3300025989: Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_10C_0N_303 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025989
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116045 | Ga0207998
• Sample Name: Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_10C_0N_303 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: Y
• Use Policy: Open

Dataset Contents

• Total Genome Size: 78844665
• Sequencing Scaffolds: 39
• Novel Protein Genes: 40
• Associated Families: 39

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Thermoanaerobaculia → Thermoanaerobaculales → Thermoanaerobaculaceae → Thermoanaerobaculum → Thermoanaerobaculum aquaticum	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	13
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Acidobacteria	3
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	4
Not Available	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	3
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Wetlands → Unclassified → Rice Paddy Soil → Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): terrestrial biome → paddy field → paddy field soil
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: Twitchell Island, California
• Coordinates
  • Lat. (^o): 38.1087
  • Long. (^o): -121.653
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001148	Metagenome / Metatranscriptome	765	Y
F001519	Metagenome / Metatranscriptome	679	Y
F001743	Metagenome / Metatranscriptome	643	Y
F003762	Metagenome / Metatranscriptome	470	Y
F004033	Metagenome / Metatranscriptome	456	Y
F004159	Metagenome / Metatranscriptome	450	Y
F004483	Metagenome / Metatranscriptome	436	Y
F007538	Metagenome / Metatranscriptome	349	Y
F008039	Metagenome / Metatranscriptome	340	Y
F008145	Metagenome / Metatranscriptome	338	Y
F010716	Metagenome	300	Y
F013809	Metagenome / Metatranscriptome	268	Y
F013963	Metagenome / Metatranscriptome	267	Y
F018649	Metagenome / Metatranscriptome	234	Y
F020329	Metagenome	224	Y
F020420	Metagenome / Metatranscriptome	224	Y
F023736	Metagenome / Metatranscriptome	209	Y
F023923	Metagenome / Metatranscriptome	208	Y
F025813	Metagenome / Metatranscriptome	200	Y
F034247	Metagenome / Metatranscriptome	175	Y
F034733	Metagenome / Metatranscriptome	174	Y
F036744	Metagenome	169	Y
F039729	Metagenome / Metatranscriptome	163	Y
F041828	Metagenome / Metatranscriptome	159	Y
F045386	Metagenome	153	Y
F046435	Metagenome / Metatranscriptome	151	Y
F049183	Metagenome / Metatranscriptome	147	Y
F049545	Metagenome / Metatranscriptome	146	Y
F050731	Metagenome / Metatranscriptome	145	Y
F054771	Metagenome	139	Y
F056794	Metagenome	137	Y
F063064	Metagenome / Metatranscriptome	130	Y
F063498	Metagenome / Metatranscriptome	129	Y
F073602	Metagenome	120	N
F080370	Metagenome / Metatranscriptome	115	Y
F089247	Metagenome / Metatranscriptome	109	Y
F089466	Metagenome / Metatranscriptome	109	Y
F093160	Metagenome / Metatranscriptome	106	Y
F095937	Metagenome	105	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0207998_1002114	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1402
