3300001866: Bioremediated contaminated groundwater from EPA Superfund site, New Mexico - Sample SAE3-23

Overview

Basic Information

• IMG/M Taxon OID: 3300001866
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0095509 | Gp0056884 | Ga0004714
• Sample Name: Bioremediated contaminated groundwater from EPA Superfund site, New Mexico - Sample SAE3-23
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: Y
• Use Policy: Open

Dataset Contents

• Total Genome Size: 168772898
• Sequencing Scaffolds: 20
• Novel Protein Genes: 20
• Associated Families: 9

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula formicica	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanotrichales → Methanotrichaceae → Methanothrix → unclassified Methanothrix → Methanosaeta sp. PtaB.Bin039	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon	8
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanotrichales → Methanotrichaceae → Methanothrix	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → unclassified Hyphomicrobiaceae → Hyphomicrobiaceae bacterium	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales	2
Not Available	3
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanotrichales → Methanotrichaceae → Methanothrix → unclassified Methanothrix → Methanosaeta sp. PtaU1.Bin060	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → unclassified Methanomicrobiales → Methanomicrobiales archaeon	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Bioremediated Contaminated Groundwater Microbial Communities From North Railroad Avenue Plume (Nrap), New Mexico
• Type: Engineered
• Taxonomy: Engineered → Bioremediation → Tetrachloroethylene And Derivatives → Tetrachloroethylene → Unclassified → Bioremediated Contaminated Groundwater → Bioremediated Contaminated Groundwater Microbial Communities From North Railroad Avenue Plume (Nrap), New Mexico

Alternative Ecosystem Assignments

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

Location Information

• Location: Espanola, New Mexico, United States
• Coordinates
  • Lat. (^o): 35.992
  • Long. (^o): -106.0797
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F038519	Metagenome	165	Y
F046981	Metagenome / Metatranscriptome	150	Y
F060548	Metagenome	132	Y
F071903	Metagenome	121	Y
F083634	Metagenome	112	Y
F089576	Metagenome	109	Y
F089758	Metagenome	108	N
F094797	Metagenome	105	N
F103319	Metagenome / Metatranscriptome	101	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI24729J20445_1000537	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula formicica	19612
JGI24729J20445_1003050	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanotrichales → Methanotrichaceae → Methanothrix → unclassified Methanothrix → Methanosaeta sp. PtaB.Bin039	5501
JGI24729J20445_1005038	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon	3856
JGI24729J20445_1007234	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanotrichales → Methanotrichaceae → Methanothrix	2987
JGI24729J20445_1008704	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → unclassified Hyphomicrobiaceae → Hyphomicrobiaceae bacterium	2580
JGI24729J20445_1008859	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales	2544
JGI24729J20445_1011297	Not Available	2111
JGI24729J20445_1011470	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon	2089
JGI24729J20445_1011979	Not Available	2019
JGI24729J20445_1015753	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanotrichales → Methanotrichaceae → Methanothrix → unclassified Methanothrix → Methanosaeta sp. PtaU1.Bin060	1601
JGI24729J20445_1027196	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon	988
JGI24729J20445_1032514	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon	847
JGI24729J20445_1037156	Not Available	756
JGI24729J20445_1045513	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon	642
JGI24729J20445_1048153	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon	614
JGI24729J20445_1048991	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → unclassified Methanomicrobiales → Methanomicrobiales archaeon	605
JGI24729J20445_1049157	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon	604
JGI24729J20445_1050865	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia	588
JGI24729J20445_1053354	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon	567
JGI24729J20445_1057986	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales	532

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI24729J20445_1000537	JGI24729J20445_10005372	F089576	MFGLPDITIAAVGGVVVIVIIALLYWGLTFQGHD*
JGI24729J20445_1003050	JGI24729J20445_10030502	F103319	MADSYNSIGHHPKSGYMTSEGCALHNLSGLDLVIDIAGVYFPLRSLQYAANHNISDEHGTGSHDPYALTNQEHTYTGSFSYASFLVNGDNVLTQKDVLMLSQLLHDQADEGVSKYFDIYIIEVQGKRTPGSGQTFEELVETTLQNESMVGYIEALVDAKVTKVNRDIPEKNTVISSREFKFSYKIPR*
JGI24729J20445_1005038	JGI24729J20445_10050383	F038519	MIDEGSDPKMRMFAIEYGGEDAEGPYTDEDLLKKTLVIIRQIEPNADIIGRECNPWSEQILAELLPYRIHVDLVDGIPQLPADVTLTWPPSETEGIQFGNLECREYFVWAESEKAALRKLATLNRAAPNYNPKAAAMCEE*
JGI24729J20445_1007234	JGI24729J20445_10072341	F089758	MALIEEKPGYPGDFGKAFESEDCLRIARELCRTGNLLKNSDDRVYGTPPGLVSIVDLSHEMHRACSTLAKVLEDAGWFQVLE
JGI24729J20445_1008704	JGI24729J20445_10087041	F046981	MALGIEQIDDFVAGIHQKFAGEERLAAQDISLPLQEYKYASRLFSGNLKKDTMSTSQCKWKVKVNTNDNFQVVGLYHRDASTRVNVLDEGELKWGLTTNNYHYDIDEEIFRTGGRQIYDYIESLENDLLTSFYTGMEDLMFGPGPSSPTQSPFPPVSLLWWITATDDSTTENNSEEGFDGYEPLGW
JGI24729J20445_1008859	JGI24729J20445_10088592	F089576	MFGLPDITIIVFGIVTIIAIALLVWWGLIFKGHD*
JGI24729J20445_1011297	JGI24729J20445_10112974	F060548	TNRPRQRRVTDFVDKQVATLIKDHAGEELCIEDLVDAAKREMPNFEWTNDKIRHSVTRLEKKRLVASEHVIRSKKLCRIPHLI*
JGI24729J20445_1011470	JGI24729J20445_10114705	F060548	MTSITNRPRQRRVTDFVDKQVATLIKDHAGEELCIEDLVDAAKREMPNFEWTNDKIRHSVTRLEKKRLVASEHEIRSKKLCRVPHLL*
JGI24729J20445_1011979	JGI24729J20445_10119793	F060548	GEGMSTVTNRPRQRKVTDFVDMQVFTLIKHHAGEELCIDDFVAAAIKEMPGFEWKDDKIRHSVNRLEKRGRLASKYVVRSKRLCRVPYLI*
JGI24729J20445_1015753	JGI24729J20445_10157531	F038519	MRMFAIEYGADDACGPYTDEDLLKKTLAIIRQIEPNAEIIGRKCNPFSDQIQAGLLPFRIHVDLVDGMPQLPADITLTWPPSETEGIQFGNLECREYFVWAESEKAALRKLATL
JGI24729J20445_1027196	JGI24729J20445_10271962	F094797	VSGSEDLEDLVDPGELPDPETFFPTPSEARALSKDKGFETIWKGGILAGCHLVLKLQISFNAKGRLLYNGKPYSRGIWGWRPPKFIRLQGREAKEEPNSRNSHPEIYLTTLNGEELKLDACPCGGELVKDSCECLYCRDCGTVYDHHR*
JGI24729J20445_1032514	JGI24729J20445_10325141	F038519	MKMFAVDYAAGEDAAGPYTDEVLLQKTLEIIRQIDPDAEVLSRECNPFSNQILAGLLPFRIHVDLLDGMPQLPAEVQITWPPGEMEGIQVGNLEFREYFVWAESEKAALRKLATLNKATPQPSNSKAVTAEAF*
JGI24729J20445_1037156	JGI24729J20445_10371562	F071903	MNRTEQAAARHEAELQEALGHLEYFKRTALALDQAMKVMANDLQVCRKNEQIWEKRIAKMQEKA*
JGI24729J20445_1045513	JGI24729J20445_10455131	F094797	EAKALSRDKGFETIWKGGILKGCHLVLKLQVSFNAKGRLLYNGRTYNRDSWTWRPPKFIRLQGREAKEEHNSRNNHPEIYLTTLNGQELKLDACPCGGELVKDRCECLYCRDCGMVYSHF
JGI24729J20445_1048153	JGI24729J20445_10481531	F094797	VSDSEALEDLLDPIDSDPETYFATPSEAKALSRDRGFETIWKGGILKGCHLVLRLQVSFNAKGRLLYNGRLYNRDSWTWRPPKFIRLQGREAKEEHNSRNNHPEIYLTTLNGQELKLDACPCGGELVKDRCECLYCRDCGMVYNHHQ*
JGI24729J20445_1048991	JGI24729J20445_10489911	F089576	MFGLPDITVLSMGVVVGLIVLALLYWGLKFNPKSDA*
JGI24729J20445_1049157	JGI24729J20445_10491572	F089758	MAIVPAQPGYPGDFGKPFESEACLRKARKLCKKGNLLKDSEGKASGTPPGLVSIVDLSHEMHRACSTLAKVLEDAGWFQ
JGI24729J20445_1050865	JGI24729J20445_10508652	F083634	MLKLANQVIVLDRLNINGRLHRLSRELQIIVGHTEDRLTLSNDEFGLLVSAPTLEEGIAGISDELSMLWEIYVAEKPANLTRDALRLRSNLKSLVA
JGI24729J20445_1053354	JGI24729J20445_10533542	F038519	SDKVAKANQRNRVVKKMRMFAIEYGAEDAYGPYTDEDLLQKTLGIIRQIAPNAEIIGRECNPFSDQIQAGLLPFRIHVDLVDGMPQLPADVTLTWPPSETEGIQFGNLECRVYFVWAESEKAALRKLATLNRASPNYNPKAAAMCEE*
JGI24729J20445_1057986	JGI24729J20445_10579862	F089576	MLGLPDITIIAVGGIVVVIIALLLYWGLTFRGHD*