3300007769: Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_C_D1_MG

Overview

Basic Information

• IMG/M Taxon OID: 3300007769
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114514 | Gp0125948 | Ga0102952
• Sample Name: Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_C_D1_MG
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 456622735
• Sequencing Scaffolds: 49
• Novel Protein Genes: 54
• Associated Families: 48

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	15
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Sorangiineae → Polyangiaceae → Chondromyces	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	2
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	4
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
Not Available	12
All Organisms → cellular organisms → Archaea	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Candidatus Sulfotelmatomonas → Candidatus Sulfotelmatomonas gaucii	1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Salt Pond Water, Soil And Salt Crust Microbial Communities From South San Francisco Under Conditions Of Wetland Restoration.
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Wetlands → Unclassified → Soil → Salt Pond Water, Soil And Salt Crust Microbial Communities From South San Francisco Under Conditions Of Wetland Restoration.

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): terrestrial biome → wetland area → soil
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Soil (non-saline)

Location Information

• Location: South San Francisco, USA
• Coordinates
  • Lat. (^o): 37.4965
  • Long. (^o): -122.1329
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F003187	Metagenome / Metatranscriptome	502	Y
F007437	Metagenome / Metatranscriptome	351	Y
F008098	Metagenome / Metatranscriptome	339	Y
F010527	Metagenome	302	Y
F012579	Metagenome / Metatranscriptome	279	N
F012695	Metagenome / Metatranscriptome	278	Y
F019205	Metagenome / Metatranscriptome	231	Y
F021102	Metagenome / Metatranscriptome	220	Y
F023884	Metagenome / Metatranscriptome	208	Y
F026377	Metagenome / Metatranscriptome	198	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0102952_1000569	All Organisms → cellular organisms → Bacteria	13539
Ga0102952_1000972	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Sorangiineae → Polyangiaceae → Chondromyces	9893
Ga0102952_1002571	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	5888
Ga0102952_1007844	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	3323
Ga0102952_1010173	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium	2891
Ga0102952_1010645	All Organisms → cellular organisms → Bacteria	2824
Ga0102952_1013011	All Organisms → cellular organisms → Bacteria	2548
Ga0102952_1017350	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	2191
Ga0102952_1020304	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	2014
Ga0102952_1023394	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	1869

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0102952_1000569	Ga0102952_10005699	F047069	SQCVVPPVQRLGLLTSVGTPAACDGKFAQDLNALWCPTCPKPAKNPGAGATVQIQLWYRDPQNTSNQSTSFSEGLEFLTCP*
Ga0102952_1000972	Ga0102952_10009723	F047069	VAPPVKRGGLLPGSGTVGLCDGTFQQDLNALWCPLCTRPNANPGAGAVVQAQLWYRDPQNTSNQTTSLSDAIEFPVGP*
Ga0102952_1002571	Ga0102952_10025712	F060093	MANESYIGNGTALSINGEAGADYAFSVEGLADGAGRVSAQIDLGAAPRPSIYQWSCEAQFQATPTQYGTLDLYIAEAPDGDSTQISGDVGSSDAALGDVDMLRNLKPIGSVVSENAAASEKCVTSRELMTLARYISIVAYNDSGASVNATDSNFRFDLQPKYWQGQ*
Ga0102952_1007844	Ga0102952_10078442	F003187	MGGVIMKKILVIVCSAILAIGVAGCAGKAPVGKGKAPVVHTKG*
Ga0102952_1010173	Ga0102952_10101732	F047069	RQANSWGNGTSFQCVAPPVLRGGLLTGTGTSGACDGAFAQDLNARWCPSCPKPNQTPLPGVPLQIQLWYRDPLNTSNQSTSLSDALEVEVCP*
Ga0102952_1010645	Ga0102952_10106452	F047069	VERAGILAATGTGEPCSGAFAQDLNALWCPTCPKPTKNPGTGAVVQAQLWYRDPFSTSNQTTSLSDALEFTVAP*
Ga0102952_1013011	Ga0102952_10130112	F036294	MGRGSSEEAIVGVKPIADEDAVTYLRVKLSESDREVGAEGRNM*
Ga0102952_1017350	Ga0102952_10173503	F008098	MQFILGVIVGAALMVGSAYLHDTGRLKAGPAQPFVNWDTVAGMWR*
Ga0102952_1020304	Ga0102952_10203043	F081809	TSQQELSVKSLRARVAFVVALSSIALITLAAPATAAPSISGTAVLADQRFKWFYWLGVVLVAGLVLWLLATLVGYYVRVIRPKHRGREIS*
Ga0102952_1023394	Ga0102952_10233943	F026377	MNQQELTQVVDDALERFRGRDLVASAEVVDVLLDLRLLLLEVESLEQLLDEPAATPAG*
Ga0102952_1031406	Ga0102952_10314063	F047069	SFQCVTPPVNRLGLQPGNGTVGLCDGTKSRDLNALWNAKPAKNPGSGTVVQVQLWYRDPQNTSNQTTSLSDAIEFTVGL*
Ga0102952_1032605	Ga0102952_10326052	F065159	VSDDFEPTTEYPPTNWESDAVFVAPGPLSRPLANYLAMCAPRSPRSSSANRFRGRSDLVLAGVASVN*
Ga0102952_1032809	Ga0102952_10328093	F010527	MSQNAKRKEATKQAVLVELENLRQGRHARYQTLVGRFARCPKLIRAAALFAAAVDANARAYSRTPLDAPPGSLPPIS*
Ga0102952_1034197	Ga0102952_10341971	F093897	MKLGFYISIGVAIGALVVGFVLLNDIQQEKDAKTVWIQKIPTQCNDVWNAEYSEYYEINPEMKEISGEESKAILETILKNHYENQGISILDLNLEVDYYDGARCEACSCLGWDRLSIQISQNDLDGIPVSEGWEVLN*
Ga0102952_1042023	Ga0102952_10420232	F041403	MAIREQKIRGRWRLLVGSVTLGVAALGLSSCGFPSTTASTNEAPSGTNIVECRSGTITNGDVQTSSLFVAKVPAGVHPDLPGDCTVQTG*
Ga0102952_1045399	Ga0102952_10453992	F061237	MDTPEQHPPVEDGSTEEGPLVDRRAVARGALFGLCVLIAASVVEAILDRNVDNFKDTGWIYPLFVAILFGYGLGGWQAGRAAPEGGLTNGTLAGLGAFGLWIPVRIVIWLVRDEHKGLFTGHSPALRPGQLFGQIVIAAGLGMLGGFVGSRAAARARGTTP*
Ga0102952_1053755	Ga0102952_10537551	F056659	MNDETLQVFAGSAIDPEELLVLAEFAAPSHFVSDEHLRDAAENLADWTDHHPTTIHDARRLATRRDVRSSVVELLEEAAAVSGGGIRGLRLARAS*
Ga0102952_1054655	Ga0102952_10546552	F037288	MAIGLLTLALLGTLALAATAFAGYRVPGDPSFVRQHFLLALGATTLLVMAHSFIMFFLIATGVELKNMEKERGWGDSFRRRTVAMKGRVFPAMTLAIALVMANFILGAAAHTKALPAWFHELLAWSTLLACVVTLYREYRVLGENNRLIAEAARKRRAPTRSQG*
