3300022177: Enriched culture of PCE-dechlorinating microbial communities from Ithaca, New York, USA - SJ1.S

Overview

Basic Information

• IMG/M Taxon OID: 3300022177
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0132855 | Gp0267135 | Ga0228536
• Sample Name: Enriched culture of PCE-dechlorinating microbial communities from Ithaca, New York, USA - SJ1.S
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 268134221
• Sequencing Scaffolds: 31
• Novel Protein Genes: 41
• Associated Families: 23

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → FCB group → Candidatus Cloacimonetes	2
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	6
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria	9
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	3
All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Ecdysozoa → Panarthropoda → Arthropoda → Mandibulata → Pancrustacea → Hexapoda → Insecta → Dicondylia → Pterygota → Neoptera → Endopterygota → Coleoptera → Polyphaga → Cucujiformia → Curculionoidea → Curculionidae → Entiminae → Celeuthetini → Syntrophus	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae	1
Not Available	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Anaerolineae → Anaerolineales → Anaerolineaceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium 4572_187	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Anaerolineae → Anaerolineales → Anaerolineaceae → unclassified Anaerolineaceae → Anaerolineaceae bacterium	1
All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium	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
F021795	Metagenome / Metatranscriptome	217	Y
F031111	Metagenome / Metatranscriptome	183	N
F041155	Metagenome	160	Y
F041288	Metagenome / Metatranscriptome	160	Y
F041847	Metagenome / Metatranscriptome	159	Y
F045834	Metagenome / Metatranscriptome	152	Y
F048134	Metagenome / Metatranscriptome	148	Y
F055830	Metagenome / Metatranscriptome	138	Y
F059711	Metagenome	133	Y
F069913	Metagenome / Metatranscriptome	123	Y
F071210	Metagenome / Metatranscriptome	122	N
F073159	Metagenome / Metatranscriptome	120	Y
F075047	Metagenome / Metatranscriptome	119	Y
F077462	Metagenome / Metatranscriptome	117	Y
F088079	Metagenome / Metatranscriptome	109	N
F088355	Metagenome / Metatranscriptome	109	Y
F088944	Metagenome / Metatranscriptome	109	N
F103105	Metagenome / Metatranscriptome	101	Y
F103516	Metagenome / Metatranscriptome	101	N
F105253	Metagenome / Metatranscriptome	100	N
F105449	Metagenome / Metatranscriptome	100	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0228536_1000016	All Organisms → cellular organisms → Bacteria → FCB group → Candidatus Cloacimonetes	505042
Ga0228536_1000046	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	299064
Ga0228536_1000087	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	229002
Ga0228536_1000260	All Organisms → cellular organisms → Bacteria → FCB group → Candidatus Cloacimonetes	126794
Ga0228536_1000293	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	112664
Ga0228536_1000321	All Organisms → cellular organisms → Bacteria → Proteobacteria	102446
