Sample 3300000701

Overview

Basic Information
IMG/M Taxon OID	3300000701 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0075432 \| Gp0054287 \| Ga0001927
Sample Name	Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 4
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	9270690
Sequencing Scaffolds	20
Novel Protein Genes	20
Associated Families	18

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Rhizobiaceae → Rhizobium/Agrobacterium group → Rhizobium → Rhizobium mongolense → Rhizobium mongolense USDA 1844	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Acidisarcina → Acidisarcina polymorpha	1
Not Available	8
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Rhizobiaceae → Sinorhizobium/Ensifer group → Ensifer → Ensifer sesbaniae	1
All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Ecdysozoa → Panarthropoda → Arthropoda → Mandibulata → Pancrustacea → Hexapoda → Insecta → Dicondylia → Pterygota → Neoptera → Endopterygota → Diptera → Brachycera → Muscomorpha → Eremoneura → Cyclorrhapha → Schizophora → Calyptratae → Hippoboscoidea → Glossinidae → Glossina → Glossina	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. AS23.2	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	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?
F000466	Metagenome / Metatranscriptome	1105	Y
F005155	Metagenome / Metatranscriptome	410	Y
F008634	Metagenome / Metatranscriptome	330	Y
F012657	Metagenome	278	Y
F014658	Metagenome / Metatranscriptome	261	Y
F018438	Metagenome / Metatranscriptome	235	Y
F024403	Metagenome / Metatranscriptome	206	Y
F025163	Metagenome / Metatranscriptome	203	Y
F050959	Metagenome / Metatranscriptome	144	N
F055339	Metagenome / Metatranscriptome	138	Y
F063348	Metagenome	129	N
F064047	Metagenome / Metatranscriptome	129	Y
F065924	Metagenome / Metatranscriptome	127	Y
F065994	Metagenome / Metatranscriptome	127	Y
F069634	Metagenome	123	Y
F078037	Metagenome	116	N
F078614	Metagenome	116	Y
F083542	Metagenome / Metatranscriptome	112	N

Family

Category

Number of Sequences

3D Structure?

