3300000909: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 37

Overview

Basic Information

• IMG/M Taxon OID: 3300000909
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0075432 | Gp0054358 | Ga0001960
• Sample Name: Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 37
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 26999708
• Sequencing Scaffolds: 43
• Novel Protein Genes: 46
• Associated Families: 46

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	1
All Organisms → cellular organisms → Bacteria	9
All Organisms → cellular organisms → Bacteria → Acidobacteria	4
Not Available	17
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → Rhodospirillaceae → Magnetospirillum	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → Pseudolabrys taiwanensis	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Candidatus Koribacter → Candidatus Koribacter versatilis	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?
F000466	Metagenome / Metatranscriptome	1105	Y
F001023	Metagenome / Metatranscriptome	804	Y
F001343	Metagenome / Metatranscriptome	719	Y
F002758	Metagenome / Metatranscriptome	532	Y
F002851	Metagenome / Metatranscriptome	526	Y
F002989	Metagenome / Metatranscriptome	515	Y
F003446	Metagenome / Metatranscriptome	486	Y
F004609	Metagenome / Metatranscriptome	431	Y
F005718	Metagenome / Metatranscriptome	392	Y
F005756	Metagenome / Metatranscriptome	391	Y
F006122	Metagenome / Metatranscriptome	381	Y
F006520	Metagenome / Metatranscriptome	371	Y
F006633	Metagenome / Metatranscriptome	368	Y
F012657	Metagenome	278	Y
F012694	Metagenome / Metatranscriptome	278	Y
F014866	Metagenome / Metatranscriptome	259	Y
F016424	Metagenome / Metatranscriptome	247	Y
F019842	Metagenome / Metatranscriptome	227	Y
F022259	Metagenome / Metatranscriptome	215	Y
F025073	Metagenome / Metatranscriptome	203	Y
F025544	Metagenome / Metatranscriptome	201	Y
F025548	Metagenome / Metatranscriptome	201	Y
F026658	Metagenome / Metatranscriptome	197	Y
F029348	Metagenome / Metatranscriptome	188	Y
F031318	Metagenome	182	Y
F031584	Metagenome / Metatranscriptome	182	Y
F032686	Metagenome	179	Y
F034415	Metagenome / Metatranscriptome	175	Y
F035091	Metagenome / Metatranscriptome	173	Y
F036023	Metagenome / Metatranscriptome	171	Y
F047330	Metagenome	150	Y
F050117	Metagenome / Metatranscriptome	145	Y
F053456	Metagenome / Metatranscriptome	141	Y
F063348	Metagenome	129	N
F064047	Metagenome / Metatranscriptome	129	Y
F065502	Metagenome / Metatranscriptome	127	N
F069634	Metagenome	123	Y
F078037	Metagenome	116	N
F083188	Metagenome / Metatranscriptome	113	Y