Ga0228536_1000493	All Organisms → cellular organisms → Bacteria	70810
Ga0228536_1000575	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	61353
Ga0228536_1000618	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	57879
Ga0228536_1000632	All Organisms → cellular organisms → Bacteria	56382
Ga0228536_1000653	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	54916
Ga0228536_1000752	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	48234
Ga0228536_1000907	All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Ecdysozoa → Panarthropoda → Arthropoda → Mandibulata → Pancrustacea → Hexapoda → Insecta → Dicondylia → Pterygota → Neoptera → Endopterygota → Coleoptera → Polyphaga → Cucujiformia → Curculionoidea → Curculionidae → Entiminae → Celeuthetini → Syntrophus	39328
Ga0228536_1001025	All Organisms → cellular organisms → Bacteria	34066
Ga0228536_1001026	All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Ecdysozoa → Panarthropoda → Arthropoda → Mandibulata → Pancrustacea → Hexapoda → Insecta → Dicondylia → Pterygota → Neoptera → Endopterygota → Coleoptera → Polyphaga → Cucujiformia → Curculionoidea → Curculionidae → Entiminae → Celeuthetini → Syntrophus	34055
Ga0228536_1001089	All Organisms → cellular organisms → Bacteria	31941
Ga0228536_1001104	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae	31445
Ga0228536_1001136	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	30334
Ga0228536_1001159	All Organisms → cellular organisms → Bacteria	29330
Ga0228536_1001466	All Organisms → cellular organisms → Bacteria → Proteobacteria	21817
Ga0228536_1002046	Not Available	13939
Ga0228536_1002130	All Organisms → cellular organisms → Bacteria	13276
Ga0228536_1002432	Not Available	10834
Ga0228536_1002784	All Organisms → cellular organisms → Bacteria	8879
Ga0228536_1002856	All Organisms → cellular organisms → Bacteria	8565
Ga0228536_1004239	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	5341
Ga0228536_1004314	All Organisms → cellular organisms → Bacteria	5249
Ga0228536_1014298	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Anaerolineae → Anaerolineales → Anaerolineaceae	1805
Ga0228536_1014812	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium 4572_187	1758
Ga0228536_1018358	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Anaerolineae → Anaerolineales → Anaerolineaceae → unclassified Anaerolineaceae → Anaerolineaceae bacterium	1496
Ga0228536_1048086	All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium	732

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0228536_1000016	Ga0228536_10000162	F031111	MNNQVLFSIFKNKTRRKKEKSRFLIGKKRCISYIPQNSYYQTIVNIPAAYNFSCYYPQNLPSSQIGKQVKEISKPLNLALIKLFKPKLTFP
Ga0228536_1000024	Ga0228536_100002493	F105253	MKKIVFLLVFISLVGYLIGQYVPVEIVNNAEDYLGRQLVTRFRDEIRKSHSYTVTYSSDEPHFKVKIDTMDRYKGDSLYEGISTIYNYTILIAVNGIDIYCYSQLGYAGKDVLNEVAFQIYSDLDEFIETFKSYLIKLLEEYE
Ga0228536_1000046	Ga0228536_1000046136	F088079	MLIEKAIWLENVPFRSIDEAIGGQNCSVYFVESMFVGQSCTFCTSIFGNLAPNAYRMLTRLDVFIHICEIYKVDITFFKSNVVSTK
