3300003380: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant M2 S PM

Overview

Basic Information

• IMG/M Taxon OID: 3300003380
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0110179 | Gp0089083 | Ga0008485
• Sample Name: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant M2 S PM
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 11532438
• Sequencing Scaffolds: 21
• Novel Protein Genes: 22
• Associated Families: 22

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea	15
Not Available	3
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	1
All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	1
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp. SCGC AG-212-E16	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Arabidopsis Thaliana Rhizosphere Microbial Communities From The Joint Genome Institute, Usa, That Affect Carbon Cycling
• Type: Host-Associated
• Taxonomy: Host-Associated → Plants → Rhizoplane → Epiphytes → Unclassified → Arabidopsis Thaliana Rhizosphere → Arabidopsis Thaliana Rhizosphere Microbial Communities From The Joint Genome Institute, Usa, That Affect Carbon Cycling

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): Host-associated → Plant → Plant rhizosphere

Location Information

• Location: Joint Genome Institute, California, USA
• Coordinates
  • Lat. (^o): 37.931388
  • Long. (^o): -122.021761
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F005683	Metagenome / Metatranscriptome	393	Y
F006898	Metagenome / Metatranscriptome	362	Y
F007651	Metagenome / Metatranscriptome	347	N
F010272	Metagenome / Metatranscriptome	306	Y
F012397	Metagenome	281	Y
F013352	Metagenome / Metatranscriptome	272	Y
F016471	Metagenome / Metatranscriptome	247	Y
F017423	Metagenome / Metatranscriptome	241	N
F020931	Metagenome / Metatranscriptome	221	Y
F023901	Metagenome / Metatranscriptome	208	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI26144J50225_100089	All Organisms → cellular organisms → Archaea	4269
JGI26144J50225_100399	All Organisms → cellular organisms → Archaea	1757
JGI26144J50225_100475	All Organisms → cellular organisms → Archaea	1516
JGI26144J50225_100508	All Organisms → cellular organisms → Archaea	1441
JGI26144J50225_100687	All Organisms → cellular organisms → Archaea	1127
JGI26144J50225_100697	All Organisms → cellular organisms → Archaea	1118
JGI26144J50225_100746	All Organisms → cellular organisms → Archaea	1062
JGI26144J50225_100986	All Organisms → cellular organisms → Archaea	877
JGI26144J50225_101287	All Organisms → cellular organisms → Archaea	741
JGI26144J50225_101412	Not Available	708