Ga0102952_1055294	Ga0102952_10552942	F087388	MARTTREIAREIMERLDRGEPLEQALTIALSGDDIDEQTRLELEVAGLRDAVVHEAFHELLEWHGNFGGLAEFLEIDEAIHRTADRIGHDFDEPTGHDDEAAPRLVH*
Ga0102952_1058880	Ga0102952_10588802	F027211	MVRTYWLVPVFYEASGNLDLRPFARTDQIEACRPRAMWLPIVRGQVG*
Ga0102952_1064988	Ga0102952_10649883	F084079	YDGIPYEKGDRVEVHPSTDLWIRGARYARVIGTSITPDDRVRVRFDVLPQRIFGGSADTFRKIR*
Ga0102952_1064990	Ga0102952_10649902	F019205	MASEGDRRVELMFDSKKSFSHKAADAADLVIDFATLGEYGLEPVEQPSRACEGRSRIGSPRSTGAWSAAIARFATQA*
Ga0102952_1071739	Ga0102952_10717391	F082563	MKAFVDIGANREFKLSEAVLVYQSGGDGAFASLHKVEQNQDGAAYLAAGEPLTTAFVRTLAEGLG
Ga0102952_1075004	Ga0102952_10750044	F032367	MSRKRDIKQFRQACKGAGLTAQERREASEALHAEKQGGHVQRDMSYGELLDWLRQWRG*
Ga0102952_1075221	Ga0102952_10752212	F045062	ILFVTLSVPLKQLAARWAEVCNEIIIRRCPICEQDSIVGHGRRRKQAHDEFHEWIWIRRGRCLLCGTTFTFLPLFSLPYTHFSLLARSRALWRRFQEQCSWEKAMPQLKSADRVPDGSTVRRWGTGLDGSQLADSFLRQMMNRVAGWLQHGKQDDRNALPLPWMVSALEGLWPLRL*
Ga0102952_1095423	Ga0102952_10954232	F038836	MEDGWTIDIDAAGDPADVDEHFDDRVAEFEHALEPWSGAVEASSDHFGARFSYDTDAVNPVQVLEEGLDIFHDAAVAAGLPPWQVVRCEILTYAEDDARGGEDDEE
Ga0102952_1099802	Ga0102952_10998021	F084079	MPKTYDTVYGYDGSGYTVGDRVELHPATDLGMRGVRYGTVTRLSLTPNDRVHVELDKRPGRTFAGSADTFRRVEG*
Ga0102952_1101114	Ga0102952_11011141	F048463	DGWPYPDALSLDPGASTVGGPVPDADDGVDLDLLELRADPHAYADLTELEYFAVSWRYGVGDGAAPHSMKELAAELGCTHAEARDVLGGALDKLRRRLLTE*
Ga0102952_1102186	Ga0102952_11021861	F083203	MSTEVAIPEAQSERFEASLEAEHAAERDLMMSLIKSIAISMPIMIAIFVLMTAIAISDKADWWVWLGLGVGLGAVAALLL
Ga0102952_1104432	Ga0102952_11044321	F052025	FGVIDPDVPAADEAARNNDRPETQAWAARLLEIVDGPPEYHHYDELYRTDR*
Ga0102952_1105791	Ga0102952_11057911	F047517	MLKALRQHPVLIGTAEVLSDAIRYVAIVLVVLVVLGQVVAALGS*
Ga0102952_1127582	Ga0102952_11275822	F090930	RDLGGAGGADVNVVVLVATDATAAPLGETARALETDDTRAAVFVGDVTTAEGRTALQEFVAELFDPGPS*
Ga0102952_1133933	Ga0102952_11339331	F023884	GTTKVCWHSHWRKLQTIPFVGNARRRNLGRIAYCESAPHRLWVTLSRVRTTTGKWEIWYLISNHSRPAKATAAEYARRFGCEEGFRDVKWELGFAQARITDIHAWARLFALFALALLAVVSLAMKLLVPGGARAVALLRRVASRRQGRWDLSWVSAMVALLKEDKSLFGYLSACIKFQLNARLAYVS*
Ga0102952_1150242	Ga0102952_11502421	F040773	MYIGLGVFAVLAAVCVFAGAVAMKRRREYGDSEGEGEMGEAEFRKYEGFDE*
Ga0102952_1152503	Ga0102952_11525031	F055517	MSAMQARLKPEHTLRYPRLSPHMWYEVSPIFPGVTTRRVDIFGRRITRIRTTRDYETVQAAHFEFRAKPVAEEQAALA*
Ga0102952_1157769	Ga0102952_11577691	F082716	DIKHMPVTFIIAPVVLISLVYIVFITSNDMIEEKEFIVSLSCPELREYTQSQIIDSKLYFGHEVFLSYAEERYDTSC*
Ga0102952_1164534	Ga0102952_11645342	F039975	AQVALTLRTVAGLETPEIARGYPYAIVTGMRAEYDPYMSPGPGGQAAAQAGQFVTFIVASWIRETGFRATTKIDAPRAEREHLAVAAGLGKLNGDGKLTAPKYGAKIYIADIIFTDLPMAADG*