Ga0228536_1000087	Ga0228536_1000087140	F088079	MLIEKAIWLENVPFRSIDEAIGGQNCSVYFVESMFVGQNCTFCTSRLGNLAPNPYRMLTRLDVFIHICEIYKVDITFFKPNVFSTK
Ga0228536_1000260	Ga0228536_100026082	F088944	MKNEEFEKEHFEIYLDSLEDRFDFDEGKEKIESLTTEAGEANIIVEQNNIEPIETQVLGTIRQLSHSGKLINYVPVALQENGLYLVMKVSPFIHYALDTDIIAPGYSGQYLIDPYNNFLLYPEEIEDSVVLDYLDLMTIFELQEALEKSIKEKQEGKGIDYSAIQDKWKLEFRFKEYQLTSYFRFRDLDANALDLTPMVDLLVKKEGLAMNKYAAARPTLTQAFDLMRQPETSNIFYALTHTLVKEPDGRVLLYPDEDYIGKLGKIYICTECVFEGYIPKQLWLGLRGFKDLKYIQEWLNISIKIEGEEKK
Ga0228536_1000260	Ga0228536_100026098	F031111	MKNQVLFSIFKNKTRRKKEKSRFLIGKKRCISNIPQNSYYQTIVNIPAAYNFCCYYPQNLPSSQIGKQVKKILKPLNLALIKLSKPKLTFP
Ga0228536_1000293	Ga0228536_100029364	F088079	MLTEKAIWLENVPFRSIDGAIGRQNCSVYFVESMIVGQSCTFCTSILGNLAPNPYRMLTRLDVFIHICEIYKVDITFFKSNVVSTK
Ga0228536_1000321	Ga0228536_100032112	F105449	MAVKCVECGKTVLKVNAKNKCEECARKDESMKSYFTRLFFINESCARLVPAT
Ga0228536_1000321	Ga0228536_100032134	F077462	MMSAGRLKTGVLITAILILFFGPLAVERTFCDVTRELKKLSEEREKSVGYAKIAKVSFKKQPKKLTHAMLYYTDAKSIGNPIIQQLQTSLASRSMKESQLREMLSEDVKRLVTVNEKFRAFIESGSSSNRALPGLAAVAGMAGPITDACVNLWKEYKDADKKRVDAMVEVLEGYKWADWDKI
Ga0228536_1000493	Ga0228536_100049320	F018395	MSSGLKLDRADTAYAEKAHELSLKNRNWLRHGIGTTADKIDEMLLDGATIEQMAKKAKTTKATVSVHLTHLRKVHKLAIARKDGVLMYDVDGMKEKQRVRGRKTK
Ga0228536_1000493	Ga0228536_100049321	F020198	MLVIPHKKLKSREATMEFLLDPARLKTFVLDLRAYLKSTQHQFHKVGFENDPKHCVHRGMYDRPETVLFRRFNHFCYEQGLDWEGAREMVELMLNERFLCECEILWRLKDEQVEERLSSR
Ga0228536_1000575	Ga0228536_100057525	F088079	MLTEKAIWLEKGPFRNVDEAIGRQNCSVYFVESMFVGQNCTFCTSRLGNLAPNPYRMLTRLDVFIHICEIYKVDITFFKPNVFSTK
Ga0228536_1000618	Ga0228536_100061836	F075047	MKKHLVFLMACLVTTWGCASVVFVSQETGKGQLLSATDEVPLQPSALFVTAHDDTMPDVTRNGRWVAFKRVVGGADRIIVRQVGDAAGTTERDVAQGIRPRWSPSGSWVLFRNQGKIYQVRPDGTSLMQLTSPPANMTDNFGHDYWNATTVVFGRGTGTGPGQVAALYLLDLASSALTGPVLGCSQPVVSHDGSRMTCEIKYYYGWGIMHYVQVYAVPSLQALGSIGFTYGPNATTIQNVGGIAFSADDERLLFSAVPPGETKREIYSIRLDGSGLTRLTNNGWDDVSPDGYKPQLW
Ga0228536_1000632	Ga0228536_100063218	F020198	MVIIPHKKLKSREATMTFLLDPAQLKSFVQDLRAYLKSTQHLCQMKGCENEPRHCAHRGMYDKPEPVLFRRFNHFCTERAGLDWEACREMMEIMLEKHFLCECEMVWRLKDEQVEVRFAGNEMK
Ga0228536_1000632	Ga0228536_100063219	F018395	MSAGLKLDRADTAYAEKAHELSLKNRNWLRHGIGTTADKIDVMLLDGATIEQMAKGAKTTKATVSVHLTHLRKEHKLAIVKKDGVLRYDVKPVKETKKAPRKSRKTG
Ga0228536_1000632	Ga0228536_100063232	F055830	MKRWKDLAVHRAGCPYKGVAVYGTDAEIAKYHSGNCPGCNVQVKWEEELQEKQTASQLKP
Ga0228536_1000653	Ga0228536_100065331	F088079	MLTEKAIWLENVPFRSIDEAIGGQNCSVYFVESMIVGQSCTFCTSILGNLAPNPYRMLTRLDVFIHICEIYKVDITFFKSNVVSTK
Ga0228536_1000752	Ga0228536_100075228	F088079	MLTEKAIWLENVPFRSIDGAIGGQNCSVYFVESMFVGQSCTFCTSRLGNLAPNPYRMLTRLDVFIHICEIYKVDITFFKSNVVSTK
Ga0228536_1000907	Ga0228536_100090728	F041847	MNEKKGMHFGKLVVDFANAPAAEEAGVAFIRGAAKAFGYGPEFLAKALDRYPTLERFAKALPADDRELVDLLLEERRLLSVINNLPCNISLSSYDYDGGRTLLFKIQPLEPRWDCENPYEEDDVRISVGAEGKTWLDEVAEMFDDRAPLTEDMDEVKGRLLGCMEEYIRLGDRILAIRRAIPAEKTHEAQKWAAYHSRIEAEQEVLAELLERWRATLGEIVDAGDLSRSQALLDLLVVYNVVNRRELAVGEDGAIYEKPLFGESYFTERAGLADEYYHNVLVYALVEFLKVPGNRRKLRKCRQCGAFFISPPGRPAGTECGRCGRRKGRGTGG
Ga0228536_1001025	Ga0228536_10010259	F103105	VIPAPYNSWPVVMSTNKAAQLLGVDRKTLAKNKNMLARCSETIGGKSKVIRDRLLRELKI
Ga0228536_1001026	Ga0228536_100102629	F041288	MFKRFSSSLYFLQLGVAITFLILAGIASSATLLKSRLLPTEQILKSSLGSEKFNTLRFETYGGLPENRMIGYFLYREGISVKGDGPQIESIGKLSLNEVLADHERVARAKFYGRLGHVMIREITREGDVVGYAVNDPKMEITLWDVTKYPSAISLELRYKDLQPKGERYDAGPR
Ga0228536_1001089	Ga0228536_10010891	F041155	AESVEVGVHRGLRADGVMSTVGFDLSAFRSLVMPQFVESII
Ga0228536_1001104	Ga0228536_10011041	F045834	MKRQNDTRMLLFLMTGTAFLFLAAAVPLSGVGFFLLVQATALVLGGVTLVSLFRRYHGLDLFSAASIYVLYVLMIALFSPGVVNGLAAYLTR
Ga0228536_1001136	Ga0228536_10011367	F021795	MKKEADRIRRWRERKKAEGKSSFTVVLSHQAREILAEEKEKTGESYAVIMEKALLGLKKQGYTPPILRHFPRREEVLARVAAQDSPPAPASNAGRVNHEGDRQPRILIDDLANYPTLEDIEREQAAKELNGVHDLKSSEGLITRLLRSSAGPFGRKKKWFK
Ga0228536_1001159	Ga0228536_100115926	F020198	MLTIPHRKIKSREATMTYLLDPVRLESFILELRIYLRSTQQLFQKEGFENDPRQCVHRTMYDRPEPVLFRRFNRFCTERGLDWEGAREMMEVMLSERFLCECEMVWRQKDEQVGER
Ga0228536_1001159	Ga0228536_100115927	F018395	MSAGQKSDRTDTAYAAKAHELSLKNRNWLRHGKGTTAGKIDEMLLDGATIEQMAKRAKTTKAAVSVHLTHLRKEHKLAIVKKDGVYRYDVKQAK
Ga0228536_1001466	Ga0228536_100146626	F018395	MSSGLKLDRADTAYAEKAHELSLKNRNWLRHGIGTTADKIDEMLLDGATIEQMAKKAKTTKATVSVHLTHLRKEHKLAIVKKDGVLRYDVDIMNGRK
Ga0228536_1002046	Ga0228536_100204621	F071210	MNEKEKRWLGTQKYEIHCFYCGGFHITGNCPQVVKAMNGWKYDRSCSETGHIKIVPNGDEYPTVLAFNGYHYRVVGLWGIPGRLLWLELERFYGDTIVAATFCPDELMEMDLGMSDDEQLSSWLGGLPFLSVSPPEFNGSEAEVDVKTTTGESL
Ga0228536_1002130	Ga0228536_10021301	F103516	MRTALILFLAALLAGCGAATNVQVMKPVNGEIQSFLTPELLKSRCYNFMSAGREGEMIAKKSNVLLNECNLTAKDAVNRVTYLTYTTKDAYVAESGENQVISKRVMGNKDIEIESRLFYEKEGGVRGIQVLINDFVDKNYVKGYEPEWVVRALYREVKLQDGKIVVVRDGMTRDEFMKEDEIEHYKKLNRMLK
Ga0228536_1002432	Ga0228536_100243210	F069913	MTLEEYNLLEEELINSGLDNKSFLTSRGIKLHKYYYWKRKSRDLKENSLQAEGQFLPIDVHSGGLIKPSKRGKGLKPPFITRGEIEIELRTLSGAELRIRGIMDSLMVSTIIASTGGRRN
Ga0228536_1002784	Ga0228536_100278412	F018395	MSSGMKYDRADTAYAEKAHELSLKNRNWLRHGKGTTAGKIDQMLLDGATIEQMAKGAKTTKATVSVHLTHLRKEHMLAIVKKDGVLRYDVKKMNGKK
Ga0228536_1002784	Ga0228536_100278413	F020198	MVIIPHKKLKSREATMTFLLDPVRLKSFVLDLRANLKSTQHLFQKEGFENDPKQCVHRGMYDRPEPVLFRRFNMFCTERGLDWEACKEMMEIMLEKRFLCECEMVWRLEDEQVEGRLADIKR
Ga0228536_1002856	Ga0228536_10028566	F018395	MSSGMKLDRADTAYAEKAHELSLKNRNWLRHGIGTAAGRIDEMLLDGATIEQMAKGAKTTKATVSVHLTHLRKGHKLAIVRKDGVLRYDVDKMNGKKKTGKKFKKAN
Ga0228536_1004239	Ga0228536_10042394	F018395	MSSGLKLDRADTAFAEKAHELSLKNRNWLRHGSKTSAGKMDEMLFDGATVEQMAKGAKTTKASVYVHLNHLRKVHKLAVVKKDGVFRYDMERMNGKKKTVGTKKGK
Ga0228536_1004239	Ga0228536_10042395	F020198	MITIPHKKIKSREATMTYLLDPSRLITFILNLRAHLKSTQHLCQKEGLENNPRNCVHRILYNRPETLMFRRFGHICYGRGLDWEGAREMMELMLNERFMCECEMVWRLSDEQVEEIFEGIMRSK
Ga0228536_1004314	Ga0228536_10043142	F048134	MESSKNVQINLSIPEQYRNLLRRMAAERVMSDPREVVTGASIATELLVTTLKEISREKKEGEFQND
Ga0228536_1014298	Ga0228536_10142983	F088355	MKNLTNKANLFASHKGQLVLAILTIALFVLAAGAPNATLGIGR
Ga0228536_1014298	Ga0228536_10142985	F088355	MKNTINNIRLFASHKGQLVLAILTIALFVLAAGAPNATL
Ga0228536_1014812	Ga0228536_10148122	F059711	MRKRNFHTSINLLIEPSTYQRLKMIAGLQKTTMSKFIREGIKLRLAQYDKENNSMVEG
Ga0228536_1018358	Ga0228536_10183583	F088355	MKNLTSKVSLFVSHKGQFVLAILAIALFVLAAGAPNATLGIGR
Ga0228536_1048086	Ga0228536_10480861	F073159	MAGRRKGAVRPGHGVMCNICGKNCGKGGALKTHIEGAHPPVTYEVYKICFYGKSKNTLADAWDDSVSTKNGDTVVTHVLARRFVQEPGPRGATRAVCKQKA