3300022181: Enriched culture of PCE-dechlorinating microbial communities from Ithaca, New York, USA - SJ1

Overview

Basic Information

• IMG/M Taxon OID: 3300022181
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0132855 | Gp0267134 | Ga0228535
• Sample Name: Enriched culture of PCE-dechlorinating microbial communities from Ithaca, New York, USA - SJ1
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 376029271
• Sequencing Scaffolds: 11
• Novel Protein Genes: 12
• Associated Families: 11

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Nitrosomonadales → Thiobacillaceae → Thiobacillus → Thiobacillus denitrificans	1
All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfovibrionales	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia	1
Not Available	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Enriched Cultures Of Pce-Dechlorinating Microbial Communities From Ithaca, New York, Usa
• Type: Engineered
• Taxonomy: Engineered → Modeled → Simulated Communities (Microbial Mixture) → Unclassified → Unclassified → Defined Medium → Enriched Cultures Of Pce-Dechlorinating Microbial Communities From Ithaca, New York, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): na → na → na

Location Information

• Location: USA: New York
• Coordinates
  • Lat. (^o): 42.4447
  • Long. (^o): -76.485
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F018395	Metagenome / Metatranscriptome	235	Y
F020198	Metagenome	225	Y
F025668	Metagenome	200	Y
F025775	Metagenome	200	Y
F039153	Metagenome / Metatranscriptome	164	Y
F041847	Metagenome / Metatranscriptome	159	Y
F059711	Metagenome	133	Y
F072821	Metagenome / Metatranscriptome	121	N
F073159	Metagenome / Metatranscriptome	120	Y
F081507	Metagenome	114	Y
F088355	Metagenome / Metatranscriptome	109	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0228535_1000041	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	398623
Ga0228535_1000060	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	317415
Ga0228535_1000282	All Organisms → cellular organisms → Bacteria	163991
Ga0228535_1000633	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Nitrosomonadales → Thiobacillaceae → Thiobacillus → Thiobacillus denitrificans	87537
Ga0228535_1005606	All Organisms → cellular organisms → Bacteria	6423
Ga0228535_1006786	All Organisms → cellular organisms → Bacteria	5161
Ga0228535_1007299	All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium	4759
Ga0228535_1016118	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfovibrionales	2176
Ga0228535_1023819	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia	1527
Ga0228535_1074743	Not Available	610
Ga0228535_1074831	All Organisms → cellular organisms → Bacteria	610

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0228535_1000041	Ga0228535_100004152	F018395	MKYDRADTAYAEKAHELSLKNRNWLRHGKGTTAGKIDQMLLDGATIEQMAKGAKTTKATVSVHLTHLRKEHMLAIVKKDGVLRYDVKKMNGKK
Ga0228535_1000060	Ga0228535_1000060143	F020198	MITIPHRKIKSREATMTYLLDPARLRSFIVDLRAYLRSTQHLFQKKGCENDPRNCKHRGMHDRPEPVLFRRFHHFCYERGFDWEAAREMMELMLSDRFLCECEMVWRLSDDRVEERLAGKRR
Ga0228535_1000060	Ga0228535_1000060293	F041847	MAMNEKKGMHFGKLVVDFANAPAAEEAGVAFIRGAAKAFGYGPEFLAKALDRYPTLERFAKALPADDRELVDLLLEERRLLSVINNLPCNISLSSYDYDGGRTLLFKIQPLEPRWDCENPYEEDDVRISVGAEGKTWLDEVAEMFDDRAPLTEDMDEVKGRLLGCMEEYIRLGDRILAIRRAIPAEKTHEAQKWAAYHSRIEAEQEVLAELLERWRATLGEIVDAGDLSRSQALLDLLVVYNVVNRRELAVGEDGAIYEKPLFGESYFTERAGLADEYYHNVLVYALVEFLKVPGNRRKLRKCRQCGAFFISPPGRPAGTECGRCGRRKGRGTGG
Ga0228535_1000282	Ga0228535_100028234	F088355	MKNTINNIRLFASHKGQLVLAILTIALFVLAAGAPNATLGIGR
Ga0228535_1000633	Ga0228535_100063371	F025775	MKQLLTFQGFPMVVVVGLIIWAWISILSVLIGSFF
Ga0228535_1005606	Ga0228535_10056068	F025668	MTKESIIEAQEYLRVKTEYGCKRIIDIKSLLESHNDGEVIKFLKDYLREKEKTLKNMILIDKSHPKVDQIVAAMFRISMAIKSLEEGEGVIKLERSQQGTEESGRFHKRDSGGHSGTGKWQDAGHDGKDRKPGQAIQRAA
Ga0228535_1006786	Ga0228535_10067863	F059711	MRNRTFHTSINLLIEPDTYQRLKMIAGLQKTTMSKFIREGIKLRLAQHDKENNSIVEG
Ga0228535_1007299	Ga0228535_10072996	F073159	RRKKHAVRPGAGVMCNVCGVNCGKGGALKKHVEGAHKVDYKQYKTCFSGCVKTLIADSWDDSVKTSTGKIVITHVLVRRFIGDPSKRGVSWKNP
Ga0228535_1016118	Ga0228535_10161182	F081507	MKKQFCIAIVIVAVLLLTAGMTSAAKLPNLVGTWSGGIHFVGWNSAADPQFYYASYVFTYEIENQDPATGNFYGHESGYPFTGNVSTNKVVTIIEYETAGEYRIITGKVSGKKITGTMQHWKPDQVDTGTFVLEKQ
Ga0228535_1023819	Ga0228535_10238192	F039153	MLYSVITPEREQKYHTEVKFFNNSKQASRLNFSPLHKEIKQWAKSQGYTPKLYLRSVAVECINPSLPKEPECIMEDLIQVIANGQAYLIAITIYGPPYENNLNYILEEHAKLRKAIYVTAECLDDVICEIQDNEHNHKGVPCVPDIKSRRSFQGDYSILFSPENLTWKTARNERA
Ga0228535_1074743	Ga0228535_10747432	F025668	VQEELRRVVYGGCGMTKESIIEAQEYLRVKTEYGCKRIIDIKSLLESHNDGEVIKFLKDYLREKEKTLKNMILIDKTHPKVDQIVAAMFRISMAIKSLEEGEGGIKLERSQQGTEESGRFHKRDSGGHSGPGKWQDARHDGKDRKPGQAVQRAA
Ga0228535_1074831	Ga0228535_10748311	F072821	EIYLRAVEDHKCPHCGEKLNRRPRRLWQKAVSFAVPLRHYKCEGCYHRFFALSPRWKQMKKGERWLRVAATGVVWIAGIFIVFRILFSVLYAVMS