Ga0102952_1168921	Ga0102952_11689211	F012579	MQTMQTPETTKVIYGVNELDLDLAGRSVRGIWKTLEQVFNIPRDAVVTVNGTRADDEYVVRPGDEIEFQKAAGVKGMPA*
Ga0102952_1184726	Ga0102952_11847261	F012695	IGHIQLVGVSPAMQAKVDLLASRQAGISFDTENTAIGLQHVFEDLYRQEGYVAVKVDVARVNPLIVSDQSIHVPYTVTIKEGGIYKLGSIDLPAGALVTRREVKKILSKEHASGRPLDLFLLAACSAYRANGYLDCSVVPHPVFNQAAHIVNYNLEITAGSQYRLAAVQFDGAPDAMAARLHAVWKMAPGAIFDESYCSNFAALAKKKDRHLAKWMRT
Ga0102952_1195043	Ga0102952_11950431	F007437	MEGSAMGSSNPRLDLYGPKTLEALGQAFDSSWVVLQARDPFRDFERDLDLKTALSLKLTALAADGVIDPVELREWALESLPLR*
Ga0102952_1197063	Ga0102952_11970632	F090930	LPDRVVVLVGTDAVALGEVARGLASSGLRTAVFVGDVTDPDGRAALEEFVAELFPAEHG*
Ga0102952_1202539	Ga0102952_12025392	F063452	VNVDPIPQNLIAVHDLLSETFTIANEDAARFGWGVAIFPRTGRFDAPVFGVVTCGGESTTLTYRLLQTLMELPVFVSGRVPATIRDGMAFGPRRSTPPPALLDQPVLHIMLTCCIGLTREDLDRTMPLESTVFAGDLKAPIILLTENRPDGWPR*
Ga0102952_1217784	Ga0102952_12177842	F056029	MSVLMSWARSTLANVENAFDRSDRWFDRMLVGTLVLLAVAIVLLFVAT*
Ga0102952_1228462	Ga0102952_12284622	F051351	VGLNPFRSQVNRRSDIVIVAVALVVVLALVLWGLFG*
Ga0102952_1231855	Ga0102952_12318551	F088485	TGAAEERGSRIADALEVPVADLRHAWEHGLPRALGLEDDA*
Ga0102952_1235535	Ga0102952_12355352	F059048	MTVWVVVVVLGIGAAAAAYAARRHTDEVEPSVREFTEFRDAISRQVDGVHGDTRTLRQHLDRQPVGPPTTAVPPRNHDRSSPTGPGTERRGR*
Ga0102952_1242745	Ga0102952_12427452	F087446	MGGGGSAVVDTYDIAVDFMDMTDEQRLWVRAEDARAGFVVEVGRYAVVGDDDADPKVARIVEISSDGNLLLEVLPGPVEAHRDVLARA*
Ga0102952_1267211	Ga0102952_12672111	F054932	QVHQALLYVELTGMVKWVMVGHDALAAAEAEAPEAQRLEVARDAWAGQEQRLQDIQQYLQRDGHGDISKPWQKLAEVAPAVLDGYIRMRESFVKPDPLSPLPKKIMELAIIAADIVQAHPWGAVRHTQRFIKDGGTVPELIEAVALAMVEDGVQGYATSGRAVIEAAENTGRTGMMASSASQGS
Ga0102952_1290817	Ga0102952_12908172	F030395	SILESATPLWARDALSTAQDNPIWEHDTEAPVVNREEEFIGVISYADLRRAYRQLTRADGADSTGELAEVTELIAIGAGSLWQSIGDLIGAERRRR*
Ga0102952_1305772	Ga0102952_13057721	F021102	VRRESPVKRRNPSGEIVWVARYTGRDGKHHIAKPAWNRGKGTFERKADAQRAIEEAYGLADRPDTLGEYAKTWTERHPRSERTNATNDHRIGRVLDVQIEGIALADWPLRELRRRHALSLVDHMLRAEGRATTGVVGILRALSVMAEDAITDEV
Ga0102952_1315181	Ga0102952_13151811	F105828	MVAYILLVALIALAVLAAVSFLGSQMTGKFNTEGSIISSAGS*
Ga0102952_1325352	Ga0102952_13253521	F103749	MPTNLVVDADGHCQEPDTGLAEWLPEKFKHLAPNRVTDSSGYSHLMIESRLAARRRWGGGPDRGAVFADHIETSRPGMTDAT
Ga0102952_1325990	Ga0102952_13259901	F097083	ENCSKLPTEIPPATIRGTITYQAPPAPASMLYFIGAEHMYPLEVPAGSPMATFELQVAPDTYQLVAFPIGSENLTNRTAAAYTTGSGIGVLTVSAGQVVEGIHLQNINSDRCVNYAFPASPDGRFPAIEENCSKLISETAPATVRGTITYQAPPSPASMLYFISGEQW
Ga0102952_1330737	Ga0102952_13307371	F062264	PKVLSDFYQVYFGFEECKVFPSGSRMVIDPRFNLAFLQSRGDVAGAVVGTHRADGAEVQRDPGIHHYGFLVDDLNQAVAKLPSSLSRGASPQVSAGVGGPEGARPAEMRFIDPWGNNVDLSSRGFLGRDETRLPGVRLLAVQVPDPDEACEFYQKQFGLNVETKLFL