F000466

Metagenome / Metatranscriptome

1105

F005155

Metagenome / Metatranscriptome

410

F008634

Metagenome / Metatranscriptome

330

F012657

Metagenome

278

F014658

Metagenome / Metatranscriptome

261

F018438

Metagenome / Metatranscriptome

235

F024403

Metagenome / Metatranscriptome

206

F025163

Metagenome / Metatranscriptome

203

F050959

Metagenome / Metatranscriptome

144

F055339

Metagenome / Metatranscriptome

138

F063348

Metagenome

129

F064047

Metagenome / Metatranscriptome

129

F065924

Metagenome / Metatranscriptome

127

F065994

Metagenome / Metatranscriptome

127

F069634

Metagenome

123

F078037

Metagenome

116

F078614

Metagenome

116

F083542

Metagenome / Metatranscriptome

112

Scaffold	Taxonomy	Length	IMG/M Link
JGI12340J11893_100281	All Organisms → cellular organisms → Bacteria	1423	Open in IMG/M
JGI12340J11893_100397	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Rhizobiaceae → Rhizobium/Agrobacterium group → Rhizobium → Rhizobium mongolense → Rhizobium mongolense USDA 1844	1272	Open in IMG/M
JGI12340J11893_100600	All Organisms → cellular organisms → Bacteria	1070	Open in IMG/M
JGI12340J11893_101232	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Acidisarcina → Acidisarcina polymorpha	784	Open in IMG/M
JGI12340J11893_101247	Not Available	780	Open in IMG/M
JGI12340J11893_101324	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Rhizobiaceae → Sinorhizobium/Ensifer group → Ensifer → Ensifer sesbaniae	760	Open in IMG/M
JGI12340J11893_101512	Not Available	711	Open in IMG/M
JGI12340J11893_101634	All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Ecdysozoa → Panarthropoda → Arthropoda → Mandibulata → Pancrustacea → Hexapoda → Insecta → Dicondylia → Pterygota → Neoptera → Endopterygota → Diptera → Brachycera → Muscomorpha → Eremoneura → Cyclorrhapha → Schizophora → Calyptratae → Hippoboscoidea → Glossinidae → Glossina → Glossina	688	Open in IMG/M
JGI12340J11893_101643	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	687	Open in IMG/M
JGI12340J11893_101646	Not Available	687	Open in IMG/M
JGI12340J11893_101883	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. AS23.2	651	Open in IMG/M
JGI12340J11893_102380	Not Available	588	Open in IMG/M
JGI12340J11893_102411	All Organisms → cellular organisms → Bacteria	585	Open in IMG/M
JGI12340J11893_102519	All Organisms → cellular organisms → Bacteria → Acidobacteria	575	Open in IMG/M
JGI12340J11893_102527	Not Available	574	Open in IMG/M
JGI12340J11893_102569	Not Available	570	Open in IMG/M
JGI12340J11893_102867	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	543	Open in IMG/M
JGI12340J11893_103410	All Organisms → cellular organisms → Bacteria	504	Open in IMG/M
JGI12340J11893_103448	Not Available	502	Open in IMG/M
JGI12340J11893_103475	Not Available	500	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

JGI12340J11893_100281

All Organisms → cellular organisms → Bacteria

1423

Open in IMG/M

JGI12340J11893_100397

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Rhizobiaceae → Rhizobium/Agrobacterium group → Rhizobium → Rhizobium mongolense → Rhizobium mongolense USDA 1844

1272

Open in IMG/M

JGI12340J11893_100600

All Organisms → cellular organisms → Bacteria

1070

Open in IMG/M

JGI12340J11893_101232

All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Acidisarcina → Acidisarcina polymorpha

784

Open in IMG/M

JGI12340J11893_101247

Not Available

780

Open in IMG/M

JGI12340J11893_101324

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Rhizobiaceae → Sinorhizobium/Ensifer group → Ensifer → Ensifer sesbaniae

760

Open in IMG/M

JGI12340J11893_101512

Not Available

711

Open in IMG/M

JGI12340J11893_101634

All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Ecdysozoa → Panarthropoda → Arthropoda → Mandibulata → Pancrustacea → Hexapoda → Insecta → Dicondylia → Pterygota → Neoptera → Endopterygota → Diptera → Brachycera → Muscomorpha → Eremoneura → Cyclorrhapha → Schizophora → Calyptratae → Hippoboscoidea → Glossinidae → Glossina → Glossina

