3300027057: Marine sediment microbial community from Union City, CA, USA - Pond 1C Sediment 1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300027057
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053056 | Gp0053695 | Ga0207796
• Sample Name: Marine sediment microbial community from Union City, CA, USA - Pond 1C Sediment 1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 146770160
• Sequencing Scaffolds: 13
• Novel Protein Genes: 15
• Associated Families: 13

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	5
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Anaerolineae → Anaerolineales → unclassified Anaerolineales → Anaerolineales bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Anaerolineae → Anaerolineales → Anaerolineaceae → unclassified Anaerolineaceae → Anaerolineaceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2
Not Available	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Porticoccaceae → unclassified Porticoccaceae → Porticoccaceae bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Environmental Microbial Communities From Fremont, Ca And La Paraguera, Puerto Rico
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Marine → Unclassified → Unclassified → Enviromental → Environmental Microbial Communities From Fremont, Ca And La Paraguera, Puerto Rico

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): marine biome → pond → sediment
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: Eden Landing Ponds, San Francisco, CA, USA
• Coordinates
  • Lat. (^o): 37.569083
  • Long. (^o): -122.103267
  • Alt. (m): N/A
  • Depth (m): .32

Associated Families

Family	Category	Number of Sequences	3D Structure?
F021885	Metagenome / Metatranscriptome	217	Y
F029111	Metagenome / Metatranscriptome	189	Y
F033789	Metagenome / Metatranscriptome	176	Y
F037736	Metagenome / Metatranscriptome	167	Y
F049303	Metagenome / Metatranscriptome	147	Y
F052283	Metagenome / Metatranscriptome	143	Y
F070128	Metagenome / Metatranscriptome	123	Y
F080659	Metagenome	115	Y
F085223	Metagenome / Metatranscriptome	111	Y
F090093	Metagenome	108	N
F092306	Metagenome / Metatranscriptome	107	Y
F094909	Metagenome	105	Y
F102576	Metagenome	101	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0207796_1000018	All Organisms → cellular organisms → Bacteria	75427
Ga0207796_1000305	All Organisms → cellular organisms → Bacteria	20299
Ga0207796_1000476	All Organisms → cellular organisms → Bacteria	16167
Ga0207796_1002534	All Organisms → cellular organisms → Bacteria	5108
Ga0207796_1002888	All Organisms → cellular organisms → Bacteria	4644
Ga0207796_1003826	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Anaerolineae → Anaerolineales → unclassified Anaerolineales → Anaerolineales bacterium	3815
Ga0207796_1009807	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Anaerolineae → Anaerolineales → Anaerolineaceae → unclassified Anaerolineaceae → Anaerolineaceae bacterium	1861
Ga0207796_1012451	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1571
Ga0207796_1020174	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1130
Ga0207796_1026162	Not Available	950
Ga0207796_1030534	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Porticoccaceae → unclassified Porticoccaceae → Porticoccaceae bacterium	859
Ga0207796_1047401	Not Available	647
Ga0207796_1053683	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	597