F083637	Metagenome / Metatranscriptome	112	N
F085919	Metagenome	111	Y
F086431	Metagenome / Metatranscriptome	110	Y
F091102	Metagenome	107	N
F094186	Metagenome / Metatranscriptome	106	Y
F095279	Metagenome	105	N
F104209	Metagenome	100	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI12488J12863_100017	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	5112
JGI12488J12863_100159	All Organisms → cellular organisms → Bacteria	2714
JGI12488J12863_100474	All Organisms → cellular organisms → Bacteria → Acidobacteria	1944
JGI12488J12863_100582	Not Available	1798
JGI12488J12863_100797	All Organisms → cellular organisms → Bacteria	1595
JGI12488J12863_100934	All Organisms → cellular organisms → Bacteria	1495
JGI12488J12863_101186	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1367
JGI12488J12863_101609	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1208
JGI12488J12863_101951	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1104
JGI12488J12863_102146	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → Rhodospirillaceae → Magnetospirillum	1055
JGI12488J12863_102445	Not Available	992
JGI12488J12863_102714	All Organisms → cellular organisms → Bacteria → Acidobacteria	945
JGI12488J12863_102804	Not Available	931
JGI12488J12863_102846	All Organisms → cellular organisms → Bacteria	925
JGI12488J12863_102930	Not Available	912
JGI12488J12863_103059	All Organisms → cellular organisms → Bacteria	896
JGI12488J12863_103293	All Organisms → cellular organisms → Bacteria	866
JGI12488J12863_103710	All Organisms → cellular organisms → Bacteria → Acidobacteria	816
JGI12488J12863_103829	Not Available	804
JGI12488J12863_104448	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	751
JGI12488J12863_104544	Not Available	742
JGI12488J12863_104752	Not Available	728
JGI12488J12863_106265	Not Available	645
JGI12488J12863_106419	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	638
JGI12488J12863_106520	Not Available	633
JGI12488J12863_106625	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	628
JGI12488J12863_106944	Not Available	615
JGI12488J12863_107147	Not Available	606
JGI12488J12863_107470	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	595
JGI12488J12863_107527	Not Available	593
JGI12488J12863_107803	Not Available	584
JGI12488J12863_107984	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → Pseudolabrys taiwanensis	578
JGI12488J12863_108151	All Organisms → cellular organisms → Bacteria	573
JGI12488J12863_108522	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	562
JGI12488J12863_109630	Not Available	535
