3300026131: Salt pond soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG SF2_B_D2_MG (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026131
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114514 | Gp0125956 | Ga0209928
• Sample Name: Salt pond soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG SF2_B_D2_MG (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 153084004
• Sequencing Scaffolds: 20
• Novel Protein Genes: 20
• Associated Families: 18

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	7
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius sp. associated proteobacterium Delta 1	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Halieaceae → Pseudohalioglobus → Pseudohalioglobus sediminis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → unclassified Syntrophobacterales → Syntrophobacterales bacterium CG23_combo_of_CG06-09_8_20_14_all_48_27	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales 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): 37.4972
  • Long. (^o): -122.1293
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F012874	Metagenome / Metatranscriptome	276	Y
F030933	Metagenome / Metatranscriptome	184	Y
F037736	Metagenome / Metatranscriptome	167	Y
F038247	Metagenome / Metatranscriptome	166	Y
F042355	Metagenome / Metatranscriptome	158	Y
F042909	Metagenome	157	Y
F044506	Metagenome / Metatranscriptome	154	Y
F045765	Metagenome / Metatranscriptome	152	N
F047065	Metagenome / Metatranscriptome	150	Y
F054047	Metagenome / Metatranscriptome	140	Y
F058158	Metagenome / Metatranscriptome	135	Y
F059981	Metagenome / Metatranscriptome	133	Y
F078289	Metagenome / Metatranscriptome	116	N
F082775	Metagenome / Metatranscriptome	113	Y
F084253	Metagenome	112	Y
F084254	Metagenome / Metatranscriptome	112	Y
F087950	Metagenome / Metatranscriptome	110	Y
F090406	Metagenome	108	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0209928_1006068	Not Available	1784
Ga0209928_1007214	All Organisms → cellular organisms → Bacteria	1637
Ga0209928_1013147	All Organisms → cellular organisms → Bacteria → Proteobacteria	1224
Ga0209928_1015241	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1140
Ga0209928_1018738	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae	1028
Ga0209928_1018803	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	1026
Ga0209928_1019135	Not Available	1017
Ga0209928_1019347	All Organisms → cellular organisms → Bacteria	1010
Ga0209928_1021406	Not Available	961
Ga0209928_1021900	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius sp. associated proteobacterium Delta 1	950
Ga0209928_1032216	Not Available	784
Ga0209928_1032845	All Organisms → cellular organisms → Bacteria	777
Ga0209928_1034499	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Halieaceae → Pseudohalioglobus → Pseudohalioglobus sediminis	758
