3300026184: Salt pond soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2_restored_D_shore_MG (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026184
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114514 | Gp0125931 | Ga0209918
• Sample Name: Salt pond soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2_restored_D_shore_MG (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 311291575
• Sequencing Scaffolds: 31
• Novel Protein Genes: 31
• Associated Families: 22

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	17
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → Candidatus Nitrosocosmicus	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	7
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → unclassified Ignavibacteria → Ignavibacteria bacterium	1
All Organisms → cellular organisms → Archaea	2
All Organisms → Viruses → Predicted Viral	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Halobacteria	1
All Organisms → Viruses → unclassified archaeal viruses → ANMV-1 virus	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 → Pond 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): 37.4958
  • Long. (^o): -122.1331
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001667	Metagenome / Metatranscriptome	654	Y
F005874	Metagenome	387	Y
F008189	Metagenome / Metatranscriptome	337	Y
F015275	Metagenome / Metatranscriptome	256	Y
F015411	Metagenome	255	Y
F022369	Metagenome / Metatranscriptome	214	Y
F029940	Metagenome / Metatranscriptome	187	Y
F032166	Metagenome	180	Y
F033186	Metagenome	178	Y
F033343	Metagenome	177	Y
F042291	Metagenome	158	Y
F050177	Metagenome	145	N
F056354	Metagenome	137	N
F057184	Metagenome	136	N
F073153	Metagenome	120	N
F074420	Metagenome	119	N
F075754	Metagenome	118	N
F079748	Metagenome	115	Y
F080661	Metagenome	115	Y
F086649	Metagenome / Metatranscriptome	110	Y
F086685	Metagenome	110	N
F096272	Metagenome	105	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0209918_1000903	Not Available	17635
Ga0209918_1001401	Not Available	12968
Ga0209918_1009672	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → Candidatus Nitrosocosmicus	3190
Ga0209918_1018764	Not Available	2029
Ga0209918_1020418	Not Available	1921
Ga0209918_1024441	Not Available	1702
Ga0209918_1030107	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	1487
Ga0209918_1031769	Not Available	1438
Ga0209918_1031977	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → unclassified Ignavibacteria → Ignavibacteria bacterium	1431
Ga0209918_1033608	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	1386
Ga0209918_1039173	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	1255
Ga0209918_1044654	All Organisms → cellular organisms → Archaea	1154
Ga0209918_1044904	Not Available	1150
Ga0209918_1045567	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	1139