JGI12488J12863_110114	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Candidatus Koribacter → Candidatus Koribacter versatilis	524
JGI12488J12863_110247	Not Available	521
JGI12488J12863_110384	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	518
JGI12488J12863_110490	Not Available	516
JGI12488J12863_110556	All Organisms → cellular organisms → Bacteria	515
JGI12488J12863_110666	All Organisms → cellular organisms → Bacteria → Acidobacteria	513
JGI12488J12863_110924	Not Available	507
JGI12488J12863_111309	All Organisms → cellular organisms → Bacteria	500

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI12488J12863_100017	JGI12488J12863_1000177	F083637	MKKMLVVICSLVLALSLAGCGWGPWAGKGPIIGKGKAPAPVVTKG*
JGI12488J12863_100159	JGI12488J12863_1001591	F104209	SAHGDEGTHAHSTLSAETTHVQVFYRFHPLYSSTLQILRRPKRGDGAVCVSDPMGRRLKIPMWMLLPNSAEMKIAEQAYLSKEALLSLVLLVSTPREIENRVHANLLQAVVDTCKGGQRATTTTPGAGDRKSGGHGADRRRDTNRTDRSHGPHSGGGLSNGRRKSR*
JGI12488J12863_100474	JGI12488J12863_1004742	F036023	MKRLFPQCSVLALMLTLALSAVAKPKTENITLYHDARVNGTSLPAGDYVVKYDVEGTNVQLKXMQGNKEVASTTGQVKTLDKMVGSNQVVLNNQDRSIAEIDFRGNGSAITFGSPSTMGGK*
JGI12488J12863_100582	JGI12488J12863_1005821	F091102	MKQWKLLPLICGAWVVTWYPSWAIEKRFLEIPGPHDSIVTFDLDTVQIIQPGRFTVVSTEIDNPEVMQFRLNVLEHLRTHCAHAEGKYPAPPELFTLGRPDIAVGDIEVAHVSGSKFVRWFYPYRLLSPTLENYEILFCDGESNYFEMRTLIANGSRHKDVYDCTRGLYGTMHDENDPTSALLIVVPEGSYLFDYYVAVCRAVTHEEPYLPQKH*
JGI12488J12863_100797	JGI12488J12863_1007973	F016424	VAKSSSKSARKTVRDEKSEFGKDRRRRHHHYLVTVNYADGETFGRVYTDKEKATKFAERQRRSPIVKSARVTQVS*
JGI12488J12863_100934	JGI12488J12863_1009342	F006633	VSTRSSAPVVRLSVCLISCLMLLAAALSVTSVAAQDRKVPQTVGVDNSKMGPYRALAQLAYAASQKGDNATAAMLAKILERTWDKAEDYGGDTALSKTNHALFEEIDKAMDQFGNMLIDHPNSAPDQAKLKAAYTYYLEKLKLGD*
JGI12488J12863_101186	JGI12488J12863_1011861	F083188	MAFCEGVPKRLFATSIAIAIAVCMMGALAAAQTTLQPRAEVFGGYSWLNPDGYVDWGKVNSIAHGWNASSTFYFPNARNLGAVIDGSGHYNGQEANVGLGLLGLQYKFRNDQFSPF
JGI12488J12863_101609	JGI12488J12863_1016092	F000466	MAHLLTYMTTPEAWQRWKKLPSQGVVKRDWVPTGRIDFATRFYGNLEDSDQPSEFKLIVEERRIVESITGNENLEIQWRLATLNEAKVVVAQYXKYLSENSLIKSVFDEPASLPPPKRIQKIQESTAA*
JGI12488J12863_101951	JGI12488J12863_1019511	F047330	GPDPEQIAIDHVHAKIAVADKALLNFCAKFNKLPSKIGADDIEVLRTYGFGEQHILEAIVTVGFAQFANTVAFGLGTVPDFHNRRIQEELGKARAVELGVHVPAAG*
JGI12488J12863_102146	JGI12488J12863_1021463	F005718	VLECTTKYARLIRFVAQRFDEMAKRKKRVATVNRKLGISINCRVQKPFLKDLDAYRKPLKLSRPAALVKLATEHLAGLKEPAEKLWEGAVERMFPAAS
JGI12488J12863_102445	JGI12488J12863_1024454	F031318	MRTTTFLSVTTVVLAFLIVAHSRTVGLTTGSPLQNTMSIYDLDVGHPNMKNLPVQE
JGI12488J12863_102714	JGI12488J12863_1027142	F094186	GAITRNIFMKAPEPREQAIIAHGNFVNLPDEEKRTYENRVVTFFLTRLPINAAPPVAAPTKTAKVVKASN*
