3300000719: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 44

Overview

Basic Information

• IMG/M Taxon OID: 3300000719
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0075432 | Gp0054563 | Ga0001967
• Sample Name: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 44
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 14139040
• Sequencing Scaffolds: 17
• Novel Protein Genes: 17
• Associated Families: 15

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
Not Available	10
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Patescibacteria group → Parcubacteria group → unclassified Parcubacteria group → Parcubacteria group bacterium GW2011_GWA2_47_8	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Verrucomicrobiae → Verrucomicrobiales → Verrucomicrobia subdivision 3 → Pedosphaera → Pedosphaera parvula	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?
F001169	Metagenome / Metatranscriptome	758	Y
F007624	Metagenome / Metatranscriptome	348	N
F008634	Metagenome / Metatranscriptome	330	Y
F012657	Metagenome	278	Y
F014460	Metagenome / Metatranscriptome	263	Y
F015418	Metagenome / Metatranscriptome	255	Y
F027605	Metagenome / Metatranscriptome	194	Y
F034030	Metagenome / Metatranscriptome	175	Y
F037757	Metagenome / Metatranscriptome	167	Y
F046870	Metagenome / Metatranscriptome	150	N
F047205	Metagenome / Metatranscriptome	150	Y
F057789	Metagenome	135	N
F073875	Metagenome / Metatranscriptome	120	Y
F075781	Metagenome / Metatranscriptome	118	Y
F078037	Metagenome	116	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI12378J11916_100024	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	3279
JGI12378J11916_100091	Not Available	2250
JGI12378J11916_100223	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1799
JGI12378J11916_100231	Not Available	1781
JGI12378J11916_101149	Not Available	1014
JGI12378J11916_101840	Not Available	825
JGI12378J11916_102720	Not Available	689
JGI12378J11916_103360	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	630
JGI12378J11916_103634	Not Available	606
JGI12378J11916_103677	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Patescibacteria group → Parcubacteria group → unclassified Parcubacteria group → Parcubacteria group bacterium GW2011_GWA2_47_8	604
JGI12378J11916_104069	Not Available	577
JGI12378J11916_104152	Not Available	572
JGI12378J11916_104701	All Organisms → cellular organisms → Bacteria → Acidobacteria	541
JGI12378J11916_104790	Not Available	536
JGI12378J11916_105246	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Verrucomicrobiae → Verrucomicrobiales → Verrucomicrobia subdivision 3 → Pedosphaera → Pedosphaera parvula	515
JGI12378J11916_105481	Not Available	505
JGI12378J11916_105603	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	500