688

Open in IMG/M

JGI12340J11893_101643

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium

687

Open in IMG/M

JGI12340J11893_101646

Not Available

687

Open in IMG/M

JGI12340J11893_101883

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. AS23.2

651

Open in IMG/M

JGI12340J11893_102380

Not Available

588

Open in IMG/M

JGI12340J11893_102411

All Organisms → cellular organisms → Bacteria

585

Open in IMG/M

JGI12340J11893_102519

All Organisms → cellular organisms → Bacteria → Acidobacteria

575

Open in IMG/M

JGI12340J11893_102527

Not Available

574

Open in IMG/M

JGI12340J11893_102569

Not Available

570

Open in IMG/M

JGI12340J11893_102867

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium

543

Open in IMG/M

JGI12340J11893_103410

All Organisms → cellular organisms → Bacteria

504

Open in IMG/M

JGI12340J11893_103448

Not Available

502

Open in IMG/M

JGI12340J11893_103475

Not Available

500

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
JGI12340J11893_100281	JGI12340J11893_1002812	F014658	MSTETRMAIEQSTPMPQRSESGVSVRYETKVLSHWDRQALAEVNDAFTYEIAWIPERQCWRSFLCSVSKLT*
JGI12340J11893_100397	JGI12340J11893_1003973	F065994	MPVERRGQVTDVGSEPTGNRRSSNSRREAAAFVRWHEPDDARVSRPDL*
JGI12340J11893_100600	JGI12340J11893_1006002	F024403	MWFLLRLDCLVDAKELLLNALDLILRGFRLLAIHLRSRRPRQSPMGAVHNRHHHLQIA*
JGI12340J11893_101232	JGI12340J11893_1012321	F018438	MGIDDKSSHPELCLEVAGGVTRTIVGLFREPDAGNPPVRFDEREQETELCQTGLRRRCKNFVNSHRETNATAPVLDSTQNPPQWLL
JGI12340J11893_101247	JGI12340J11893_1012472	F012657	KRLLSASPVMIAASLHQMAEKYDPQVAPTTLHLPEAVHADFREKVFLYREANVLLALVDRVNPSSDGRDSLFEPVFWEYERIIFRESSDHFGELSDHPILRAARRESVAAALQDLNFRMHPPRVNKWDFAVDWSRNWFAGIGHNELNPARLERFSEFWSREYTAVQQALDATVTTGR*
JGI12340J11893_101324	JGI12340J11893_1013242	F008634	MYGKGRELEIGNATSAIVISLLQALVDKHVLSNTEARAVLTKAADKLGPHDYTAPVKGAIGIILDDILQQFPENGGD*
JGI12340J11893_101512	JGI12340J11893_1015121	F055339	MKKATFLAALMMLAFCAFVVAQTAQQTAPKVKVGTQLNAKAATPAPGSNAKNTTQKASVGKGATSVKASQPSSFWTEELDVDDDGTVENSQYLYDAKRGILYTYREDDFACPNGNPESGSILMALYANGNPANKPVGSGWYLVNLNAGQCAAKKAGTFGCKFDANGNATECGAAAVNDAT
JGI12340J11893_101634	JGI12340J11893_1016342	F050959	YQDGDEPAPAAERAFYHLQDVREFLNVLGVGAQYVRDALRELAAGRSAFLTNIALTEKAIKNAGFSALLAAARG*
JGI12340J11893_101643	JGI12340J11893_1016432	F000466	WKKLPSQGVVKRDWVPTGRIDFATRFYGNLEDSDQPSEFKLIVEERRIVESITGNENLEIQWRLATLNEAKVVVAQYHKYLSENSLIKSVFDEPASLPPPKRIQKIQESTAA*
JGI12340J11893_101646	JGI12340J11893_1016462	F064047	MTLMKSPRAGRLALAFGVVLSVFLSVAAFDASYAQPAPGAAP
JGI12340J11893_101883	JGI12340J11893_1018831	F065924	EATTVCGHAKGYVTSACGPSVWTGRALQAESDDLEVIGLAHLYPACNGTFVPGQYGYPRALDLIRVSAPKAIRAT*
JGI12340J11893_102380	JGI12340J11893_1023802	F005155	VPRVRELMNLYEVTLHGTDSVYVLAPSKYRALELVGDYLADAGQPDVLKNGKFVVRQVNLNDEQILRPEKCRACPLNE*
JGI12340J11893_102411	JGI12340J11893_1024111	F078614	LLLFGLSPVVREVLQLSRLLKIFEIYENEQQALSA*
JGI12340J11893_102519	JGI12340J11893_1025191	F083542	KRIGAVLSRREFARRAALLSATSVVSPAAMLDLPSAGGGDYQVDAGGPKLSPEGQAEASARYQQVLSLYGERLNDEQKTRVKKMCAELQPALDHIRSYELENGNAPALYLKPLYEREKRQQSTSANGKP*
JGI12340J11893_102527	JGI12340J11893_1025271	F063348	PDRQGVPSVNVKKAEIEDLAFRFRDEVKAEILQHRGSNAVGVVGSFVVNIEAHRARYAKKLEAIRAGADAATVFLADEVGREIDALATKEIKRVRDAGRVEFEPGAADHQIPLEIHKIGLSDNQLEVIMRTAEPLAEEKCQEFLQRVAAILPMRGQISDDXVSVAVHRALSDIIRNSAVWKEWNQNSPPTL
JGI12340J11893_102569	JGI12340J11893_1025692	F012657	MIAMPSFKKKRRLRTSPVMLAASLHQMAERDDPQVAPETFRLPEAFHDRFREKILLYREANILLVLMDRVNPSRDGRDPLFEPVFWEYERIVFWELPRIFGESFNPDRAARRQSVAVALRDLNVRMHPPIGNRYDFALSWSRNWFAGIGHNEINPATLARFSSFW
JGI12340J11893_102867	JGI12340J11893_1028672	F000466	WKKLPSQGVVKRDWVPTGRIDFATRFYGNLEDSDQPSEFKLIVEERRIVESITGNENLEIQWRLATLNEAKVVVAQYXKYLSENSLIKSVFDEPASLPPPKRIQKIQESTAA*
JGI12340J11893_103410	JGI12340J11893_1034101	F025163	MQLTLAFLEPSPPARPSPSQKLDAETCAEALNILGRIIAQACETTQHTEATDE*
JGI12340J11893_103448	JGI12340J11893_1034482	F078037	MDVKLITAXLVTAFTASAALAQGPSTEKLKADAQEVVKIISSDSAKAQAYCETIKLGDQMDQAEQNNDSDKAEGLSNKIDELNQKLGPEYLKLGQDLQDIDPNSPDGLDLARTLAA
JGI12340J11893_103475	JGI12340J11893_1034751	F069634	IHAPSKPAVVVSLLLAILALIGYFVDSSFAFLIAMFAYIIGALGVLVEI*