JGI12488J12863_102804	JGI12488J12863_1028041	F078037	MDAKVSAVILVTAFTASAAPAQGPSTEKLKADAQEVVKIISSDSAKAQAYCETIKLGDQMDQAEQNNDSDKAEGLSNKIDELNQKLGPEYLKLGQDLQDIDPNSPDGLDLARTLAALDKLCK*
JGI12488J12863_102846	JGI12488J12863_1028461	F031584	YALGHVWTAPWQELSDVAAALVGCGHVSGLLMRRMCRWP*
JGI12488J12863_102930	JGI12488J12863_1029301	F035091	MTDAKSYWHVVVFRCVHCGKNEAFAEESSAVEPREEQVRRKTYQAICRHCGWQGEARGISAIE
JGI12488J12863_103059	JGI12488J12863_1030591	F022259	MATAAGLTEAVLYDALVNYLVSMARTVESAMNRALDAIVGFDSP
JGI12488J12863_103293	JGI12488J12863_1032933	F006122	MAIILDADVVIRGEKGTFDLAKWVTSRPNDRFEIAAITVAELWHG
JGI12488J12863_103710	JGI12488J12863_1037101	F001023	FQPVGEKELWGDLADTLHLVYVFSAKGDPLRKTLAERHFDAVYLGDKKMGFISEEFRSQMLEIWKVKYLEMARLRMVITSIPTEIQLEHFLNDGDSPDIPIPVYVEYLNKIREMARAGK*
JGI12488J12863_103829	JGI12488J12863_1038291	F064047	MTLKKSSRAGLLALAFGVLLGLFLSVASFDASYAQTPA
JGI12488J12863_104448	JGI12488J12863_1044482	F053456	VNSAFYVPLAGIAVMAIGLIVVGTAAWRTHKTSSRLEFIRSLGNEAELYTEPVQVPERVTTSLLTRIFGPLKNGLRHNLARLYPSKETDRVHADLLKAGLTGSVRAEEFVAVQVGAVLLGFGAGLIALVSGFVSVK
JGI12488J12863_104544	JGI12488J12863_1045441	F012657	MIAMPSFKKKRRLRTSPVMLAASLHQMAERDDPQVAPETFRLPEAFHDRFREKIXLYREANILLVLMDRVNPSRDGRDPLFEPVFWEYERIVFWELPRIFGESFNPDRAARRQSVAVALRDLNVRMHPPIGNRYDFALSWSRNWFAGIGHNEINPATLARFSSFWSSEYTAVQKVLDAAVKTSRRLIDFTFIKRRILNLWSGG*
JGI12488J12863_104752	JGI12488J12863_1047521	F006520	MWILVIYVSIVAISETVVALLGLTLDRIYPALSLPISLSLFFAVLWLAWIVAVRLTKPKHAKADT
JGI12488J12863_106265	JGI12488J12863_1062651	F063348	NLKKAEIEDLAFRFRDEVKAEILQHRGSNAIGVVGSFVVNIEAHRARYAKKLEAIRAGADAATVFLADEVGREIDALATKEIKRVRDAGRVEFEPGAADHQIPLEIHKIGLSDNQLEVIMRTAEPLAEEKCQEFLQRVAAILPMRGQISDDDVSVAVHRALSDIIRNSAVWKEWNQNSPPTLQDGQVSDAA*
JGI12488J12863_106419	JGI12488J12863_1064192	F032686	GGAIRYTHVVRLHDAAEATAEEGTGTLKGDDISLQGSWKGGNRQYEAKYSGTFVRRHAALKGTQTWSDGGKTVSRDCVGIIKRPLKVFLPRDKK*
JGI12488J12863_106520	JGI12488J12863_1065201	F086431	VVPNQGLQGIAFFEATVCLTLLVLFVHLKRDNSSAFYRLWLLGWVCLTFSSFTELTMFYGQFARLHLLASGTDVAALALFFASVVQLTVAQNRLYVPMLWLAGVMALVTCYYESGPTGWWETRWETSLLESATCLCAGWF
JGI12488J12863_106625	JGI12488J12863_1066251	F005756	QSIIVTHVRRKLIWCSILGGVFITLLAIMLRFAGINGPVPYLTYAGAYLMETFFQRFLEWIPWKYADNLISEVVLFLVLNISSYAFIIFLLLRIFFPDRSSELPPLTGKK*
JGI12488J12863_106944	JGI12488J12863_1069441	F034415	MAVAEGTHRSLQLVEGEAYRRIMSGEAPATLTEFAQQLLDWFRASRSDATPITQAAVENQIRDTWHRRHDMIRGGAS*
JGI12488J12863_107147	JGI12488J12863_1071471	F095279	TFSPHHQGIPLGARRAEGKILIHLRQSAPVVEKRSLAAYERVANGGGR*
JGI12488J12863_107470	JGI12488J12863_1074701	F002989	MARFQAEEPNGVAVQQLEVLVRTAVFKSANLLVGWLLQKAADQIDGAYQPQPGQHYKGRIGSQIEGMFGSFPLERDYYYHEGKRQG
