3300002963: Feedstock adapted compost microbial communities from Newby Island compost facility, Milpitas, CA, USA - starting DNA

Overview

Basic Information

• IMG/M Taxon OID: 3300002963
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053053 | Gp0053414 | Ga0053370
• Sample Name: Feedstock adapted compost microbial communities from Newby Island compost facility, Milpitas, CA, USA - starting DNA
• Sequencing Status: Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 306997490
• Sequencing Scaffolds: 14
• Novel Protein Genes: 15
• Associated Families: 10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	1
All Organisms → Viruses → Predicted Viral	1
All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Eubacteriales → Clostridiaceae → unclassified Clostridiaceae → Clostridiaceae bacterium	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Bacillales → Bacillaceae	1
Not Available	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Klebsiella/Raoultella group → Klebsiella → Klebsiella pneumoniae	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Eubacteriales → Syntrophomonadaceae → unclassified Syntrophomonadaceae → Syntrophomonadaceae bacterium	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Feedstock Adapted Compost Microbial Communities From Newby Island Compost Facility, Milpitas Ca
• Type: Engineered
• Taxonomy: Engineered → Solid Waste → Feedstock → Composting → Unclassified → Feedstock Adapted Compost → Feedstock Adapted Compost Microbial Communities From Newby Island Compost Facility, Milpitas Ca

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Soil (non-saline)

Location Information

• Location: Newby Island compost facility, Milpitas, CA
• Coordinates
  • Lat. (^o): 37.454581
  • Long. (^o): -121.928712
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001938	Metagenome / Metatranscriptome	614	Y
F029085	Metagenome / Metatranscriptome	189	N
F036251	Metagenome / Metatranscriptome	170	Y
F036417	Metagenome / Metatranscriptome	170	Y
F047639	Metagenome / Metatranscriptome	149	Y
F079824	Metagenome / Metatranscriptome	115	N
F088752	Metagenome / Metatranscriptome	109	N
F098955	Metagenome / Metatranscriptome	103	Y
F101228	Metagenome / Metatranscriptome	102	Y
F101423	Metagenome / Metatranscriptome	102	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI1652J44930_10004772	All Organisms → cellular organisms → Bacteria	4657
JGI1652J44930_10019070	All Organisms → Viruses → Predicted Viral	2086
JGI1652J44930_10020334	All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium	2006
JGI1652J44930_10023147	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Eubacteriales → Clostridiaceae → unclassified Clostridiaceae → Clostridiaceae bacterium	1852
JGI1652J44930_10028438	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Eubacteriales → Clostridiaceae → unclassified Clostridiaceae → Clostridiaceae bacterium	1617
JGI1652J44930_10030602	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Bacillales → Bacillaceae	1540
JGI1652J44930_10048304	Not Available	1132
JGI1652J44930_10049001	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Klebsiella/Raoultella group → Klebsiella → Klebsiella pneumoniae	1121
JGI1652J44930_10056083	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes	1019
JGI1652J44930_10060345	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Clostridia → Eubacteriales → Syntrophomonadaceae → unclassified Syntrophomonadaceae → Syntrophomonadaceae bacterium	969
JGI1652J44930_10071668	Not Available	859
JGI1652J44930_10086528	Not Available	754
JGI1652J44930_10094203	Not Available	711
JGI1652J44930_10120594	All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium	598