Scaffold ID

Protein ID

Family

Sequence

JGI12340J11893_100281

JGI12340J11893_1002812

F014658

MSTETRMAIEQSTPMPQRSESGVSVRYETKVLSHWDRQALAEVNDAFTYEIAWIPERQCWRSFLCSVSKLT*

JGI12340J11893_100397

JGI12340J11893_1003973

F065994

MPVERRGQVTDVGSEPTGNRRSSNSRREAAAFVRWHEPDDARVSRPDL*

JGI12340J11893_100600

JGI12340J11893_1006002

F024403

MWFLLRLDCLVDAKELLLNALDLILRGFRLLAIHLRSRRPRQSPMGAVHNRHHHLQIA*

JGI12340J11893_101232

JGI12340J11893_1012321

F018438

MGIDDKSSHPELCLEVAGGVTRTIVGLFREPDAGNPPVRFDEREQETELCQTGLRRRCKNFVNSHRETNATAPVLDSTQNPPQWLL

JGI12340J11893_101247

JGI12340J11893_1012472

F012657

KRLLSASPVMIAASLHQMAEKYDPQVAPTTLHLPEAVHADFREKVFLYREANVLLALVDRVNPSSDGRDSLFEPVFWEYERIIFRESSDHFGELSDHPILRAARRESVAAALQDLNFRMHPPRVNKWDFAVDWSRNWFAGIGHNELNPARLERFSEFWSREYTAVQQALDATVTTGR*

JGI12340J11893_101324

JGI12340J11893_1013242

F008634

MYGKGRELEIGNATSAIVISLLQALVDKHVLSNTEARAVLTKAADKLGPHDYTAPVKGAIGIILDDILQQFPENGGD*

JGI12340J11893_101512

JGI12340J11893_1015121

F055339

MKKATFLAALMMLAFCAFVVAQTAQQTAPKVKVGTQLNAKAATPAPGSNAKNTTQKASVGKGATSVKASQPSSFWTEELDVDDDGTVENSQYLYDAKRGILYTYREDDFACPNGNPESGSILMALYANGNPANKPVGSGWYLVNLNAGQCAAKKAGTFGCKFDANGNATECGAAAVNDAT