Ga0209918_1048203	All Organisms → Viruses → Predicted Viral	1099
Ga0209918_1057640	Not Available	978
Ga0209918_1062185	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Halobacteria	932
Ga0209918_1064065	Not Available	915
Ga0209918_1069146	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	870
Ga0209918_1070237	Not Available	862
Ga0209918_1072881	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	841
Ga0209918_1074812	Not Available	827
Ga0209918_1083034	Not Available	773
Ga0209918_1086392	All Organisms → Viruses → unclassified archaeal viruses → ANMV-1 virus	753
Ga0209918_1115254	Not Available	622
Ga0209918_1122279	Not Available	597
Ga0209918_1135788	All Organisms → cellular organisms → Archaea	555
Ga0209918_1136305	Not Available	554
Ga0209918_1136953	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	552
Ga0209918_1138535	Not Available	548
Ga0209918_1142622	Not Available	537

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0209918_1000903	Ga0209918_10009039	F029940	MNDKPENNVGKELFLDKIEKLSLQIEKLTSEISQMKHKLDKSNKINRSFGLKSLQKSEPLNFTKEVFGIGSPTKRYLLSIRAITEIWKNRKNDFLITIRQQDKETHKDLKALGIRIPIENIKQIRTLSREIISLLYVACELKNVEINEILREILLEINEEGLDMVREIKNIMVLKSHP
Ga0209918_1001401	Ga0209918_10014018	F029940	MSHEYDKNINKELFLNKFEKLFLKIEQLTEEVSKLKHKIDKENKINRSFGLKSLKNSSPLTFTKDIFGIGSPTKRYLLSIRAITELWKNRKNDYFLVIRQQEKETQQDLKALGIRIPIDDIKKLRTLSREILSLLYIGCELKGVEINEVLRDILLEINERGNTLVQEIKKKMIS
Ga0209918_1009672	Ga0209918_10096722	F022369	MSKHKLIELQKIIEEKIGSLKEEVEIGTNVKLNPLYIADRQDEIEFLQWTIRIIYSILNRGNDERQQLGVTKKRLEMLETIEFEKTLQERVQELNLKLKESNNLRESDILINEIDTLESILGSLSDLKYGDKVCAIEVAEADNNYQQANRLRKQLIKMQDLETEISAQCSLNWRNTIGSKCIKGEKFFI
Ga0209918_1018764	Ga0209918_10187641	F056354	MILSVFIALSITAVLITGLAIRGDIPELLGAAVGAIMSIVASINALDLFVITNSGNVKDIAPQTDIALILLVIVVINLIFIFDRAFSGGN
Ga0209918_1020418	Ga0209918_10204181	F086685	VSSSPDTSMIELTTIPLVVWVIGCITFVILGHELTHYIAWLPVATSIEYHFEDQYIEAEYPDTPFARKWAVVAGISPVIVATGLVLALIATGWDPTATWHHITASAAVVLYGVSGGKSDFEALLALIKTRGSLG
Ga0209918_1024441	Ga0209918_10244413	F015275	MKTRFGFIDPSAIMGVVVSLIILAVGVFAFFVTLNEITNVADTARTRSAVNNVSDTGNSVFNIIGIVLIIGAIMSIVGLVYNYIRM
Ga0209918_1030107	Ga0209918_10301071	F033186	MNKINNIIPWGLAISTLGVTIAGAFYGTTALGLASITGGALALVAALLARQQMEKKKLNPELAMELK
Ga0209918_1031769	Ga0209918_10317694	F050177	MARIPSDPPDDALTPRQLADRVDDVVNLSVEELEAFRASEYNEEYLEYNSERAQQGNEPLDDVIRLLETPPDQWRDVDDGFNEIAEARELLDFQRRTQAQIESQGLGSNTIAEYDDMTFREAASIRWGI
Ga0209918_1031977	Ga0209918_10319776	F042291	MPIYQSFNPKIKAWVKYHFGKNGVEFTDVKQKEPQKPFKGIPKKGKRK
Ga0209918_1033608	Ga0209918_10336081	F022369	LSTYWFMQKHKLIELEKIIDERIGSLKEEVEIATNVKLNSLYIADRRDEIEFLQWITRIIHPILNRGNDERRQQLGVTKKRLEMMETIEFENALQERVQELNLKLKESNNLRESDILINEIDTLESILGRLSDLKYGDKVRAIEVAEAENNYQQANRLRKQLIRIQDIESEINAQCSFAR
Ga0209918_1039173	Ga0209918_10391732	F001667	MAVMLVGATALATEDAFAGKKKYERSQATSQANACGNGFLSTNVGCQNTASQIQGDENVVSQAAQQTFPDSEFDHGHDGKDNRD
