms → Bacteria

640

Open in IMG/M

JGI12410J11868_103111

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria

620

Open in IMG/M

JGI12410J11868_103169

Not Available

615

Open in IMG/M

JGI12410J11868_103475

All Organisms → cellular organisms → Bacteria → Acidobacteria

594

Open in IMG/M

JGI12410J11868_103627

Not Available

585

Open in IMG/M

JGI12410J11868_104252

Not Available

551

Open in IMG/M

JGI12410J11868_104291

All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium

549

Open in IMG/M

JGI12410J11868_104371

Not Available

545

Open in IMG/M

JGI12410J11868_104493

Not Available

539

Open in IMG/M

JGI12410J11868_105001

All Organisms → cellular organisms → Bacteria

517

Open in IMG/M

JGI12410J11868_105222

Not Available

510

Open in IMG/M

JGI12410J11868_105231

All Organisms → cellular organisms → Bacteria → environmental samples → uncultured bacterium

509

Open in IMG/M

JGI12410J11868_105382

All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium

504

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
JGI12410J11868_100400	JGI12410J11868_1004001	F104209	ERRNGHGGAGTHAHSTLSAETTHVQVFYRFHPLYSSTLQILRRPKRGDGAVCVSDPMGRRLKIPMWMLLPNSAEMKIAEQAYLSKEALLSLVLLVSTPREIENRVHANLLQAVVDTCKGGQRATTTTPGAGDRKSGGHGADRRRDTNRTDRSHGPHSGGGLSNGRRKSR*
JGI12410J11868_100720	JGI12410J11868_1007202	F057789	MSETALQFTGTDLRGLLDVLLEALKVIRRTGRRPTITVNGKLYASHDLRKVAALLPDEDLQRHHQALVNVMFAKKQRGYRKTAYNLADRVNSWRTEEQKLAARQAAKTSALAVAEPAPFRNRGFSERTIRALMDCSIDEPERLLFMQPANLKKIPGVGKALFDEIMRCRAKFIRSSVMKKNP*
JGI12410J11868_101393	JGI12410J11868_1013931	F066972	MCGASQKGRPVVRSAILIFLAILVSATTPARAQGTWLETRMTRAICSSEATPVANTDRLARRLNLTEPQKAALKDLTDASASAHASAKKSLCEAKALLETDEV
JGI12410J11868_102264	JGI12410J11868_1022641	F083637	VXCSVLLALSLAGCGWWAPGKGKAPIIGKGKAPAPVVTKG*
JGI12410J11868_102790	JGI12410J11868_1027901	F001022	LGYSTFSFECLRPRMKILEIVPRDRTRLYGALVAKEAAIRKSGRGTYSRVGRRSLGSARWKHKMYKGSVQLAHDPSEIVTAKVRAATPEDERKLLSSFLGFVDRHCGDYVDTITIQYRQIR*
JGI12410J11868_102844	JGI12410J11868_1028442	F070356	MGGDLIGLVAVVLTCGLPVAALYTYYRVRKLRTQERLTALEK
JGI12410J11868_103111	JGI12410J11868_1031112	F054391	GSLSDIETTIAMTAKDAAATFESAGKAAKAFRSAGHP*
JGI12410J11868_103169	JGI12410J11868_1031691	F029309	NKKYPFKQMSPGETFRLNDLDVRGAQKLAYYYRSLCKRPIQVVVTKQDDGYYCRRVA*
JGI12410J11868_103475	JGI12410J11868_1034751	F016554	EQHHERTAAEIADTVLREVDWFTQNAPLSDDRTLVVLKVK*
JGI12410J11868_103627	JGI12410J11868_1036271	F048198	PAPRTSDHDRGSSGPWLPFRLYFPEGSSLTMATSAPLSATQRLMDYSARLRVRPANRRGSPIYSANPFTPCRHPYPGGPSGCVQRCLHRWFCLRRISTGSTTTNPTTPNQVGSVTRLQRSLHATAWMCCLSCFGQDVYYRAFLGRVAPSPRSVMTGWFHRHLPSPDFHRLNWQRYGLRANKR*
JGI12410J11868_104252	JGI12410J11868_1042522	F073875	MATETMTAEKMRRKPFVQLLGTCKDCGQPVIAGQEFLRTEHGIEHALCFYEPDYAKR
JGI12410J11868_104291	JGI12410J11868_1042911	F073892	SVTFASDIRPSCELAKESILSRSSSGLAQLSNVGDMRIRCRVPPRPFPTKPGESRNGLTAATTAYVVSADGSKKLVPSEVHVFGGGGDGFGADPEPEYVDFYVHIPLDSAEADAEARRYLAKLQASMTPEQKAQFTEDAQKKALENLRALVYQHRVGHFQVDCRVLDGSRVLGSDIVEFEMV
JGI12410J11868_104371	JGI12410J11868_1043711	F027877	MGYNARNDEIHENVERMRREREAYEDSLAIVRQFN
JGI12410J11868_104493	JGI12410J11868_1044931	F015758	GKLGKGASAMNEARSATKTMMAQSAKSELKGRIRKIRLEESLVDMACDLCMEQVPIELAFQQIQDRAMEKMVPLLDTKILDQADIVQSCLEMVAEESERVAWSALRKGTELLEEGLAILEEGKIELPRDGYVN*
JGI12410J11868_105001	JGI12410J11868_1050011	F040312	VLYAIYFQLARTAAWRGARASKLCVFNFALVILSFTVVNLYLSQHHRYF*
JGI12410J11868_105222	JGI12410J11868_1052222	F094225	KFQDDPLPFTQTRIEWLNKLAPKCHDWTLIGTRNAIRLLLSGNGVLTGTSGIQQLDIHNFSQLHVLRSEVHGDSADVYIGGLPQPNPFDLQEIRIRMVRVPDKRIWRIEEIPDATPLFAKYLDAPLPPAK*
JGI12410J11868_105231	JGI12410J11868_1052312	F092928	RRDDAHDALRSGPEHAVPFDKMVLAQGLGDEDRQASRDEEGGRGAGASLSRDHAPHLG*
JGI12410J11868_105382	JGI12410J11868_1053821	F014529	DERARLRKLLLELGGLPQPSNVSNRSRRQSRVALVK*

Scaffold ID

Protein ID

Family

Sequence

JGI12410J11868_100400

JGI12410J11868_1004001

F104209

ERRNGHGGAGTHAHSTLSAETTHVQVFYRFHPLYSSTLQILRRPKRGDGAVCVSDPMGRRLKIPMWMLLPNSAEMKIAEQAYLSKEALLSLVLLVSTPREIENRVHANLLQAVVDTCKGGQRATTTTPGAGDRKSGGHGADRRRDTNRTDRSHGPHSGGGLSNGRRKSR*

JGI12410J11868_100720

JGI12410J11868_1007202

F057789

MSETALQFTGTDLRGLLDVLLEALKVIRRTGRRPTITVNGKLYASHDLRKVAALLPDEDLQRHHQALVNVMFAKKQRGYRKTAYNLADRVNSWRTEEQKLAARQAAKTSALAVAEPAPFRNRGFSERTIRALMDCSIDEPERLLFMQPANLKKIPGVGKALFDEIMRCRAKFIRSSVMKKNP*

JGI12410J11868_101393

JGI12410J11868_1013931

F066972

MCGASQKGRPVVRSAILIFLAILVSATTPARAQGTWLETRMTRAICSSEATPVANTDRLARRLNLTEPQKAALKDLTDASASAHASAKKSLCEAKALLETDEV

JGI12410J11868_102264

JGI12410J11868_1022641

F083637

VXCSVLLALSLAGCGWWAPGKGKAPIIGKGKAPAPVVTKG*

JGI12410J11868_102790

JGI12410J11868_1027901

F001022

LGYSTFSFECLRPRMKILEIVPRDRTRLYGALVAKEAAIRKSGRGTYSRVGRRSLGSARWKHKMYKGSVQLAHDPSEIVTAKVRAATPEDERKLLSSFLGFVDRHCGDYVDTITIQYRQIR*