JGI12340J11893_101634

JGI12340J11893_1016342

F050959

YQDGDEPAPAAERAFYHLQDVREFLNVLGVGAQYVRDALRELAAGRSAFLTNIALTEKAIKNAGFSALLAAARG*

JGI12340J11893_101643

JGI12340J11893_1016432

F000466

WKKLPSQGVVKRDWVPTGRIDFATRFYGNLEDSDQPSEFKLIVEERRIVESITGNENLEIQWRLATLNEAKVVVAQYHKYLSENSLIKSVFDEPASLPPPKRIQKIQESTAA*

JGI12340J11893_101646

JGI12340J11893_1016462

F064047

MTLMKSPRAGRLALAFGVVLSVFLSVAAFDASYAQPAPGAAP

JGI12340J11893_101883

JGI12340J11893_1018831

F065924

EATTVCGHAKGYVTSACGPSVWTGRALQAESDDLEVIGLAHLYPACNGTFVPGQYGYPRALDLIRVSAPKAIRAT*

JGI12340J11893_102380

JGI12340J11893_1023802

F005155

VPRVRELMNLYEVTLHGTDSVYVLAPSKYRALELVGDYLADAGQPDVLKNGKFVVRQVNLNDEQILRPEKCRACPLNE*

JGI12340J11893_102411

JGI12340J11893_1024111

F078614

LLLFGLSPVVREVLQLSRLLKIFEIYENEQQALSA*

JGI12340J11893_102519

JGI12340J11893_1025191

F083542

KRIGAVLSRREFARRAALLSATSVVSPAAMLDLPSAGGGDYQVDAGGPKLSPEGQAEASARYQQVLSLYGERLNDEQKTRVKKMCAELQPALDHIRSYELENGNAPALYLKPLYEREKRQQSTSANGKP*

JGI12340J11893_102527

JGI12340J11893_1025271

F063348

PDRQGVPSVNVKKAEIEDLAFRFRDEVKAEILQHRGSNAVGVVGSFVVNIEAHRARYAKKLEAIRAGADAATVFLADEVGREIDALATKEIKRVRDAGRVEFEPGAADHQIPLEIHKIGLSDNQLEVIMRTAEPLAEEKCQEFLQRVAAILPMRGQISDDXVSVAVHRALSDIIRNSAVWKEWNQNSPPTL

JGI12340J11893_102569

JGI12340J11893_1025692

F012657

MIAMPSFKKKRRLRTSPVMLAASLHQMAERDDPQVAPETFRLPEAFHDRFREKILLYREANILLVLMDRVNPSRDGRDPLFEPVFWEYERIVFWELPRIFGESFNPDRAARRQSVAVALRDLNVRMHPPIGNRYDFALSWSRNWFAGIGHNEINPATLARFSSFW

JGI12340J11893_102867

JGI12340J11893_1028672

F000466

WKKLPSQGVVKRDWVPTGRIDFATRFYGNLEDSDQPSEFKLIVEERRIVESITGNENLEIQWRLATLNEAKVVVAQYXKYLSENSLIKSVFDEPASLPPPKRIQKIQESTAA*

JGI12340J11893_103410

JGI12340J11893_1034101

F025163

MQLTLAFLEPSPPARPSPSQKLDAETCAEALNILGRIIAQACETTQHTEATDE*

JGI12340J11893_103448

JGI12340J11893_1034482

F078037

MDVKLITAXLVTAFTASAALAQGPSTEKLKADAQEVVKIISSDSAKAQAYCETIKLGDQMDQAEQNNDSDKAEGLSNKIDELNQKLGPEYLKLGQDLQDIDPNSPDGLDLARTLAA

JGI12340J11893_103475

JGI12340J11893_1034751

F069634

IHAPSKPAVVVSLLLAILALIGYFVDSSFAFLIAMFAYIIGALGVLVEI*

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300000701: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 4

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences