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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |
| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300030493 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0095509 | Gp0056905 | Ga0310040 |
| Sample Name | Bioremediated contaminated groundwater from EPA Superfund site, New Mexico - Sample HSE6-23 (v2) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | Y |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 453618199 |
| Sequencing Scaffolds | 34 |
| Novel Protein Genes | 34 |
| Associated Families | 19 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria | 3 |
| All Organisms → cellular organisms → Archaea | 4 |
| All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanotrichales → Methanotrichaceae → Methanothrix → Methanothrix soehngenii | 1 |
| Not Available | 10 |
| All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia | 2 |
| All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon | 10 |
| All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → unclassified Methanoregula → Methanoregula sp. PtaU1.Bin051 | 1 |
| All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Methylococcales → Methylococcaceae | 1 |
| 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) | 35.9918 | Long. (o) | -106.0796 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F016481 | Metagenome / Metatranscriptome | 247 | Y |
| F017253 | Metagenome | 242 | Y |
| F025903 | Metagenome | 199 | Y |
| F036294 | Metagenome / Metatranscriptome | 170 | Y |
| F038519 | Metagenome | 165 | Y |
| F041560 | Metagenome | 159 | Y |
| F054136 | Metagenome | 140 | Y |
| F059711 | Metagenome | 133 | Y |
| F060548 | Metagenome | 132 | Y |
| F069913 | Metagenome / Metatranscriptome | 123 | Y |
| F071903 | Metagenome | 121 | Y |
| F072819 | Metagenome | 121 | N |
| F073009 | Metagenome | 120 | Y |
| F083634 | Metagenome | 112 | Y |
| F086459 | Metagenome | 110 | Y |
| F089758 | Metagenome | 108 | N |
| F094578 | Metagenome / Metatranscriptome | 106 | Y |
| F094797 | Metagenome | 105 | N |
| F106197 | Metagenome / Metatranscriptome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0310040_1000074 | All Organisms → cellular organisms → Bacteria | 122704 | Open in IMG/M |
| Ga0310040_1000454 | All Organisms → cellular organisms → Archaea | 38545 | Open in IMG/M |
| Ga0310040_1000551 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanotrichales → Methanotrichaceae → Methanothrix → Methanothrix soehngenii | 33823 | Open in IMG/M |
| Ga0310040_1000915 | Not Available | 24039 | Open in IMG/M |
| Ga0310040_1002131 | All Organisms → cellular organisms → Archaea | 12983 | Open in IMG/M |
| Ga0310040_1005472 | Not Available | 6234 | Open in IMG/M |
| Ga0310040_1005572 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia | 6141 | Open in IMG/M |
| Ga0310040_1008219 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon | 4598 | Open in IMG/M |
| Ga0310040_1009042 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia | 4300 | Open in IMG/M |
| Ga0310040_1009498 | All Organisms → cellular organisms → Archaea | 4138 | Open in IMG/M |
| Ga0310040_1011136 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon | 3692 | Open in IMG/M |
| Ga0310040_1012477 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon | 3383 | Open in IMG/M |
| Ga0310040_1015650 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → unclassified Methanoregula → Methanoregula sp. PtaU1.Bin051 | 2864 | Open in IMG/M |
| Ga0310040_1023130 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon | 2167 | Open in IMG/M |
| Ga0310040_1024575 | Not Available | 2079 | Open in IMG/M |
| Ga0310040_1029579 | All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes | 1828 | Open in IMG/M |
| Ga0310040_1033438 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon | 1679 | Open in IMG/M |
| Ga0310040_1034852 | Not Available | 1632 | Open in IMG/M |
| Ga0310040_1034886 | All Organisms → cellular organisms → Bacteria | 1631 | Open in IMG/M |
| Ga0310040_1038907 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon | 1517 | Open in IMG/M |
| Ga0310040_1039512 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Methylococcales → Methylococcaceae | 1503 | Open in IMG/M |
| Ga0310040_1041344 | Not Available | 1459 | Open in IMG/M |
| Ga0310040_1052850 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon | 1241 | Open in IMG/M |
| Ga0310040_1061176 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon | 1125 | Open in IMG/M |
| Ga0310040_1072475 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon | 1009 | Open in IMG/M |
| Ga0310040_1087122 | Not Available | 895 | Open in IMG/M |
| Ga0310040_1091461 | Not Available | 868 | Open in IMG/M |
| Ga0310040_1104853 | All Organisms → cellular organisms → Archaea | 793 | Open in IMG/M |
| Ga0310040_1109259 | Not Available | 772 | Open in IMG/M |
| Ga0310040_1120112 | Not Available | 726 | Open in IMG/M |
| Ga0310040_1151336 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → unclassified Methanosarcinales → Methanosarcinales archaeon | 625 | Open in IMG/M |
| Ga0310040_1156628 | All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes | 612 | Open in IMG/M |
| Ga0310040_1178567 | Not Available | 563 | Open in IMG/M |
| Ga0310040_1181574 | All Organisms → cellular organisms → Bacteria | 557 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0310040_1000074 | Ga0310040_1000074140 | F072819 | MCRGIGVYIRRPGRTGGRASIRAGITTARGIVNVTLIHGEEMFQDQIKAQEVSFRIARLEGENAVSELVNWCRNNLDELTVQCFTHKRFMSVQALVDALCEVYRDLGVEGEKGNVSAFVLFLAGKHRDKIYASHVVELNDTHRQILRDKLGLDIEEIEPGLSKLDWRADAGI |
| Ga0310040_1000454 | Ga0310040_100045410 | F038519 | MFAIEYGADDAYGPYTDEDLLKKTLGIIRQIAPNAEIIGRECNPFSDQIQAGLLPFRIHVDLVDGMPQLPAEISITWPPSEVEGIQVGNLEFREYFVWAESEKAALRKLATLNRAAPNYNQKAAAMCEE |
| Ga0310040_1000551 | Ga0310040_100055112 | F106197 | VADVKSALACFLLLLLVTGTESASADTISGQIDSQNFPSGDWYRGSNQGGANVWIKNTGDVGHLFWVSYEVMDSRGRWYSAPPESVYADAGDNATYFVSPVWTIPDDAEIGSYQADFYLYGYYDSSTGELSDQLDQVDQPNAFSVVG |
| Ga0310040_1000915 | Ga0310040_100091529 | F094797 | VSGSEDLVDLDDPGDLGPETFLPTPSEARALSRDKGFETIWKGGILTGCHLVLKLQISFNAKGRLLYNGKPYSRGIWGWRPPKFIRLQGREAKEEPNSRNSHPEIYLTTQNGVELKLDACPCGGELVKDNCECLYCRDCGTVYDHHR |
| Ga0310040_1002131 | Ga0310040_100213112 | F016481 | MEESEMDCGKSVWEHISEDKKKAFMKAKLDFKIKKVQAKLDFLKELQKIFE |
| Ga0310040_1005472 | Ga0310040_10054723 | F089758 | MVTIQEQLGYPGDFGKPFESEDCLRRAREFCKTGNLQKNSDDKVYGTPPGLVSLVDLSHEMHRACSTLAKVLEDAGWFQVLELPGYYFPPESKEGLE |
| Ga0310040_1005572 | Ga0310040_10055727 | F094797 | VDLDDPGDPDPETFLPTPSEARALSRDKGFETIWKGGILTGCHLVLKLQISFNAKGRLLYNGKPYSRGIWGWRPPKFIRLQGREAKEEPNSRNSHPEIYLTTLNGEELKLDACPCGGELVKDSCECLYCRDCGTVYDHHR |
| Ga0310040_1008219 | Ga0310040_10082198 | F094797 | VSGSEDLEDLVDPGELPDPETFFPTPAEAKALSKDKGFETIWKGGILTGCHLVLKLQISFNAKGRLLYNGKPYSRGIWGWRPPKFIRLQGREAKEEPNSRNSHPEIYLTTLNGEELKLDACPCGGELVKDSCECLYCRDCGTVYDHHR |
| Ga0310040_1009042 | Ga0310040_10090422 | F038519 | VKKMRMFAIEYGAEDAYGPYTDEDLLQKTLGIIRQIAPNAEIIGRECNPFSDQIQAGLLPFRIHVDLVDGMPQLPADVTLTWPPSETEGIQFGNLECRVYFVWAESEKAALRKLATLNRASPNYNPKAAAMCEE |
| Ga0310040_1009498 | Ga0310040_10094988 | F060548 | MKNPMMVPNRPKQHRVTDFVDMQAAMLVRNHAGEELCIEDLVDAAKRDMPNFEWNNDKIRHSVDRLEKRGKIASKYVIRRKRLCRVPYPI |
| Ga0310040_1011136 | Ga0310040_10111361 | F038519 | MKMSAIDYAAGEDAAGPYTDEVLLQKTLEIIRQIDPNAEIISRECNPWSEQILAGLLPFRIHVDLLDGMPQLPAEVSITWPPSSIEGIQVGNLEFREYFVWAESEKAALRKLATLNKAVQSYSPKAAAAEEL |
| Ga0310040_1012477 | Ga0310040_10124775 | F060548 | MGASMKEPGIIIVNRGKRNTSTDFVDMQVATLISDHVEKEPCIEDLVGLAETEMPNFAWTDDKIRNSVNRLEKRGRLMSKYVIRSKRLCRVPYPI |
| Ga0310040_1015650 | Ga0310040_10156502 | F083634 | MADQIITLDRLKINGHVRRLARELRITVGHDADRLTLTNDEFGLLVFSPTLEEGIAGISDELSTLWEVYVAGNPANLTRDALRLRSHLESLVVAGASS |
| Ga0310040_1023130 | Ga0310040_10231304 | F094797 | MDPGDLPDSETFLPTPSEARALSKDKGFETIWKGGILTGCHLVLKLQISFNAKGRLLYNGRPYSRGIWGWRPPKFIRLQGREAKEEPNSRNSHPEIYLTTLNGVELKLDACPCGGELVKDSCECLYCRDCGTVYDHHQ |
| Ga0310040_1024575 | Ga0310040_10245752 | F073009 | MLSILISDQPLDLSDDFSVSLNLKSPLFNDVGDYSYPFKVPTTARNKAILGWKNRIASSSRIYDTYEGSFRWNGIVLFKGQVRIKSAGEKTFEGILYINKGNFNYEVKDLMMNRVDLGLKEFASDQDAINYFNWSLTHFYPDVDFSMPKISNTDFFDPVATNPELMAYNYIFPDGWLHKTTSDGTQRTILVPFLYLKYVLNKLA |
| Ga0310040_1029579 | Ga0310040_10295793 | F069913 | VFKLFIFVLKLKAMTLEEYNLLEQELINSGLDNKSFLTSRGIKLHKYYYWKRKSRDLKEDPLQTEGQFLPIDVHTGGLIKASKRGKGIKQPFITHGEIEIELRTPSGAELRIRGIMDSLMVSTIIASTGGRRNV |
| Ga0310040_1033438 | Ga0310040_10334383 | F060548 | MSPTPGIIVNRPKRSAATDFVDLQVSTLVTDHADEEPCIEDLVRLAKKDMPKFDWTDDKIRHSVNRLEKRGRLTSKYVIRRKRLCRVPYPI |