Ga0209918_1044654	Ga0209918_10446541	F079748	MNTKYLVIVAAMAVMLVGASALSTTDNAFAGKKKYEKSQASSQANACGNGVLPLNVFCQNLLSQIQGDGNAVNVIGVQ
Ga0209918_1044904	Ga0209918_10449044	F042291	NPKIKAWVKYHFGKNGVEFTDVKQKEPQKPFKGIPKKGKRK
Ga0209918_1045567	Ga0209918_10455671	F001667	MQIKELRLVMLEMNSKYMVVVAAMAVMLIGATAFATDSAFAGGKKKYSQATSQANACGNGFLSTNVGCQNANSQIQGDENVVSQAAQQTFPDSEFDHG
Ga0209918_1048203	Ga0209918_10482033	F086649	MPNPAMDNLTKDSTDKQVQDAVSAEIELCMGQPAPPGAENKQKYCAGRAYGMARSKTGKELNYGT
Ga0209918_1057640	Ga0209918_10576401	F086685	MIDITTIPLVLWVLGCILFVILGHELTHYIAWLPVASSIEYHFEEQYIEAEYPDTPFARKWAVVAGISPVIVATGLLLALIATGWQPTATWHHITASVAVLLYGISGGKSD
Ga0209918_1062185	Ga0209918_10621851	F075754	MINYQAGIEWHIPMNRWEPIHARVDDTSEWYAAQVGRSEYLRDSEEDADMHHRKGGVVAEGLVKAIFAGMEWWDTHSFDTFLGGTRYDIISRGLNRGEPRQHYVHKIQAKKEERAKPSTHYYAVVRNHPDYWLIGHINSIRFWYLCDRSAPEFWDDEQFDGGFLSYEHF
Ga0209918_1064065	Ga0209918_10640651	F032166	LDDVIRLLSTPPEAWKDEDDGFNEVQEAEELLDFQRRTQAQIASQGLGMNFLGDDQDMTMREAASIRWGIDPDDEREWL
Ga0209918_1069146	Ga0209918_10691461	F057184	MSLLQPQAMMMTTLLFFIISSITMNTEVLAQNQSPVNQSHAGTIDLEIRGVSAFVPEGRNIYSITGEVFNNNTFPFNSVQVSATLYDKNDQVVGVGSGFTSPSGIPPGLKAPFKIDIFGTEIKGGIDAINNSTLQVAGDLQVQLFQ
Ga0209918_1070237	Ga0209918_10702372	F074420	MFLRLIVHYLFRRRKGVFMKTFIVIMATVILGVLIWGLILGPGENSLYSQASRLLDYGIEQLQTIP
Ga0209918_1072881	Ga0209918_10728812	F033343	CSKVLEGDSFMDLVEASMKEEGGQHVHGWENITLVEEKPVAVLKNKLVTV
Ga0209918_1074812	Ga0209918_10748121	F080661	MNSFERMWTALNLEKPDRMPIHTINLDGNVADKILGAPESSAFDVFDEMEEKFPDTWADKINSILNDIQISFFAKTIRAGHKIGFDGVGVQYIPFILESKEEMTDIFGKRHKVRNIDGNPYPDYYGGYIKDREAWEAYPKPDLKEEYKKAKKFWKGIKRKCRDIEDDICIVAQNALTSIFPPVWQGMGMANFARALKNDPKLIEERFRFTTDYT
Ga0209918_1083034	Ga0209918_10830341	F032166	EYLAANSERAQRGNEPLDDVIRLLETPPEEWRDVDDGFNEIAEARELLDFQRRTQAQIKSQGLGSNTIAEYDDMTFREAASIRWGIDPDDEREWL
Ga0209918_1086392	Ga0209918_10863924	F015411	MPRRGYGRKDGNQRGLKQGGRGINRTDKCRHPERKKGR
Ga0209918_1115254	Ga0209918_11152542	F005874	RKQTMAMIPNMPPDNDLTPAELYDRVEDITNLTVEELQAFKGSDYNEIYNARKSDAAQRKDEPLDDVIRLLSTEPAEWRDVDDGFNEVDEAEELLNFQRRTQAQIASQGLGENYLTEEEDMTMREAASIRWGIDPDEQREWL
Ga0209918_1122279	Ga0209918_11222791	F073153	MSEQDLPVRDEIRRIDGNIEGILTRLGNQSETIARIDLLVEEMQEMQTELEHIEVRLNTL
Ga0209918_1135788	Ga0209918_11357881	F096272	MEDLKKLHRKPKVSIAEINDFVLQHPKWAASIIRNAIGFEMYREFCLCCENFDKCYEKLGAIKRENSLGCICNEFLNQEHSEANRPRLRAYFKEVAVMLNL
Ga0209918_1136305	Ga0209918_11363051	F008189	NYWKPKVGQFKVKALTELEDTEPYVQKRSDGTEEVHPQAKIKILVNDEEKVWTFGKGKTPASTFGQIVELASRNNNILKDKEFTVVVKSDGVKNDYTIV
Ga0209918_1136953	Ga0209918_11369531	F001667	MNTKYLVIVAAMTVMLIGATALASTDSAFAGGKKKYEKSQALSQANACGNGKLPMNVFCSNSASQIQGDENSVGTATTQSSED
Ga0209918_1138535	Ga0209918_11385351	F032166	ETPPDEWRDVDDGFNEIAEARELLDFQRRTQAQIKSQGLGSNTIAEYDDMTFREAASIRWGIDPDDEREWL
Ga0209918_1142622	Ga0209918_11426221	F075754	MISYQAGIRWHTPVNPWEPIHARVDDTSEWYAAQVGRSEYLRDSEEDADMHHRKGGVVAEGLVKAIFPGMEWWDTHSFDTFLGGTRYDIISRGLNRGEPRQHYVHKIQAKKEERAKPSTHYYAVVRNHPDYWLIGHINSVRFWYLCDRSAPEFWDDEQFDGGFL