JGI12488J12863_107527	JGI12488J12863_1075271	F025073	APLFAQKSPAPPKAADYEDADGYVVLSILLSHVHSEVDPSFLLAPFLLSPLTVPGIKADSFQSCNRVPTEFASAAADFRDKNKQNWNLTKKIDLKFRYKFTNLTGKRPWLAPTQNAKDVPPALFETSVYQVSAVGFDASRTHAIAYVGAVCGPDCSSGSYHLLVKEKEGWKETTGSPVCQLISLNLDFLFKRSPS*
JGI12488J12863_107803	JGI12488J12863_1078031	F050117	TLPIYGVADHVAFIMSAVATLQAGDFGTIREARRKALYNVSDESFSEYLAYTQIMIGMLNRLDLYKEYRSH*
JGI12488J12863_107984	JGI12488J12863_1079842	F025544	WGPINADAVTTVQQFNARLSAKGRIWAWPTIAAALASKHHWLVIACDSCETVIDLDLRVKPREPDASIRVALHDVRCPRCNGHGRTRITALAQYPSI*
JGI12488J12863_108151	JGI12488J12863_1081511	F025548	EVRLCAGINRHEVENERVLRERSSDPLGPEFCAGYREVHSEA*
JGI12488J12863_108522	JGI12488J12863_1085221	F003446	GAQAMVKNSQESLVGAIERHIENAQRNLMTQRNELNQYLDTMATGTVERVQRNLETSRTKATERFVLRLREQVAPVMEEARADLQKLVASQAVFKEESLAIYRQVTDQLESDANARLLQTHDQLEKNSTSVVNECNEKMLELSQAFEKIARDSAQNMIASATDKGNKNLEERAAEISSHFTNQLEGH
JGI12488J12863_109408	JGI12488J12863_1094081	F085919	MDQVTHSGDWTRRRKLVVAGLISLTLVIGIMIGTVVSGKVSAMRTFSFGGTNAAPLALPDPIPSSNSFS
JGI12488J12863_109630	JGI12488J12863_1096302	F002851	MKSYIETAALITGCGSAAFWFASALCHLPGIKPGTNEQDKATELSNRLQRMSTWNFWAAGLMG
JGI12488J12863_110114	JGI12488J12863_1101141	F001343	SRRYFGKEKGAAMKFATFAKSLVMGLALLLASSAFAASKASLILQHPTIVNGTKLDAGEYKLQWDGSGPDVEVSIMKGKNVLAKVPAKVVDLPVAALNDAAVVKNSDGSSTLAGVRFQGKKIGLDIGESSDGMQAGSSK*
JGI12488J12863_110247	JGI12488J12863_1102471	F002758	MKVAALAAVSVLIALPAEAGQRHRQNIVSPSCDNGARCTTLNVAAPTSNKAPSLRGRHIGTSERKPRRVVDANGNSMMVTVRTAYGFNITVHPAYASKFQKFFALLKDRGYKVPANIVKCWAPRGTRVGGSNHYIGAACDIQTGWNRGPEFVYHMGDVVKQAGLYNGCS
JGI12488J12863_110384	JGI12488J12863_1103841	F004609	LATTLSVMLISSALARQGTKMDPNAKTMTIEGAVRDLACPVQNPDGTATNFDLKCTLDCVKHGSPIIILTKDGLIYFPISADMPDSDQREKMMPFVGKYVQVTGAVFERKGTRAIAITQIKEIKNVHPDTGGK*
JGI12488J12863_110418	JGI12488J12863_1104181	F026658	GARLEANTILVEEERLLIGADPLGVYEFRRPDRVH*
JGI12488J12863_110490	JGI12488J12863_1104901	F012694	IIGGLIMTEEINDTSNRVDPSAHHTFLAFWHGRVVYENGRVKHFETEHDAWQFLARCDAAGKIIH*
JGI12488J12863_110556	JGI12488J12863_1105561	F029348	MTQTLRNLVLFFERDVRIARTYRGPFVLELLEALFGAALFYYVARFVDSPELRQALPQGTSYFAYSLVGFVFFDYLNAALDTFDRSIL
JGI12488J12863_110666	JGI12488J12863_1106662	F014866	VVVSGLTSEQVAEIKSSIQATQKFIGELLEHASRWELEGAELRIYFPPEKSTFAGLIEGRDTTEKIRTSSNKVLGRAVRVCAKLDSGAVNDANASSRAATTQEMRAQFENDPVVKSMLQRFGGRISEVRRRTGD*
JGI12488J12863_110924	JGI12488J12863_1109242	F069634	VKVXIHSPNKPPVVVSLLLAILALIGYSVDSSFAFFIAMFAYIVGALGVLVEI*
JGI12488J12863_110962	JGI12488J12863_1109621	F065502	MRENMSLLSFWGLVFSLIAVTLFVVIYSYQKSKYANRRIVGDLRQRSVDVYLAAKTPEAESDSKIPSGQQ*
JGI12488J12863_111309	JGI12488J12863_1113091	F019842	GQISVKFSTADLTILRIRCQKCGQHTEKLVTLLLRKDAIQCSSCGERISLATPTNKILISETAASCARVGEALVKGLSLA*