3300026022: Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_5C_80N_201 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026022
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116040 | Ga0208649
• Sample Name: Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_5C_80N_201 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 67408568
• Sequencing Scaffolds: 32
• Novel Protein Genes: 33
• Associated Families: 33

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	7
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	5
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	9
Not Available	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Rubrobacteria → Rubrobacterales → Baekduiaceae → Baekduia → Baekduia soli	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales	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?
F001888	Metagenome / Metatranscriptome	622	Y
F002064	Metagenome	597	Y
F002615	Metagenome / Metatranscriptome	543	Y
F003606	Metagenome / Metatranscriptome	477	Y
F003762	Metagenome / Metatranscriptome	470	Y
F015635	Metagenome / Metatranscriptome	253	Y
F016947	Metagenome / Metatranscriptome	243	Y
F017227	Metagenome / Metatranscriptome	242	Y
F019048	Metagenome / Metatranscriptome	232	Y
F024161	Metagenome / Metatranscriptome	207	Y
F025567	Metagenome	201	Y
F026166	Metagenome	199	Y
F028276	Metagenome / Metatranscriptome	192	Y
F034584	Metagenome	174	Y
F038660	Metagenome / Metatranscriptome	165	Y
F041375	Metagenome / Metatranscriptome	160	Y
F042513	Metagenome / Metatranscriptome	158	Y
F046973	Metagenome	150	Y
F049819	Metagenome / Metatranscriptome	146	Y
F059318	Metagenome	134	Y
F061194	Metagenome	132	Y
F061931	Metagenome / Metatranscriptome	131	Y
F063664	Metagenome / Metatranscriptome	129	Y
F075217	Metagenome / Metatranscriptome	119	Y
F077667	Metagenome / Metatranscriptome	117	Y
F081653	Metagenome	114	Y
F082449	Metagenome / Metatranscriptome	113	Y
F084885	Metagenome / Metatranscriptome	112	Y
F085424	Metagenome / Metatranscriptome	111	Y
F089198	Metagenome / Metatranscriptome	109	Y
F089441	Metagenome / Metatranscriptome	109	Y
F092949	Metagenome / Metatranscriptome	107	Y
F094330	Metagenome	106	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208649_1000079	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	4379
Ga0208649_1000144	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	3649
Ga0208649_1000801	All Organisms → cellular organisms → Bacteria	1954
Ga0208649_1001170	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1702
Ga0208649_1003226	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1189
Ga0208649_1003249	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1186
Ga0208649_1004165	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1080
Ga0208649_1004974	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1012
Ga0208649_1005639	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	965
Ga0208649_1006103	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	936
Ga0208649_1006270	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	926
Ga0208649_1006289	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	925
