3300025977: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqB_D2 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025977
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101407 | Ga0210072
• Sample Name: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqB_D2 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 97025147
• Sequencing Scaffolds: 13
• Novel Protein Genes: 13
• Associated Families: 12

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	7
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	1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → Gemmatimonadaceae → unclassified Gemmatimonadaceae → Gemmatimonadaceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	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 → Aquatic → Marine → Wetlands → Unclassified → Natural And Restored Wetlands → 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): Unclassified
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: San Francisco Bay, California
• Coordinates
  • Lat. (^o): 38.131752
  • Long. (^o): -122.266335
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001196	Metagenome / Metatranscriptome	749	Y
F026610	Metagenome	197	Y
F047065	Metagenome / Metatranscriptome	150	Y
F048676	Metagenome / Metatranscriptome	148	Y
F050381	Metagenome / Metatranscriptome	145	Y
F076109	Metagenome	118	Y
F078289	Metagenome / Metatranscriptome	116	N
F080061	Metagenome	115	Y
F082105	Metagenome / Metatranscriptome	113	Y
F084253	Metagenome	112	Y
F093888	Metagenome / Metatranscriptome	106	Y
F099324	Metagenome / Metatranscriptome	103	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210072_1001608	Not Available	2323
Ga0210072_1002555	Not Available	1997
Ga0210072_1008624	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → unclassified Desulfobulbaceae → Desulfobulbaceae bacterium	1246
Ga0210072_1016245	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	948
Ga0210072_1029820	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → Gemmatimonadaceae → unclassified Gemmatimonadaceae → Gemmatimonadaceae bacterium	715
Ga0210072_1039449	Not Available	627
Ga0210072_1041519	Not Available	611
Ga0210072_1043667	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	597
Ga0210072_1044241	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales	593
Ga0210072_1047230	Not Available	575
Ga0210072_1048323	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	569
Ga0210072_1056119	Not Available	529
Ga0210072_1056954	Not Available	525

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210072_1001608	Ga0210072_10016084	F078289	IFILIIVVFPLYGFNSLVRHEDIPKMRELGISQEVIQYIISNQTSSVSSEDVIKMKQSGLNNNDIMSAIKSDLYRPEQKSTSMKEVELIAKLKESGMSDEAVLQFIQTVKSTRRVDSDGNVTKQYTNESQRTQYPTTGATFPKLDNYGYDPSNGRFLFFIKPQNQE
Ga0210072_1002555	Ga0210072_10025551	F048676	YSRLCGTASDAVNAVKLEIPKGFKLLKFKMSECLKNIVKLPISKI
Ga0210072_1008624	Ga0210072_10086242	F099324	MFKQIIFVIMLGWVLVLSGCAAIDKGEDYRTGYPPRAGYTSTTPHKALVSEACNIEANNLSAEDFMGDDRARRVYFSQCMLRNGYDADGNYVGIPPK
Ga0210072_1016245	Ga0210072_10162452	F084253	SNFVLIKAAQGFAISAHGTGRRMSLRRSRKPAENADQDKNGHLWMDTSYD
Ga0210072_1029820	Ga0210072_10298203	F026610	MESYQVVILPSERWTRVLLCHGPDELLRAILPPPSQVRHERSAPTFLESLALWLDATLPVVLSVDAQHAGFCLGLTDELGLGKCSIYYRVEVRERGGRRRGTRIRSMGNFADLRRLSLSAHGGGR
Ga0210072_1039449	Ga0210072_10394492	F080061	LFGILTLGHCGLPFDLAQGGGELVEPFGICDLKFEIF
Ga0210072_1041519	Ga0210072_10415192	F047065	MTDLLNKFSKAAKAVSSSKTPMWECVKQAYVDHLSDISTNNLPEKIQIFYDSVKLRVTSVDTLGHIDNDEASYIANDIMYMADVIRSGSRKS
Ga0210072_1043667	Ga0210072_10436672	F076109	MEVLFKIFFVIAFIAFILCMFVFVGGLFMAFKEVELPDIEDV
Ga0210072_1044241	Ga0210072_10442411	F080061	IQISDKIKRHLFGILNFGHCDLPFDLAQGGGELVEPFVICVLLFEIFYH
Ga0210072_1047230	Ga0210072_10472301	F050381	MKKLIIVLAIILLPSLALANFSIQFDNTTHKKMFYLLYWIDHNYDWPYPFNLAGGELKALETIDLSQGYKNGQYFVIWFDEGNWQNTVKMNVGEGVTSVKVTPIHFRQQK
Ga0210072_1048323	Ga0210072_10483231	F082105	AAPLMHEPPRYAGQPNVTVQRAVASTIMRIDSAGSGRVNEKKYKK
Ga0210072_1056119	Ga0210072_10561191	F093888	ASICALVIIFSLTLFGILILIRVRNIKKVLNNLNDGLDIISQKLGRQSMEFENIQPNRHKLGSHINNEIAAGGRASLEAGNGAVIAQKNGSEEHRINTEIRTKIQELLKKTGKPTPYHDLTQHLSKDYPGYNYDFFLKEAEDLQKKGKVEVQLIAGKLYFQIKKT
Ga0210072_1056954	Ga0210072_10569541	F001196	DQFRSGIFGLPWNAGKAAIEAKYPGGAWDQDDQGRARYCAASQQPLLKLPPQHQTRELCFLIGSDGTLASAMARMDASLPALLAIVNRSRTIFGDFDSVRRDEAAIQSRSTAMLWTREAPYVVQVSSANDNDGRPMEVTFTVADEANIHTVGSERVSHRPPGT