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI1652J44930_10004772	JGI1652J44930_100047722	F036417	MVYYARVPIRQLIPTVLVRLATDEGEVVFRARWNRSPLELQRSILFRLRQGTHLWFETEWGHSICFKPESVWGAVVDGR*
JGI1652J44930_10019070	JGI1652J44930_100190701	F101423	MFTKRKPKSIERFRVGKGNPGIKAFLYRILNKPYLDIRIFRGYKEITRIVTPDTGMRQFTVEGIGTFVVPVGDNLLRQYYNKHCIYLNYNIQNSNPGVPVDCEKWTEYEYPPLSPEEFQVLLEAQTVADLLSETEKDTKWIW
JGI1652J44930_10020334	JGI1652J44930_100203342	F098955	MDPSAIPVFLAGPFPVLHSANVLEREAEVQLDVGLIIGGLPTILAATSFPLDETWERVEAALSSGDARLGVAGIPHQVESPLGELEIFPSAYIGLECANGERLILAHIRGLDPDQDPESYAREVIAALLNGQSPAELGELIED*
JGI1652J44930_10023147	JGI1652J44930_100231473	F029085	MKNIKDEKIKIDELLEENISEQLENGSGDSLVSLIAISELTNLNKLKVITRLKDEQVPLLSKLYMYAETFNISFIKNLADNILQLQISIRGLGRKELVNIVRESTPQEIKRGLFGTKDVFR*
JGI1652J44930_10023147	JGI1652J44930_100231474	F047639	MRLFKHKYLRVIKFNSDKSSTISYHLSSKFKPNFLINPDHIFFYKGYRTIIVTDKAAETINPLDFXSKFNANDFQTAIESKLIKDTFNTLKPNLFDKTTFMLLLNIILTIAVIYLLMKGQGMI*
JGI1652J44930_10028438	JGI1652J44930_100284382	F079824	GKTLCLTFVGYVDYLAGRHVISNYQTSFSELVSTERIAEMVINEDIRDTTILISELQLYMNSLGVNTKELRSFVGSVIGQSRKRNTDIHYDTQRYTDVHPRIRVQTDRAFLPRKFHENGKPCQLDRCNKKHIIYLFQHDPYLEQPIIKLRADKFGALYDTNEIVALTKD*
JGI1652J44930_10030602	JGI1652J44930_100306023	F088752	MKELQSVYNQITKILKENNVLMNITPPRPYLIKKDVEERFNAEAEDLLKKGKIKEYNLKMEEKEAYKLYYDEAYKYTNFFEEGDE*
JGI1652J44930_10048304	JGI1652J44930_100483043	F036251	MSGNKRQTICFSDTGISAPIDDVERVGLTDGTVFVAQRIEIRPSLKYGEYVVFDGEDLEGKEFHGYSTSGVILQQAKALLDKYGGKDGTLTVDVLCTVRALVSESTGRKFYTLV*
JGI1652J44930_10049001	JGI1652J44930_100490013	F101228	YLLIYYITGSTIQAVFGILIFMLMCLGVLWVNRLPREDRLWCKRLVGITAILLSALVAISYYPASALTITGEPSGDQIRWEITDGEPPYTVFVNGVEIVRDYPGAVVLTDSEPGKQYTAVVMDNESVADATVIGEYYTYPLWAWLLFAALLACLVVSIWIPYAAFGAAIAGGFLLLLIAPNPDYAPYLRIFAGAAFIVGLGGLAGRMQA*
JGI1652J44930_10056083	JGI1652J44930_100560831	F001938	MIEKIYKNKYMVICDNCGDGYECNSWADVMDFMLEEGWKKRLVDGEFKHYCPECQEG
JGI1652J44930_10060345	JGI1652J44930_100603452	F079824	MIYGFFGSIPGCPHNRGNHALRGNGKTLCLTFVGYLDYLAGRHVXSXXXTSFSELVSTEKIAEMVINEDIRDTTILISELQLYMNSLGVNTKELRSFVGSVIGQSRKRNTDIHYDTQRYTDVHPRIRVQTDRAFLPRKFHEDGKPCQLDRCNKKHIIYLFQHDPYLEHPILKLQADKFIWSILS*
JGI1652J44930_10071668	JGI1652J44930_100716683	F101423	MFAKSKPKSIERFRVGKGSPALKAFTYRILNKPYLDIRIFRGYKEITRIVTPDTGMRQFTVEGIGTFVVPTGDNLLRQYYNRHCIYLNYNIQNSNPGVPVEYEKWTEYEYPPLSPEEYQVLLEAQTVADLLKETEKDMKWIWYLLIGGIVLVGLIMLMGGA*
JGI1652J44930_10086528	JGI1652J44930_100865283	F101423	MFTKRKPKSIERFRVWKGNPGIKAFLYRILNKPYLDIRIFRGYKEITRIVTPDTGMRQFTVEGIGTFVVPTGDNLLRQYYNKHCIYLNYNIQNSNPGVPVECEKWTEYEYPPLSPEEFQVLLEAQTVADLLSETEKDTKWIWYLLIGGIVLV
JGI1652J44930_10094203	JGI1652J44930_100942032	F101423	MFGKRKPKSIERFRVGKGSPALKAFWYRILNKQYLDIRIYRGYKEITRIVTPDTGMRQFTVEGVGTFVVPTGDNLLRQYYNKHCIYXNYNIQNSNPGVPVXCEKWTEYEYPPLSPEEFQVLLEAQTVADLLSETEKDTKWIWYLLIGGIVLVALIMLMGGA*
JGI1652J44930_10120594	JGI1652J44930_101205942	F036417	MVYPARVPLRTRIPTVLVRLATDDGEVVFRARWTRSPLELQRNILFRMRRGSLLWFQDEWGHDLCFRPECVYAAMVDGR*