Ga0207998_1003113	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1225
Ga0207998_1003318	All Organisms → cellular organisms → Bacteria → Terrabacteria group	1197
Ga0207998_1003932	All Organisms → cellular organisms → Bacteria → Acidobacteria → Thermoanaerobaculia → Thermoanaerobaculales → Thermoanaerobaculaceae → Thermoanaerobaculum → Thermoanaerobaculum aquaticum	1127
Ga0207998_1004509	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1076
Ga0207998_1005664	All Organisms → cellular organisms → Bacteria	992
Ga0207998_1007070	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	917
Ga0207998_1007094	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	915
Ga0207998_1008058	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	874
Ga0207998_1008485	All Organisms → cellular organisms → Bacteria → Proteobacteria	859
Ga0207998_1009119	All Organisms → cellular organisms → Bacteria → Acidobacteria	837
Ga0207998_1009412	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium	827
Ga0207998_1009729	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	817
Ga0207998_1010881	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	786
Ga0207998_1011640	Not Available	766
Ga0207998_1013350	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	729
Ga0207998_1016392	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	678
Ga0207998_1016899	All Organisms → cellular organisms → Bacteria	671
Ga0207998_1019499	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	637
Ga0207998_1020146	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	630
Ga0207998_1023183	All Organisms → cellular organisms → Bacteria	598
Ga0207998_1023411	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	596
Ga0207998_1023421	All Organisms → cellular organisms → Bacteria	596
Ga0207998_1023960	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	591
Ga0207998_1024277	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	588
Ga0207998_1026194	All Organisms → cellular organisms → Bacteria → Acidobacteria	572
Ga0207998_1026692	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	568
Ga0207998_1026773	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	568
Ga0207998_1027447	All Organisms → cellular organisms → Bacteria → Proteobacteria	562
Ga0207998_1027914	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes	559
Ga0207998_1028374	All Organisms → cellular organisms → Bacteria → Acidobacteria	556
Ga0207998_1028852	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	552
Ga0207998_1029178	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	550
Ga0207998_1029204	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	550
Ga0207998_1030232	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	543
Ga0207998_1032253	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	530
Ga0207998_1034164	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	518