Ga0209928_1035105	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → unclassified Syntrophobacterales → Syntrophobacterales bacterium CG23_combo_of_CG06-09_8_20_14_all_48_27	752
Ga0209928_1036776	All Organisms → cellular organisms → Bacteria	734
Ga0209928_1039002	Not Available	713
Ga0209928_1043547	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	675
Ga0209928_1046193	Not Available	656
Ga0209928_1050405	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius sp. associated proteobacterium Delta 1	628
Ga0209928_1060934	Not Available	570

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0209928_1006068	Ga0209928_10060681	F047065	MTDLINKFSRAAKAVTSSKSHTWECVKKAYADHLSDISTDRLPLDIQIFYDSVKLRVTSAEAFGHIDNDEASYIANDIRYMANVISSGLKNS
Ga0209928_1007214	Ga0209928_10072141	F084253	KAALVFAVRRTSVRRSRKPAENAEQDKKGHLWMETN
Ga0209928_1013147	Ga0209928_10131472	F042909	MIELLNFIGSLNLWTFIVIWTSTIFLVIFISLLLFCVSQMNKETIKISKKVKILIEGLSEKLKLGNDDIIF
Ga0209928_1015241	Ga0209928_10152411	F078289	MKKTVIILMTLFIVVPLYGFNSLVRHEDIPKMRELGVSQEVIQYFISNQTSSVSSEDVIKMKQSGLKNDDIMSAIKSDLYRPEQKSTSMKEAELIAKLKESGMSDEAVLQFIQTVKSARRVDSDGNVTKQYTNESQRTQYPTEGATFPKPDNYGYDPINGRFLLLVNPQN
Ga0209928_1018738	Ga0209928_10187382	F044506	MMEQWNSGIMGFGMMQCLINGPATGGIDDKIKMVNILLKTNIPSFHPSIIPFPEKIRRPKKSPYSQ
Ga0209928_1018803	Ga0209928_10188032	F045765	MKYHSSKGENTTTIKIDDRLYDLLRKFCDKEGRRLKDFVEDALENAIYTDESIKILNAEIKSLKKKEAKYDYAFRRGFQKGFYISFCALHGQILLGPDDEEYEILKNDPYRVSKGAQLDLFR
Ga0209928_1019135	Ga0209928_10191353	F037736	AQGSKTRPLVLLDPRKSSVPYRVQLDGLQILWLLANPLRTHGIGESGSKTITGWLLMSAADANHIWWLNAKPFTGLLLHLNSYRILHLPCGFLNMLCFLLLCHRQRNDNY
Ga0209928_1019347	Ga0209928_10193472	F087950	MQCWINGPATGGIDDKIKMAIILLKTNIPAFHHSIIPF
Ga0209928_1021406	Ga0209928_10214062	F047065	MTDLLNKFSEAAKVVSSSKTRMWECVYGAYVDHLSDISTDSLPEEIQIFYDSIKLRITSVEAFGHIDNDEACYIANDIMYMADVISSGLRKP
Ga0209928_1021900	Ga0209928_10219001	F058158	RIDKRIVNQKSYMSDFTKTEKEDIDIWELHVKEREYILTQIAKDRRTSKIRTWIELIFMLGFIYYMLYDIYKDGDLDTIIKFLKT
Ga0209928_1032216	Ga0209928_10322162	F059981	MEREKIICIFCGRIAKIKEQDDLKIVVCPKCKRETELVAYQDIFDQWLGDIRNKDGER
Ga0209928_1032845	Ga0209928_10328453	F038247	MKSVFFWSEEEARAHRKNNPEPKGIYLSLRQGEIINRPIQSVLFGFARE
Ga0209928_1034499	Ga0209928_10344991	F090406	DKDGGNVYALPPTVVDQMLKDAMSTEISTGTLRRGSTPYPSYLGEVTWGSLDKDTITASARPAKGRKLDGTIIDGYVFEVSRKGTAPATGEPTVKRIFAKLQNDAELTGAGVAFVEFTD
Ga0209928_1035105	Ga0209928_10351051	F054047	IGHGLFVGWVEHPDIFCWVSFLYPTYLPAIFVLSVKPNKMAED
Ga0209928_1036776	Ga0209928_10367763	F042355	MSTELKQVNKLKKTSRRNENVNDATFIERLIKISRVTKVTK
Ga0209928_1039002	Ga0209928_10390021	F054047	GSNIGHGLFVGWVEHPDIFCWVSFLYPTYLPAIFLLSAKPNKMAEDRTVP
Ga0209928_1043547	Ga0209928_10435471	F030933	ELRRKRAQAVKTAWVLGTIALLIFATFIGSAIIGR
Ga0209928_1046193	Ga0209928_10461932	F084254	LSLQTGRIPVFISESMVIEILAEVIRQSKRHPRADQVASALAMRGLPIAQKDVMTVFDQYDIEKKIVDTY
Ga0209928_1050405	Ga0209928_10504051	F012874	MPAKAGIQNYLKTLDSRLRGNDVKGRFKTFYETIDIQRSM
Ga0209928_1060934	Ga0209928_10609342	F082775	MTEPDILYPAIFVFSMLLIGLLLTMWEFSRLYKRQQQKVENDKRFTGLDSRVYRENVRNVSHF