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI26144J50225_100089	JGI26144J50225_1000895	F023901	MKDNCSLKMRSRHNEQGQSCEGGVPLDPNKFGGYEFAINTKGWDAKREPTHNCHDQHKSGLIPTNLENDKAVRLRQTVKDESGKVHQIGEIDYMDGNGFHKVMDIFDSSPNPWMVDRNLYETKSYFWIRNNGSGYITVRDVSLEILS*
JGI26144J50225_100399	JGI26144J50225_1003992	F100610	MPVIISLFGNEDMEITEFPLTNKSVFYRCSYGECFRFIADKCMHCCANPIPDTEMHINYLRRLPDIKKAVTDLGI*
JGI26144J50225_100475	JGI26144J50225_1004751	F005683	MEKSNGTKIMGILLVFGLVVYSIYFGQISFAEGVELKTVGKGAISCGNGEEVKGVRINFFVSYDEETPFAEWNMDHKELGSAGGETPFAEWNMDHKELGSAGGMITNVKTSSDSFVLKGFEAFDSICDVETPSDVKLSGNCGEGTVRLVSDNGNKGTFASNVKCG*
JGI26144J50225_100508	JGI26144J50225_1005082	F010272	MYMNHERKLILIAIGAFVTLSLFVFPSTNMIAYSQSENKTQGKEQAQEKLFELAQKFNKILKDSNVNLTLPQNGDLSSKLQELKDSGAFKELSEKFSQAVQELGQGNKTEELKQEAGADLSTLMQKLQSLRNNSTQ*
JGI26144J50225_100571	JGI26144J50225_1005712	F073212	EPGFNIVINANGFTPNGTVAWKFVGSDSKILXYGYFETNSTGGFNDVTFADDLKQDHYKLYFADDVNTDGTFDIGAKRIYSNVTIPCGQ*
JGI26144J50225_100687	JGI26144J50225_1006872	F057496	MAGVYRNHTKVAEDHSSAYCKDEYVFGXKGEPLRLSHLIAFNVIEDAEHISGILTVEFDYYSDDDSIKYRDMHYSNPRLIKHIEGNPTVMKNIDAYLRNNLLESEYGLKL*
JGI26144J50225_100697	JGI26144J50225_1006971	F068543	ESAIDQAGNSLSPGDLITPQKVTYLFSAQASETVQALEEEGPQDYQYECALDDESFNSCNSPMTYELDEGKHDFVVRLVP*
JGI26144J50225_100746	JGI26144J50225_1007462	F013352	MASSTNAQIEVTVDENVSTPISNSTLSEDAEPRPDILYSALNKDTIVGEVLNNFSYPIELVRITATVYDKNGIIVATGDKYVNDYLIKPGSRSGFDIFLDETLPSKSKYALTTSFEKSEDDKPEALQLSVGKNSKSSNTFRVLGEVMNQGKNDANAVKVSAIFYDEKHKVMDTDYVFTNPDIISPNKKAPFEFSFYVDNPEKIKSMAFNVQSDEFSLITDNGQNNTISQQ
JGI26144J50225_100986	JGI26144J50225_1009861	F088429	QPETNASLNVPEPQPETNASLNVPEPQPETNASDIITPRSIDLNITVGKDPIARSENQMVTVVALDPTTGKVLDRVFIKLEIKDPVGILVKNYTGTVGNLTRTFKIGENAIGTFIISATASQAGVQSTKSLPFQVQ*
JGI26144J50225_101287	JGI26144J50225_1012871	F006898	MYLILTTTLLLFSLFSLPGAFGAEMFKGLSFSIDIPNTWAYTETPEAPIERALGVSSYTSVVLVPVQFAELLIQEKGDIGMGNGSTAIVFAKASDYSVKNAPLDLYVKYRMNEDDSLNVTSQQDTTIGKEKAVRIDGNKNNNASNIRLLEYLLLHNDEPYVIRYIASMDDFE
JGI26144J50225_101412	JGI26144J50225_1014121	F050439	MLYDVLHVTEGWGPLQAVEISITLLYCIDFFYLQSDLGSDQLPQGNWRDTMLDAAIAVVFGAAYWQASDRKLFTCYALLAVAGALIVAYHFTPNRRFLWAILPHSVLTVLFVSLAWLARGLENVTWTFAVVSWFPTIWYGTYVFWLAHRILPSGK*
JGI26144J50225_101570	JGI26144J50225_1015703	F007651	MSNDLNELIARKDKLEGELHLELSSDYNELMKNLSESFRDMHENSVQYYKQKANEELDKMEKNIQSGNKLSAINQ
JGI26144J50225_101979	JGI26144J50225_1019791	F012397	KLRSVGYVSVRIKRNKNNKKGVRWNRILILIVLVTTLSLLSGPSLSFSEIKNEINVTPPLNWEPSPTNNSTTMIWFQNYTKSIFAITKAPDDLVFPLFIAGPFMTGYLKYKGVLESADRLTFGHSNYGYRYFLNLSSPSKLLDSSSGLIPKNEFLSKIPEGYDVPFKGMLIXTQKHXELYAIIFLNPKEKFDSMLNQIQPT
JGI26144J50225_102022	JGI26144J50225_1020221	F086321	MNPSKKEIYKILERFTSQKGGILIILHNSFSSDSKPPQEQTSVVRDDERKSAIFEINFGTVAGLSMLCECEKALADQVMSLDFLDSG
JGI26144J50225_102077	JGI26144J50225_1020771	F020931	LSPRFGFFKRKTPDYFHDKESQANSVHSVSNKELLEIVENEKKVLQKDLIDNLEPTRNLVLDCLNRLRKNADELEEQEIKAESPQFESLINTSKKILITSIKKESLIESYQIKSYEDAIKFKNNLELLINRFGQVGDSHNRILNEFMRKQINKLKSE
JGI26144J50225_102188	JGI26144J50225_1021881	F016471	MTEADKFGAVKDATVAIGLANKDTKDVISSFGTGFFIGGEYIVSSAHIFSQCIKYNAQNKDKNKGMEGIYSAFNITTNGDQLELNTYHMNNGMEGIYSAFNITTNGDQLELNTYHIIKAIRLPPVKEVTGFTGSVDLDIGIGKLDRHSDNF
JGI26144J50225_102190	JGI26144J50225_1021901	F073748	VNNFLLNLRGCVLFTCLIAGLQICLTAPGWSEEVHFGCEYDEEKTHETSTSNSGPERRSTHGEARYTIDWQSKRVQGFSGEYELKFSDAELRIQRKTQNSSGEWLNKASESIIINRYTGEYVFSEKVEGESVKGISRYWYTYKTRKGICKKIDKSLF*
JGI26144J50225_102210	JGI26144J50225_1022101	F090038	MAFLSKKLSQELLNLDIDEGIRIESNKNIKCKMYINKRTSGYFVLEIEDTNSTNIKEFRFYRDIKPIYRLIDKIFGKQYSITIY*
JGI26144J50225_102506	JGI26144J50225_1025061	F083220	YNKSTHVVTNLGGRGVSLKYHVVVVGLDAWVCAAGPGTQNTYRQIFCLNPRNPSQTKFIDILKRTINGVYQSDPNWPTSAPYQTIGIHAMYGSATGTWLDVGFHRASWGAGGDSVFNLSTNKWSLLKANRYSSGHSSIGTRFVNGSGSINGMYSGGACVRNPSNLMDATRYTFIMQPPSA
JGI26144J50225_102784	JGI26144J50225_1027841	F017423	EKYQIAFQYPSDWTIKEKSNKLEEGTEIDVSNKKIGDGKIGIHFYDDLLEGFGSTDLEFAFSDFYKHRITDDLKFEYKTIQPPSLLEIDGHKTGSFHIMFSQKDEIDPISGEVQYWITFVGENGYMIEFLSIPENFDTPDNTEMRDRFISSINFLGLSNTTDTSGRISSVAMSY
JGI26144J50225_102884	JGI26144J50225_1028841	F032058	MSPEQSPGQGTLIVAALIVLGIVFAGHWIVSYVQSSNPWAIIPWYGVAAVLIIV
JGI26144J50225_103058	JGI26144J50225_1030582	F098876	ESKDVNSSVHIQSQIVAGKNPSIEFSLHLKLTHESRYPNIKFSSSGEKISVQEDRLMTKDEVSQDMIPEYYDKELITEEFVKEXLIRXIKSXFDKDWQSFYS*