Ga0208649_1007120	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	886
Ga0208649_1008237	Not Available	839
Ga0208649_1008517	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	829
Ga0208649_1008851	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	817
Ga0208649_1010848	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	758
Ga0208649_1011382	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	744
Ga0208649_1013629	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	694
Ga0208649_1015255	All Organisms → cellular organisms → Bacteria	664
Ga0208649_1017163	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Rubrobacteria → Rubrobacterales → Baekduiaceae → Baekduia → Baekduia soli	634
Ga0208649_1018433	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	619
Ga0208649_1018704	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	615
Ga0208649_1018754	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	614
Ga0208649_1018970	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales	612
Ga0208649_1021618	All Organisms → cellular organisms → Bacteria	582
Ga0208649_1022293	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	575
Ga0208649_1023259	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	566
Ga0208649_1027438	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	530
Ga0208649_1027520	Not Available	530
Ga0208649_1029175	All Organisms → cellular organisms → Bacteria	517
Ga0208649_1029971	Not Available	512

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208649_1000079	Ga0208649_10000791	F001888	MHHHRHGWGGPRMLFRGGFPNRQELLERLESYQRDLEQELANLDDVIRHLRGPAAEPAGD
Ga0208649_1000144	Ga0208649_10001441	F049819	MAESRNVQAVREAYELARRADHKTLRTRILDDATWRPAKEGAWNPCRDADQIVRTLLWRAHANRLRPGEVIDLGDRVLVQLKGVRLGRLGGRGLFPRLHQIVVVRDGKIVRMQDYPGREEALAAAGLRG
Ga0208649_1000801	Ga0208649_10008014	F042513	SEAAMERSNPELASAMRKMQRSGALRDPQRAQAAMSQLTAQERRALLEMQEQQGALAPEATNRQMRRRLDKAKKRR
Ga0208649_1001170	Ga0208649_10011701	F003762	TDTLNAACERPAEGETAERAVRAAELVAATAGEPPDDLSAEEREWAETHGVPPEDLLELACRSMKCVAGLSDDWHERLNDLRYRLGDVAAP
Ga0208649_1003226	Ga0208649_10032261	F089198	RWVYGVEDRAAYVNQLGKCRVEELGVKQHAYAAAADFGY
Ga0208649_1003249	Ga0208649_10032491	F002064	VETAQNTLSEQQLNLMIQYTVEAYKTFEKLAENLPNPIAATMFKQFAVDERENRDLLEMKIQAAGANRVRVTLGGDLLFQDILEGDLSYRETTEFLIARERTMEKKLVDYSRSASPVDRNLLIYLAAGKRAHIVELERELELIRIDPDWFKREDAQWRIVHGSTQE
Ga0208649_1004165	Ga0208649_10041653	F003606	VRPRSANEWRDFWRDGGERALHAQLDEFAPYSVRIATLLGSNAPLRALVAELGRIRAHELGTEPAPARDAEVAQR
Ga0208649_1004974	Ga0208649_10049742	F081653	NRAGSVQKCSLRRFEMEKMKLSLVILLVSSVLAFPNSSVAQTAVEMNSGAGSICVLPNSPEPPTRISPGGEYNPQTLTVHVDHKKLISWPHKEPVLIEGLDLRKRHLVVLTSDGKRIESFFFKFSKSDDARLCIYFDGYQGVQLGNQTNALWCKVKKRDCWR
Ga0208649_1005639	Ga0208649_10056392	F034584	VTTRGTLPVIVAFIALPAVAAPPTTCAQTDVYGKALCAYQMRHFDDAEAGFREIVGRGAKDAETLHATYFLARTEMKRGQWKAGSDLLIRIYGLDRAFYDTWSCDFLLGECRKGLGKE
Ga0208649_1006103	Ga0208649_10061031	F059318	LAQRAFHDLRDAIVAASPNMAVESFEPGTELATVLDSYRTMSLFSAARLLIIPEMNAFVSARELGSLYDKAAGDWKTAKTDRKRTTAAAKLLHVLGLVGADLEMTDRQIADVIGMPLDALLTDMLAFCRTTGKKVGRGEGDAALLTEAVTRGGASGTVLLMRTGELPRDSATLDLIERRGAVVPCDVTRENFDGALSSAIEEIAGEAGVRFDPKAIAALRRRLGIDRMLGDKFSRDVPDLRSALSEAERLATLAGDGGRVTAEIVEREVEALEGGARYELASLFSEGKMVEAVSKLRDLVAQSRRDDVRAPA