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0207796_1000018	Ga0207796_100001850	F102576	MNDLLLLERYFPGGKLEGGIALANRLDWGLSVQMSGNDYVVSSGNEPILRTESKDALQSFIYGMGLAYAVLPENLFLALEKTLREL
Ga0207796_1000305	Ga0207796_100030523	F094909	MVVMYNEKILDWVEGYVLTRMLIFGDFVGTVDRTELMFDLDTSSDYFRIHEGQRIQALSLPVKSRRLCTLLGEIEACFQRGWPLLDAGEWTKADFDEVYDLSMQISDEIMLLREEFQQKMPSEPRPSSVNPD
Ga0207796_1000476	Ga0207796_10004763	F052283	MNSRQKSVFTGAILGAALGAVGGYLFTRGLDLSREGREQPDELSLKSVPPGEMVKVFIAIMAVLRGIAELGERL
Ga0207796_1002534	Ga0207796_10025346	F094909	MVVMYNEKVLDWIEGYVLTRMLIFGDFVGTVNRTELMFDLDTGSDYFRIYEGQRIQALSLPVKSRNLCTLLGEIESFFQRGWPLLDAGEWTEADFNQVYELSKRISDEIMILRKEIQEKKNSVSATASVNPDPNP
Ga0207796_1002888	Ga0207796_10028882	F102576	MNDLLMLERYFPGGKLEGGIELANRLDWGLSVQRAGDDFVVSSGNEPILRTGSKDALQSFIYGMGLAYAILPERLFKMLEKSLREL
Ga0207796_1003826	Ga0207796_10038263	F092306	MTTIFYSGPDVQQSSEPHTFVEVQESDCWPVDDRSASGTKDQLADGLHPVIAIGGRTAADGRPFNLTGVVVSCNISTAGTATDRIVVNIADGTIVRNYVANILTYSGGSAATYETAPVMGQPVFVDDSADLAAGVTLSMSPLNSADVRNPLAGYLWYCQDEIADGQVGGSRSTATFDTALSDSLVEQTYCVLLINAARELA
Ga0207796_1009807	Ga0207796_10098072	F080659	MTGIPILDTILDLIMQYRLGIAMVGLAVIAIGLIARPIAPEWSAHNRTAVAMMVIGGIVLILLPTLAAAIVGT
Ga0207796_1012451	Ga0207796_10124512	F070128	MLLVGGFGSVSSGSLDATAIMALSLASSLILLDLAGTPQPRSPRAIIGFSLLAIAIGAALVMVFERVSS
Ga0207796_1020174	Ga0207796_10201742	F029111	MAIGRETGLVWKCWIGSGGGGNRTAGNSPDSDDSRTVSRTGFDENTSKEHEQNALPDILMTMSQIPDVNRELAEVGTMFAVFDALRRSGER
Ga0207796_1026162	Ga0207796_10261621	F090093	MNIRTIVVIACLYVSFFGLPNIELPNVQPPAPETPDVREPTAELRDAVQDVADICEKMDAFDRLVWMSTWEECSTIVAGEDDDVSLVFDNTLGLRLFTDSTFDVAWSRLANASQKYRGLGEAVEKAFTQVIGNDV
Ga0207796_1026162	Ga0207796_10261622	F049303	MSTLINDPVRVLAVVAAAAVLLAPYLPAVLKRLKAAWASLPSVPKTPPDGIGVSDLTMVLDLANRLRLDGHEKATDLAKQLLDAMLEVPQK
Ga0207796_1026162	Ga0207796_10261623	F021885	MNIFEKLKLLAEWSPLLTFAQQLAAEDDIHAKAVIVTEAMEWVADRTSVEWDDELASHISDILISEEGEAFVRWILERMQVSDVDVD
Ga0207796_1030534	Ga0207796_10305342	F033789	MFEDLPCPFMIGDIKVWPAHSRPGQRWFIAYEGKPYWFRSKNEAKLFAMDRQAMEDPEGLCD
Ga0207796_1047401	Ga0207796_10474011	F037736	VQLDGLQILWLLANPLWTHGIGESGSKTITGWLLMDAAAANHIWWLNTNPFTGLLLHINSYRIRHLPFGFLTASEFQSRSTCLIKK
Ga0207796_1053683	Ga0207796_10536831	F085223	LAEYEKMIATEDGIQALIRRVEIADSLNWGHLADGHQPTCPRQLHFTHHDSYERWAKHFDGSQSLVTILRVRCLECGAVFTIQPSFIVRYKRYDTDAIEKYMVLLFITEDSYRMAGVSQALGMDTQQAGTWLALTEAERDPISPTALWALVQWLGELSPAQLNLALGVEPPTHVIEDEKHVKECGEKAYVPIVYAPRE