JGI12410J11868_102844

JGI12410J11868_1028442

F070356

MGGDLIGLVAVVLTCGLPVAALYTYYRVRKLRTQERLTALEK

JGI12410J11868_103111

JGI12410J11868_1031112

F054391

GSLSDIETTIAMTAKDAAATFESAGKAAKAFRSAGHP*

JGI12410J11868_103169

JGI12410J11868_1031691

F029309

NKKYPFKQMSPGETFRLNDLDVRGAQKLAYYYRSLCKRPIQVVVTKQDDGYYCRRVA*

JGI12410J11868_103475

JGI12410J11868_1034751

F016554

EQHHERTAAEIADTVLREVDWFTQNAPLSDDRTLVVLKVK*

JGI12410J11868_103627

JGI12410J11868_1036271

F048198

PAPRTSDHDRGSSGPWLPFRLYFPEGSSLTMATSAPLSATQRLMDYSARLRVRPANRRGSPIYSANPFTPCRHPYPGGPSGCVQRCLHRWFCLRRISTGSTTTNPTTPNQVGSVTRLQRSLHATAWMCCLSCFGQDVYYRAFLGRVAPSPRSVMTGWFHRHLPSPDFHRLNWQRYGLRANKR*

JGI12410J11868_104252

JGI12410J11868_1042522

F073875

MATETMTAEKMRRKPFVQLLGTCKDCGQPVIAGQEFLRTEHGIEHALCFYEPDYAKR

JGI12410J11868_104291

JGI12410J11868_1042911

F073892

SVTFASDIRPSCELAKESILSRSSSGLAQLSNVGDMRIRCRVPPRPFPTKPGESRNGLTAATTAYVVSADGSKKLVPSEVHVFGGGGDGFGADPEPEYVDFYVHIPLDSAEADAEARRYLAKLQASMTPEQKAQFTEDAQKKALENLRALVYQHRVGHFQVDCRVLDGSRVLGSDIVEFEMV

JGI12410J11868_104371

JGI12410J11868_1043711

F027877

MGYNARNDEIHENVERMRREREAYEDSLAIVRQFN

JGI12410J11868_104493

JGI12410J11868_1044931

F015758

GKLGKGASAMNEARSATKTMMAQSAKSELKGRIRKIRLEESLVDMACDLCMEQVPIELAFQQIQDRAMEKMVPLLDTKILDQADIVQSCLEMVAEESERVAWSALRKGTELLEEGLAILEEGKIELPRDGYVN*

JGI12410J11868_105001

JGI12410J11868_1050011

F040312

VLYAIYFQLARTAAWRGARASKLCVFNFALVILSFTVVNLYLSQHHRYF*

JGI12410J11868_105222

JGI12410J11868_1052222

F094225

KFQDDPLPFTQTRIEWLNKLAPKCHDWTLIGTRNAIRLLLSGNGVLTGTSGIQQLDIHNFSQLHVLRSEVHGDSADVYIGGLPQPNPFDLQEIRIRMVRVPDKRIWRIEEIPDATPLFAKYLDAPLPPAK*

JGI12410J11868_105231

JGI12410J11868_1052312

F092928

RRDDAHDALRSGPEHAVPFDKMVLAQGLGDEDRQASRDEEGGRGAGASLSRDHAPHLG*

JGI12410J11868_105382

JGI12410J11868_1053821

F014529

DERARLRKLLLELGGLPQPSNVSNRSRRQSRVALVK*

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300000721: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 41

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences