3300009060: Salt pond soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG SF2_C_D2_MG

Overview

Basic Information

• IMG/M Taxon OID: 3300009060
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114514 | Gp0125958 | Ga0102962
• Sample Name: Salt pond soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG SF2_C_D2_MG
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 390551898
• Sequencing Scaffolds: 41
• Novel Protein Genes: 43
• Associated Families: 35

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → Desulfosarcina → unclassified Desulfosarcina → Desulfosarcina sp.	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	2
Not Available	11
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	5
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → Desulfosarcina → Desulfosarcina variabilis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	2
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → unclassified Desulfobulbaceae → Desulfobulbaceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Archaea	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacterales incertae sedis → Candidatus Desulfatibia → Candidatus Desulfatibia profunda	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): 37.4973
  • Long. (^o): -122.1295
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F004928	Metagenome / Metatranscriptome	418	Y
F007072	Metagenome	358	Y
F008223	Metagenome / Metatranscriptome	337	Y
F024001	Metagenome / Metatranscriptome	208	Y
F024682	Metagenome / Metatranscriptome	205	Y
F025653	Metagenome / Metatranscriptome	200	Y
F031307	Metagenome	183	Y
F032166	Metagenome	180	Y
F037736	Metagenome / Metatranscriptome	167	Y
F041201	Metagenome / Metatranscriptome	160	Y
F042460	Metagenome	158	Y
F044506	Metagenome / Metatranscriptome	154	Y
F044508	Metagenome / Metatranscriptome	154	Y
F045765	Metagenome / Metatranscriptome	152	N
F048318	Metagenome / Metatranscriptome	148	Y
F048676	Metagenome / Metatranscriptome	148	Y
F053305	Metagenome / Metatranscriptome	141	Y
F054044	Metagenome / Metatranscriptome	140	Y
F054047	Metagenome / Metatranscriptome	140	Y
F057781	Metagenome / Metatranscriptome	136	Y
F059980	Metagenome / Metatranscriptome	133	Y
F059981	Metagenome / Metatranscriptome	133	Y
F075754	Metagenome	118	N
F081352	Metagenome / Metatranscriptome	114	Y
F084253	Metagenome	112	Y
F084254	Metagenome / Metatranscriptome	112	Y
F085724	Metagenome	111	Y
F087210	Metagenome / Metatranscriptome	110	Y
F087679	Metagenome	110	Y
F087950	Metagenome / Metatranscriptome	110	Y
F090406	Metagenome	108	N
F095489	Metagenome	105	Y
F098287	Metagenome	104	Y
F099324	Metagenome / Metatranscriptome	103	Y
F101186	Metagenome	102	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0102962_1022088	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	1891