Ga0208649_1006270	Ga0208649_10062702	F075217	MVTVPAEGRWSIRALSDDDGGPALSFLRRDPLINVYLVSRLLEERFVAATQIVEVRYGGEIVLVASLATNV
Ga0208649_1006289	Ga0208649_10062892	F017227	QELRDRIHTAVYTVGNREVSLRSQDGFPQALRLVDAILEARRAA
Ga0208649_1007120	Ga0208649_10071202	F019048	VTMSDDASPEQPVEIVCPHCKKTFSANLIDGSAERYRGFKCPHCRLFVPAARVKS
Ga0208649_1008237	Ga0208649_10082372	F092949	MEASSSTSSAGSSRADGLWRAVGEAAGPVGEMTPLLEKVRDCAWRITDADVAGLSADELYEAVLPVAFAVADEKRRRAYEAIDAD
Ga0208649_1008517	Ga0208649_10085172	F063664	RYVPAEQVGRIEEGAVRLTITREQAEALGEYREPATSAEIEPDSKGGAGEAIASDVREVEAKAFAPIERHEHPMNVWRRIAFFFRRMVR
Ga0208649_1008851	Ga0208649_10088512	F094330	MRGKKGLCKSMRDLAIKSRVLGDGYYYLPVELWPKPKGKVVVHNHDWTVIGSIPRTSRSSKRRSKAAHDRA
Ga0208649_1010848	Ga0208649_10108481	F038660	GKYMDAYLPNRRCLGARARDRTGMIAARAQFTEHCPRVTAEWQLLGATVDVSGIGFWNPVRTTRGALPNGAELRPLTNLHIVAGCGVG
Ga0208649_1011382	Ga0208649_10113822	F015635	MQASQRSSFQPAEAGAILAGTVGVCAGGGALVGWGAGNVGYGVLGGVVAGLPAGVFAVYRRFKGYFS
Ga0208649_1013629	Ga0208649_10136291	F041375	MKRVYLAGPPFADEYRRRASELVRAHGWEPVDPMRRDFRGRTEGHEREIVEGDLADIDS
Ga0208649_1015255	Ga0208649_10152552	F002615	AYIAPGEDGTATGNWEHFANAKATGLLAQWKTTLDPKKQQTIATQLQKIWLDQLPIVPLFIGPRWSTYSTRYFHNFTTKRNFWGDPIFSTFPDNILSFTRITPGGKAGA
Ga0208649_1016294	Ga0208649_10162942	F028276	AAAADDAEPAWDPSFHKTRDFFHGFRMAVHGHTLYNYGSLDGGVGAVWSARQAWYVSGGLRHTKALPEIYNPAMAQQWAELARIARGRYHRALHFAGVMTQGTSSCNCGLRPPAAHRVLVRALDAQGLGHIPLPVGGTNIIG
Ga0208649_1017163	Ga0208649_10171631	F026166	AYPLPADEIVVDEESGGTRRFLSGPLEFGSAMLITPSCSMGAQGAAGYGHPVRTLVPVLPVTELVERGVVKETALDDLRRFDHLINYMYLPPLEVDELEFSIPESVALLYMPVTLHHAFLEGQRVSQLAYSGAQQLQRKLAWFYSGWLEDDLDLFDPPMD
Ga0208649_1018433	Ga0208649_10184332	F061194	SELPFERRRGALEEGLNALLSVQLFEVSQHLDAEGKLNVYQFISDQKALLETA
Ga0208649_1018704	Ga0208649_10187042	F082449	MRAALVACLVALALGGIAQGAAGARKASCPGAWAKGWQVLANKVQAPVYCPTWMPNPLDAKIGGDYQDAYGIGKDRSYLVSFLEHGDLGSGDVHVN
Ga0208649_1018754	Ga0208649_10187542	F085424	MKIHQWEVWKSRPPGFERDHWFVIISGQERCDEPRQLNVNGLACFTLRGPLLKSQVQLNSADGFAAPTALQCDYLYGLEKKGLHSSQGLVSWERQQAIKSKVREVLRF
Ga0208649_1018970	Ga0208649_10189702	F089441	TAYDVALELVELGRGDEYLAATEGAPGHLWLEAARTAASGELGSASDLYGSFGARFAQAWAALLAAERGDTSRLDAALAYFEEQRATPYVQRCRALLQASA
Ga0208649_1021618	Ga0208649_10216181	F061931	MKNGSANADSERFQSEADKYAAYLETPEGGLRLDLAFVNLQEFLPQDTASLRAL
Ga0208649_1022293	Ga0208649_10222931	F025567	SLIAAPPASSDRLVSTHELTEFVVRTVPVRIDVEAAAGRVHLAISPDQVILKPGEGIEWDFRYVGGADVIVDELIIEFEKPSPFSQSNFRSRRPGTARPHRQLSGAAHKNAAGRTAQYTIRALNGFKTEMAVARPSVTIVP
Ga0208649_1023259	Ga0208649_10232592	F077667	VIASIGTLLIPLWILLGLLVLMGVLALLGRIQGGRYLRPLIQLIAKVPLFRRWLEKASNAALERSNPELASAMKKMQR
Ga0208649_1027438	Ga0208649_10274381	F016947	HNDETRQDAISLTDYQKKELADVETRQATIIKQADADAAQITKAIADLRARRETELAKAGQWNAEDARIENDYKAKMSEYANKKAAYEKAKAEYDSANFLKRKLMREPVDPGVPPVREENKILKPALLAELDSQIKAKEDELTAVNNKRRDSVAQVEADARRLRQEFDTRSTSQRA
Ga0208649_1027520	Ga0208649_10275201	F046973	MPAPDNTVQEVRASVLHYLRLYEQGSLTLGDLAAELSIMAPAYDEAMGGIADHFGELLETAYKYCVQSSADARTSYEELERVLTEFRRAEAAWE
Ga0208649_1029175	Ga0208649_10291751	F024161	LRKIVVDLAEQLDRSLTEQNKYQSLLRELLEAQRNRKSEQLSKEQLALFEAAWKVQSTEDESSADDDDLDGDTGAGSK
Ga0208649_1029971	Ga0208649_10299712	F084885	MKLYLIFLLIDVLVLLAYPFVYVIHKIRTIFQVKR