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI12378J11916_100024	JGI12378J11916_1000244	F007624	PMQLREGSFHGPRPTCPKHPKQRVHRHGFYVRFENCDSQRRLRIERFVCPRCGRTLSVLPKNRLPYVAVNTTILESDFDARASGTDPPSCSEKERGCLGRAFERFADRVAPLCALLGQMIRPIKPSVSECWRALRQLDNLEGILLLLGTKFNTSLLADYRCLQPGF*
JGI12378J11916_100091	JGI12378J11916_1000911	F034030	MPFDQKGRRMRRREFILLGAYVIAGCVAAVTSADLALAQAKNSTSMEDRLSAKIRCQDFQKNSDGKWTSSSKAKIGKIDFSNHTFGVDEVDIGGADLATFLNRKCAAH*
JGI12378J11916_100223	JGI12378J11916_1002233	F012657	QMAERDDPQVAPETFRLPEAFHDRFREKILLYREANILLVLMDRVNPSRDGRDPLFEPVFWEYERIVFWELPRIFGESFNPDRAARRQSVAVALRDLNVRMHPPIGNRYDFALSWSRNWFAGIGHNEINPATLARFSSFWSSEYTAVQKVLDAAVKTSRRLIDFTFIKRRILNLWSGG*
JGI12378J11916_100231	JGI12378J11916_1002311	F057789	MSETALQFTGTDLRGLLDVLLEALKVIRRTGRRPTITVNGKLYASHDLRKVAALLPDEELQPHHQALVNVMFAKKQRGYRKTAYNLADRVNSWRTEEQKLAARQAAKTSALAVAEPAPFRNRGFSERTIRALMDCSI
JGI12378J11916_101149	JGI12378J11916_1011491	F015418	MSIVSRRTFSTGVLASALLPAHSAIGQPNDPASIAIIDTPHNAARVASKLAAQNVKVVVRFFARKPQPWLHEKVMASDGNMIDGVREPALLIRHGLSIVS
JGI12378J11916_101840	JGI12378J11916_1018401	F078037	MDAKVSAVILVTAFTASAALAQGPSTEKLKADAQEVVKIISSDSAKAQAYCETIKLGDQMDQAEQNNDSDKAEGLSNKIDELNQKLGPEYLKLGQDLQDIDPNSPDGLDLARTLAALDKL
JGI12378J11916_102720	JGI12378J11916_1027201	F037757	VTAILRRNAPFWISIACGIALWEIAGRSTSAAFMVPFSATMLRLWQLIVSDQFVEQFFDSARLFLTGFVI
JGI12378J11916_103360	JGI12378J11916_1033601	F001169	VILQGPELEECTHLQQASAAQELQVKAETRLAALMEEKLVTRISVISTLLGGGKTTERLLVRISIETHKASQDFDQSAADNAKTRIKQALGDIGHDVFIETDR*
JGI12378J11916_103634	JGI12378J11916_1036342	F014460	VAANIAEAEAQKGVRGTARRVRKALTGKQTAPKKGKK*
JGI12378J11916_103677	JGI12378J11916_1036771	F075781	KEPAMTAGAVIKKAFPVVMVSVLDSKDGSVEVIK*
JGI12378J11916_104069	JGI12378J11916_1040692	F073875	MATETMTAEKMRRKPFVQLLGTCKDCGQPVIAGQEFLRTEHGIEHALCFYEPDYAKRARELKPKTSV*
JGI12378J11916_104152	JGI12378J11916_1041521	F047205	MKTHTGKDATAAYSPTKGHSVVIYTHKFKPEHFRKGAEIVTKQFPDAQAQSKTPQKRLNIFLRRPSTHEIVNVSFFDAGPGVHDWHESEGRLKTVERLQDMLEKPIDVQVFEV
JGI12378J11916_104701	JGI12378J11916_1047012	F027605	YRFHEMTITGMSLAGERQIRDAWTIKPGDVLDKVVFEQFLTTLESHRDNIFKGLPVHYDTVGHWLQTDPEKGTVDVLLDFK*
JGI12378J11916_104790	JGI12378J11916_1047901	F012657	ETKAAASKMVAMPGLKKGEKQRILSASPVMIAASLHQMAEKDDPAVAPETLRLPEAVHAGFRQKVLLYREANVLLALMDRVNPSRGRRDPLFEPVFGEYERIIFQESPDPIVRATRRQSVTAALQDLRLRWHPPMGNKHDFARDWSRNWFAGIGYKEMNSTRFERFCWFWSAEYSAVQ
JGI12378J11916_105246	JGI12378J11916_1052461	F046870	MATTPESFVDAINSAFGKQTTQRAAHAKGVVLLGKFVPSAEA
JGI12378J11916_105481	JGI12378J11916_1054811	F012657	QVAPMTLHLPEAVHADFREKVFLYREANVLLALVDRVNPSSDGRDSLFEPVFWEYERIIFRESSDHFGELSDHPILRAARRESVAAALQDLNFRMHPPRVNKWDFAVDWSRNWFAGIGHNELNPARLERFSEFWSREYTAVQQALDATVTTGR*
JGI12378J11916_105603	JGI12378J11916_1056031	F008634	MYGKGREVEIGNATSAILISLLRTLAEKEILSNADVRSLLTNAASDLGPHEYTAPVKGAIGIILDDILPRFPEDGGD*