Ga0207998_1035337	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	512
Ga0207998_1036395	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	506

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0207998_1002114	Ga0207998_10021141	F001743	VIEVACAACGWLAITNQPAHLVWAEHESACPAVGGAVRHMPELPPLPKLLPEVRACRHRPVRRQIAVTPSGAKRYAVVCELCGRHVGG
Ga0207998_1003113	Ga0207998_10031131	F003762	MDWRDLTDTLNAACERPAEGETAERAVRAAELVAATAGEPPDDLSAEEREWAETHGVPPEDLLELACRSMKCVAALSDVWHDRLNDLRYRLGDVAAA
Ga0207998_1003318	Ga0207998_10033182	F004483	PRWSTYSTKYFHNFVTPKNFWGDPIFTTFPDNILSFTRILPGGKAGA
Ga0207998_1003932	Ga0207998_10039322	F073602	QTSFRQIYVERTGFLFDIVFLVFDGKTGDRLLQDEFKDFRERNRRRADELLGLFQNLFSLEDQVLNMFVPRERAVQRYLFTR
Ga0207998_1004509	Ga0207998_10045092	F008145	MAVRGDDVAASIDTHVRESIEKMVGEIRSSVEDVREAVDQQLKAALQSVQADVNAITFLPHIKKVIGDLEKEMEPEASPAAADASRLKAAIKSVEHGKSQVDILNALLEQAVQFGSRAALLILRGETFSGWKGMGFSSHGGNDETVKRFNAAPGLVPQLDQVLRHEHVVVWDGNNLSSRLGVSGSVKAILVPMVIKDKVAAAVYVDVIGDDVSKLDASSLEILVFATGLLIDTLAIRKKIPSPSLTEAGDSAETVMNAPPMAAPA
Ga0207998_1005664	Ga0207998_10056643	F010716	MAEQERETIEKEIERTRDDVGERIDELDRKLRTTLDFKTFASEHAGEFVAGGAVVGFLAGFGFPKLLRRAVAIGVPLALIAMKVRSAQQDGSHVLGGPPDYEI
Ga0207998_1007070	Ga0207998_10070702	F001148	VKDIYEVLRRKQAEQAQLAKQIEALQTAAEQLRTVAHLLDEEHEEGAAAGRG
Ga0207998_1007094	Ga0207998_10070941	F020420	AGGPWLAIFDFQPLTRAERQSLERWLRDRAEPLLMVRNVLLATPIAQDVFIELTPQALAAMPEGWRDAPRPILFFAPAGRSAPERRRQYLDALSRLRIPLASAGSELWAVRDFDADLMVALARLSAAGERAAFRAALDPGQTRLFDQQLPAVEAALLDDLVGARDEEDEVALDLASLSALHPAAHPLSLFAAVERAHNRRRPETARTQFSARTLEARLSARGYPERIRDCTDEFAARAPLLLPAELQRVFEAADLLAPDPA
Ga0207998_1008058	Ga0207998_10080582	F004159	MATENDHEHSAAGMDYDSRMGEKASKLGSDFAERGPEALLEEIENLLPESWREQIARFPIAAVVLGFGLGIWLGMKKGDELIAAGTSFVTSAAMSNVSQIMDRFGSQNA
Ga0207998_1008485	Ga0207998_10084852	F008039	PDQAARKLNPYVYMRDGAGDKVFLESQLWRNDPAYDQKSLTRLSEVMSGLEKRGFKGDPNAAHGWDKPEKIVRCRINMEVVNKRWRGKTGAMVDCENTGISEAEIAGSEDPKHVEKILQDFDRLFKLAKEKQAK
Ga0207998_1009119	Ga0207998_10091191	F054771	LADDLNLDELKRRLKEGDYLEISTGGGAYEVWAEPLASPPAVYFEGEQHPIAELDAIAHRIMDEMHRGEIRCRWVEDD
Ga0207998_1009412	Ga0207998_10094121	F080370	RLDPMSRVTMPVLVRLLMCAALFGVLGTASQPAWCHAQDQASFPSGKLPIKSSFSGYIIAVG
Ga0207998_1009729	Ga0207998_10097291	F056794	MADDIKVIKNERGIGTGQTRDGTTPATQADGSLPSTSNARNPIVSDPAEKGSTPRDPAGKTPGSAESGAIDPAQKSGPGKTPGTSEG
Ga0207998_1010881	Ga0207998_10108812	F013809	FHTFELIADGIVRREKALDFSGCNSRPGTGSLHPVAIGTTVEATKLSELSMERVARRLCERAGRNVSER
Ga0207998_1011640	Ga0207998_10116401	F093160	EAEEADKMAVDGSGNVYVIDDRYRVAKINGSTDKVDKVLAIPGYACEEEVPDGSTQVFPNMANNIAMMAKSGGSKLYVTSEQNTLSLIDPATMTIKATINIPNAGELDAIATDPGLNQVYITDEEKAVMWILKGACANGTGQCVVKE
Ga0207998_1013350	Ga0207998_10133503	F023923	VRWKGRGGTFRRDVGDGEHAEIALAERIYRVRVSELG
Ga0207998_1016392	Ga0207998_10163922	F013963	NYDLAIMALEGLARGPLTISVRDGAVSIEGQRESFKELARLCLLIGGGQSSEDGFDLQPGVHVTAGSVGLMLRAQLS
Ga0207998_1016899	Ga0207998_10168991	F049183	MLRRMPTDASVTTRLEPPYETNGSGIPVSGASPSTAARL
Ga0207998_1019499	Ga0207998_10194991	F018649	MRATNSNLTPEDFDWLRKLKAVADAKRGPSLVPVEIAGKLRTFGFATPIGIDGLAITDRGREALLEQNLRDAEDR