Ga0102962_1022122	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → Desulfosarcina → unclassified Desulfosarcina → Desulfosarcina sp.	1889
Ga0102962_1025213	All Organisms → cellular organisms → Bacteria → Proteobacteria	1753
Ga0102962_1030729	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales	1571
Ga0102962_1031979	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	1534
Ga0102962_1038996	Not Available	1372
Ga0102962_1041063	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1334
Ga0102962_1045619	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → Desulfosarcina → Desulfosarcina variabilis	1258
Ga0102962_1047778	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1225
Ga0102962_1060092	Not Available	1078
Ga0102962_1066581	Not Available	1018
Ga0102962_1071782	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	977
Ga0102962_1077564	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	937
Ga0102962_1078535	Not Available	931
Ga0102962_1078707	Not Available	930
Ga0102962_1083829	Not Available	898
Ga0102962_1086947	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	880
Ga0102962_1087516	Not Available	877
Ga0102962_1087734	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → unclassified Desulfobulbaceae → Desulfobulbaceae bacterium	876
Ga0102962_1101939	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont	807
Ga0102962_1114166	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	759
Ga0102962_1114983	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	756
Ga0102962_1130294	All Organisms → cellular organisms → Bacteria	708
Ga0102962_1145068	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	670
Ga0102962_1149091	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	661
Ga0102962_1154643	All Organisms → cellular organisms → Archaea	649
Ga0102962_1154734	Not Available	649
Ga0102962_1156638	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	644
Ga0102962_1157291	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium	643
Ga0102962_1160804	Not Available	636
Ga0102962_1169600	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	619
Ga0102962_1189499	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	586
Ga0102962_1194161	Not Available	579
Ga0102962_1201868	All Organisms → cellular organisms → Bacteria	569
Ga0102962_1205596	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	564
Ga0102962_1209978	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacterales incertae sedis → Candidatus Desulfatibia → Candidatus Desulfatibia profunda	558
Ga0102962_1227711	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	538
Ga0102962_1237672	Not Available	527
Ga0102962_1252735	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	512
Ga0102962_1256645	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	509
Ga0102962_1257106	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	508

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0102962_1022088	Ga0102962_10220882	F024682	MVTLKAEDELISKLKSEIGKTLPAMFAGMAENMLENNKDVIIAWLKDNKDLVKEVIES*
Ga0102962_1022122	Ga0102962_10221221	F048676	CGTASDAVDAVKLEIPQGFELLKFKMSEYLKNIVKLTISKI*
Ga0102962_1025213	Ga0102962_10252132	F081352	MCLADVSLMIRLIRKISTITLACLLVLNLTAGAAVVVEHCPPLLGSSSPMDIDHCDGMLNFAFPMQGCCGECNDIFCDLIKNPLQDANAVNASPFQGSCYPFFLGTVDPIAESGTWVASSAPRYLFFAALAWSQIPLYIENLALII*
Ga0102962_1030729	Ga0102962_10307291	F087679	VHGVGGASPRFDYYNYWMAMHSWMSAPINDDGTAYYGNSLVHRNDFTVDDGTWVCLEVHARLNPDPSSGAGAVLEVWKNDALVQRFDDEGPMGYWVRDKFCPADADGSECADYVAPATDTLDLQFRSTTDLRLDAFWPQNYITDDAMGTLMFDQMVVASRRIGCMR*
Ga0102962_1031979	Ga0102962_10319791	F084253	IFVLIKAAQGFAVRRTSVRRSRKPAENADQDKNGHLWMGNS*
Ga0102962_1038996	Ga0102962_10389963	F048676	DAVDAVKLEIPQGFKLLKFKMSEYLKNFVKVTILKI*
Ga0102962_1041063	Ga0102962_10410631	F054044	MSNTVGILVLVFALTALILLFLDFSFRSAADQEECLQLVRALGLNSLSLVPSGRPLRNPGAIDPSIDLRFDPRLGRIHLDGADFVLKVSD*
Ga0102962_1045619	Ga0102962_10456191	F087950	QCWINGPATGGIDDKIKMVNILLKTNIPSFHPSIIPFPEKIRRPKKSPYSQ*
Ga0102962_1047778	Ga0102962_10477784	F084253	VLIKAAQGFAVRRTSVRRSRKPAENADQDKNGHLWMGTS*
Ga0102962_1060092	Ga0102962_10600921	F037736	RNSSVPYRVQLDGLQILWLLANPLWTHGIGESRSKTITGWLLMGAADANHIWWLNTNPFTGLLLHLNSYRILHLPCGFLNMLCFLLLCHRQRNDNY*
Ga0102962_1066581	Ga0102962_10665812	F024001	MNKFTILGVEAPVWPCAKPQEYLDIPSFRNAVRRDASAFK
Ga0102962_1071782	Ga0102962_10717821	F098287	TREFIDYNPPSRKHISLATRYSEDVAVVTNLLKKYEPEIVITHTLGGEKLDHEGTAYMVYLAFMRAIRDEVPVGKLWMTVNGWLLDREARESGRGKPDVTIDISDYLAVKYGALDQHLSQNGGFGRDYIVINKGKVNENIEEFITVADNTK*
Ga0102962_1077564	Ga0102962_10775641	F004928	MAHALRSIESEPANTVEIVVHISETLGDERRKDLVTALENEESIVSAEFCPLRYHLMLVRYDRDISSSQDVLGSVKAQNYNARLIGPV*
Ga0102962_1078535	Ga0102962_10785352	F042460	GYFGLAHGGPTFTIYLLLVNLPYGIITALAARLIMGSKP*
Ga0102962_1078707	Ga0102962_10787072	F084254	PMVIEILAEVIRQSKRHPRADQVASALAIRGLPIAQNDVMTVFDHYDIEKKTPDSH*
Ga0102962_1083829	Ga0102962_10838292	F075754	VDDTSEWYAAQVARSEYLRDSEEDADMHHRKGGVVAEGLVKAIFAGMEWWDTHSFDTFLGGTRYDIISRGLNRGEPRQHYVHKIQAKKEERAKPSTHYYAVVRNHPDYWLIGHINSIRFWYLCDRSAPDFWDDEHFDGGFLSYEHFEQLPLAQ
Ga0102962_1086947	Ga0102962_10869473	F037736	VPYRVQLDGLQILWLLANPLWTHGIGESGSKTFTGWLLMGAAATNRIWWLDTNPFTGLLLHPKSYRIMHLPFVHSNVCLF*
Ga0102962_1087516	Ga0102962_10875162	F007072	MELRKISSNKKGQLSIGDAPTVVLLVGLVFLVMATIAFIGEKYQGSLTADSTAYNVTGDLQTEIGNNTSIAGIILTISLVGIVLTILIGVFIGVRGGTSRV*
Ga0102962_1087734	Ga0102962_10877342	F099324	MFKQIIFVIMLGWVLVLSGCAAIDKGHDIEGEDYRGGYPPRGGYTRTSQHKALVSEACNIEANNLAGDKDFMADDRARRVYFSQCMQRNGYNAAGNYVGIPPK*
Ga0102962_1094579	Ga0102962_10945793	F087210	MRFLIGALTFAGAETALAHTPESGFLSNFGHQLTSLHHSPAAMLLGVVVLVLMLVAVRKLTTR*
Ga0102962_1101939	Ga0102962_11019392	F057781	MKLPDLQMLAHWLDPALVAALETRRRKKNEWHRRRKLATLQTLWLMLAVSLNTQ
Ga0102962_1114166	Ga0102962_11141662	F024682	MVTLKAEDELVSKLKAEIGKTLPAMFAGMAENMLENNKDVIIAWLKDNKDLVKEVIES*
Ga0102962_1114983	Ga0102962_11149831	F059980	SLHLMEEAGSMGFSGGFEQGNPETALPELIRFIPGNVKRVNSQNRFCCG*
Ga0102962_1130294	Ga0102962_11302942	F054047	FVGWVKHPYIFCWVSFLYPTYTPAIFVLSAKPDKMAEDRIIPKIIKM*
Ga0102962_1145068	Ga0102962_11450682	F024682	LDPEDELISKLKAEIGKSLPAMFAGMAENMLENNKDVIITWLKDNKDLVKQVIET*
Ga0102962_1149091	Ga0102962_11490912	F095489	MGTNAATPMSKTRMNMPASNDVVDWNLVAERRFEDIEELNDLVQGWDFEFHQLKAGRSPAELLQLGRPEFMLTRF
Ga0102962_1154643	Ga0102962_11546431	F025653	MSDPMKYFESKLKNMCLAELQDYRKRLDESIKQKIEQTAPNEQIAPLILYRGRVEHEMTKRMNKMKSQ*
Ga0102962_1154734	Ga0102962_11547343	F032166	EEYLEGNSDKAQRGNEPLDDVITLLETPPEQWRDVEDGFNEIAEAREMLDFQRRTQAQIKSQGLGSNTLPEYDDMTFREAASIRWGIDPDDEREWL*
Ga0102962_1156638	Ga0102962_11566381	F037736	YRVQFDGLQILWLLANPLWTHGIGESGSKTITGWLLMDAAAANHIWWLNTNPFTGLLLHINSYRIRHLPFGFLTASEFQSRSTCLIKK*
Ga0102962_1157291	Ga0102962_11572912	F059981	MEREKIICIFCGRIARIKEQDDLKIVVCPKCKRETEMDEYQDKFDQWMGDIRNNDGKR*
Ga0102962_1160804	Ga0102962_11608041	F031307	MSKIRTYFGFKNGKLVSVLHSVNADVKKAVDCTYYITEPQEVEKQIAKWKQDNSE*
Ga0102962_1169600	Ga0102962_11696002	F044508	VAIKTNRSDKTEIKKILKISDHQQRWPRPLPGAILIPPAMLVVADLLN
Ga0102962_1189499	Ga0102962_11894992	F045765	MKNYSSKSGDTTAINIDDRLYDLLRKFCDKEGRRLKDFVEDALENAIYTEESIKVLNEEIISLKKKEAKYDYAFRRGFQKGFYISFCALHGQILLEPDDEAFEILKNDPFRISKGAQLDLFRSKEI*
Ga0102962_1194161	Ga0102962_11941611	F053305	LSRRSVSKKTKLIRNPKELKMLKKSVSMALVALFVFSFIAVATVSADETQKITGTVMSINVETGEVIVKDDAGEMKKLMADPKAEGGVDLKMLKVGDPVSVESDSNGVI
Ga0102962_1201868	Ga0102962_12018682	F059980	MEEACSMGFSGGFEQGKPETALPELIRFIPGNVKR
Ga0102962_1205596	Ga0102962_12055961	F048318	ILVMATVENVSLAITASATKPGYSDIAYSYELHPSELDCAWKREYTISTVLCGEDVIEDDVLAWGKDEHKVKFDASGPCESIKVGRIFEVETKVLDEDVFGDDEVYLIVEARSALGPDAAGENLVMGKSNIVIGNF*
Ga0102962_1209978	Ga0102962_12099781	F101186	MLFENQRKIFADFHKSVEAEGVLDEKTSHLIKVAAAMSLGCYP*
Ga0102962_1227711	Ga0102962_12277112	F085724	MNRRWKMKTILAIVMVLGMTAVYEPDSIIPKYFIDKTPQGEYRVYDSKQIVVPKYIVKPDPWGNGYRVYETGKPVL
Ga0102962_1228326	Ga0102962_12283261	F090406	KGGNVYALAPTVVDQILKDAMSTEISTGTLRRGSTPYPSYLGEVTWGSLDKDTITASARPAKGRKLDGTIVDGYVFEVSRKGTAPATGEPTVKRIFAKLQKDAELTGTGAAFVEFAD*
Ga0102962_1237672	Ga0102962_12376721	F008223	SKKPAPPSPVEEASRILERFATATSMGVDREDLSRYPAKQRQVMALHFGAIEFLAREFQLDETQMLGVFVVFLDNYFIMPITESGSISERVQGFYDKPQEREYLEAGADVCRRWHELNERRAPLQLGQMLQAS*
Ga0102962_1252735	Ga0102962_12527351	F044506	MMQCWINGPATGAIDDKIKMVDILLKTNIPSFHPSIIPFPGQIRKSQKTSIFSVGCRNYETLNYTWV
Ga0102962_1256645	Ga0102962_12566452	F048318	TVENVRLDITASTTNPGYSKIAYSYELNPSEMDCAWKREYTVSADFWGQDLIDDDVLAAGLDEHKVKFDDSGPCEPIKVERVFEIETKVLDEDLFGDDEVYLIVEACSGFGPDAAGEDPVTGRSNTVIGDF*
Ga0102962_1257106	Ga0102962_12571062	F041201	LVQDRGGAEFKTGGILLYVEDFKRGTNKDIGPKDIFEMGSKKPSGSSATY*