Ga0207998_1020146	Ga0207998_10201462	F025813	MHALHQVLHAFFNLHSFTLALPDVWAGFQVNLKMMVIAEAFVLVLA
Ga0207998_1020480	Ga0207998_10204801	F089247	GVATDSGKGLTVTPPSGANILAGGKQLSALTLGSGDYEYALLEFDGTQYRLLYATPATQSANGIARRDYPGNWIYPSTSGYAATAADNGNVLSSFNTTGGLTVTLPSTTGIAAGWSMGFTSDNGKSLAIQVNATSGGDILYPLVNGTAKTTLTLAGDNYEYVVLQYDGGGNFRVEQATPATAQQLGLAGIGGISRWSFPSVSAYSATV
Ga0207998_1023183	Ga0207998_10231831	F036744	MQPLPHLASCLRLAFDARDPAHPSGVSLASYFARAAVRGRKRSDLEPDLLFPAQVRARLGPSAAKAIALAMDGGSFRSCLAARPTVPLATREWLAEAALSLGKAEGFPLMWALLRAMSELEAVAQKLLGARTPRSVVRQILHGVGARTLRVEPFAALLVRVLKIAQAVYAA
Ga0207998_1023411	Ga0207998_10234111	F001519	MTLVNSLCAEISVFEGVGEPTGVVVERSAIRGKKGLCKSMRDLAIKSRVLGDGYYYLPVELWPKPKGKVVVHNHDWTVIGSIPRTSRSSKRRSKAAHDRA
Ga0207998_1023421	Ga0207998_10234212	F054771	LSDDLNLDELKRRLKEGDYLEISTGGGAYEVWAEPLASPPAVYFEGEQHPIAELDAIAQRIMDDIHRGEIRCRWVEDD
Ga0207998_1023960	Ga0207998_10239602	F063498	LNDSKPETALKFVDRALLLMSNQKVTDFTLYQNLIELRVQVLLVLGRQNDAISSLEEAREVLPNNPSIARWMERLKKS
Ga0207998_1024277	Ga0207998_10242771	F045386	VSLERIEITPVAVIVGEILQSRRTGYLTIIRAPLRKVLYWSQGELVLITSSAPEDSLADFLVRRGILQPDSAAQMVTDDPTDAAAKFQESGL
Ga0207998_1026194	Ga0207998_10261941	F023736	VQSLIDSRTARVLFTVLLFALALGFLYVARRTLLVFLFAIFFAYLVDPAIAKLEKLVHSRGRAIGVV
Ga0207998_1026692	Ga0207998_10266921	F046435	PAEAAGHKREELSDLDVLNEVATLTGGKLQLGNRPEQIAKAVASIEKDLRAQYLVGFTPTGRGEVQYRRISLKLARRVRAVRVRAGYLGTEPPTLRRIERKGS
Ga0207998_1026773	Ga0207998_10267732	F041828	LANPKGMRAVPKLTAEFLTNFDRFNLSAQEGYLVSLIDGRFDLQKLVILSPFDPFTTFFNLAKLQQERAITVPQ
Ga0207998_1027447	Ga0207998_10274473	F063064	ANSSGVSRGEILDQMGLKGDKSGEMSVSNALTALTKSNQVSRREGKYFASA
Ga0207998_1027914	Ga0207998_10279141	F050731	AVAGIPASVPLERASEIHLTDAGGGALQWVLHAPTCNWSLQATLWPGSLHLFVHDADDDEEQLYRARATRTQDYYLRKYPLDDE
Ga0207998_1028374	Ga0207998_10283741	F089466	TRQELESYSRKDLFLASDVRAVYGILDDNARFLYVTYDSPAESYLFDLAGDPNALHNVLTPSLKQEYDERIIDYLHQVADFYGYKPSMGSLLASSAQ
Ga0207998_1028852	Ga0207998_10288521	F095937	MYLLVSLFLPSSRRLIFGVDKRTGEVRRVESRVTFLPPHQFYRLSFEKREGSAQRDGLVRITSREGVPVTMTYRLRFSISGDRIPDARRLVADGWSAWIRARVGEAVAAVGSQVPIEDLLSPTSQFAT
Ga0207998_1029178	Ga0207998_10291782	F034247	GVEALDAIRRRWPGALEQLVGLRAPLDRFADALAFTGGKATLVLDGEG
Ga0207998_1029204	Ga0207998_10292042	F007538	EIAPNLFYRWKDEVEKGALAALGGRSAAARPDQEQVKRIKQLERALGRSALQIEILKNVLGE
Ga0207998_1030232	Ga0207998_10302321	F004033	MKKFVIGIALLLISVAGFAADVPGTPQITPPTNGGDWMKLSSTEKLFWSIGYAQGYQDALGKIDVASGPNSPCSTLAARTERQTATAGKVSGFELVSGLEKFYSDPANVQVPIGNAIRIYLLQASGKDQTTIQELIET
Ga0207998_1032253	Ga0207998_10322532	F049545	GLSRVHADAVEPTARAALAALAGVPHYEQIWAGDLRLSVQVIAIASGERVQGADFARRAQLLRQRAVSLSDRVAGEVQVLQLVLYDRPVSVHERELVLSTARVAPWWPLARGRVVTWIAALSEPALYTTRFRGWPDELSADQLRALIA
Ga0207998_1034164	Ga0207998_10341642	F020329	LQMLIPIVAILATFGFPVALVFVWKWFKLKDRELQLDSDLRRTAGNALESRVQRLESIIMALDADLRAKLDAGPAQRPELMEGPGAPESGQAGAPQEPNKIR
Ga0207998_1035337	Ga0207998_10353372	F034733	VVRADAAADQFVVRVGDRSRAVSEKAAAGLFVRPG
Ga0207998_1036395	Ga0207998_10363951	F039729	VPRLLVIDDRDQTIEMCHRHLPQFDYVTRCGKPHPCQVCEERDKGCPLKCAHDYFEAAEALSREGALPDLVVLDLHFAVPAARLLPRDRPPADASAPGALEDLRRRQS