| Ga0310040_1034852 | Ga0310040_10348521 | F054136 | MIENKAQLLADLAYVGSKVQAKTNVYLFSGAAFLWHGLKDATKDIDICCSYEEADRIVTELRMFGGMESVTGINDIHFLRMIFKSFALQIFIKEIWMGDEYQLLEAAHCDTLTFGGITFLIPDVKTLITIKDR |
| Ga0310040_1034886 | Ga0310040_10348862 | F017253 | HNVGSYTQVRIAGDFLSSRKAAWAERCPPKTTAAALDG |
| Ga0310040_1038907 | Ga0310040_10389071 | F038519 | MLESLKENSASNLGPRSPIKMYGIATDLGDDWAGPYVDQELLKKTLAIIQKVDPGAEIVSKETDPFSEQVLAGLLPFRIHVDLVDGMPQLPADVQITWPPGEMEGIQSGNLECREYFVWAESEKAALRKLATLNKATPQPSNSKAVTAEAF |
| Ga0310040_1039512 | Ga0310040_10395122 | F036294 | SDEAIVGVKPAADEDAVTYPRVKLLASDKDVGAEGRNM |
| Ga0310040_1041344 | Ga0310040_10413441 | F041560 | FEVKDIFLNRVDLGMMSFASDQQAVDYFNWSLTHFYPEVDFSMPEISNPTFYDPPATNPELMAHNYIFPDGWLRKYTTDGQCRTILTPFLYLKFVLNKLAEIFGYRLQDEFFTSSIELSRLVVYNSVSLSEVLFGLQKLYYCRLVPNVKVSEFITGLEKWFNCSFHVDTRQRVIRIVGNKEVLLRSDIVEFSRNILSLIQEIPEQITGFRFLLGPDAGDMAYQAQLDAEKGITEMIKGAVQHFSDIPTYPFTWLGDIYYIVDTNTWWQLAVNPYTFLIEWQQLPAGPMLTDKFFYKWGDEKNKFETIFSSLPDKYISVNCGNLGADYQKITPRLFWVGMAGGWGTPVRLRGFANNSNFSLRYPGPNGLFNLYWKDWVNWIMETRKSVKIEKQMDFIELKNLEFTKRYRINGINYLISEISVTLNKASIKSAQLKCFTAP |
| Ga0310040_1052850 | Ga0310040_10528503 | F089758 | MVKIPAQPGYPGDFGKPFESDDCLRIARELCKKGNLLKNSDDKVYGTPPGLVSIVDLSHEMHRACSTLAKVLEDAGGFQVL |
| Ga0310040_1061176 | Ga0310040_10611764 | F094797 | VSSSEDLEDIMDPGCLPGPETFLPTPSEARALSRDKGFETIWKGGILTGCHLVLKLQISFNAKGRLLYNGKPYSRGIWDWRPPKFIRLQGREAKEEPNSRNSHPEIYLTTQNGEELKLDACPCGGELVKDSCECLYCRDCGEVYSHY |
| Ga0310040_1072475 | Ga0310040_10724751 | F038519 | MKMFAVDYAVGEDAAGPYTDEDLLQKTLAIIRQIDPDADIISRECNPFSDQILAGLLPFKIHVDLLDGIPQLPADVQITWPPGEMEGIQFGNLECREYFVWAESEKAALRKLATLNKAAPNYNPKAAAM |
| Ga0310040_1087122 | Ga0310040_10871222 | F071903 | MNRTEQAAAKREAKLQEALGHLEYFKRTALALDQAMKVMAKDLQVCKKNELIWEKRIEKLQEKA |
| Ga0310040_1091461 | Ga0310040_10914612 | F060548 | STVTNRPKQHRVTDFVDMQVATLMRNHAGEELCIEDLVDAARRDMPNFDWNNSKIRNSVTRLEKKGLVGSKHEIRSKKLCRVPHLI |
| Ga0310040_1104853 | Ga0310040_11048533 | F094578 | WLLQRLKSMYFAVHCWKCKKFELPVEEYKKICEDNIQKIIDNLEIKEMKFREFNEIIKNSTFCKFEKRDFSNNCPICRKFGIWG |
| Ga0310040_1109259 | Ga0310040_11092594 | F060548 | MSTVTNRPKQRRVTDFVDMQVATLIRNHAGEELCIEDLVAVALKEMPGFEWKDDKIRHSVNRLEKRGKRA |
| Ga0310040_1120112 | Ga0310040_11201122 | F025903 | MIDITESPNFISFAGNPVIYEACSDNYLISLGSRASFELLVTGIDTSMGHSFKLQFAGKTLVFQTAGFTGFDGLLFEVGYLGQTFNDFANNIYQCFLENYDIQKYFNVTLDGPGTSSRNIHLQAKQSGTDGTVVFSNVNVTGVGQGT |
| Ga0310040_1151336 | Ga0310040_11513361 | F038519 | MRMFAIEYGGDDAEGPYTDEELLKKTLAIIRQIEPNAEIIGRECNPWSDQIHAGLLPFRIHVDLVDGMPQLPAEVSITWPPGEMEGIQSGNLECREYFVWAENEKAALRKLATLNKATPQPSISKAVTAEAF |
| Ga0310040_1156628 | Ga0310040_11566281 | F017253 | MRQCVKLVTLVANVGSYTQGRIAGDFLSSRNAARAERYPPKTTAAELA |
| Ga0310040_1178567 | Ga0310040_11785671 | F086459 | MIYAKDRVLAELDSAGAQLASLTADLKASRAVLQARLKMPPPFMPLEEYDCHFANAFTHIEKAKMAVRAMHPVCHQADFLKKKTEKNRR |
| Ga0310040_1181574 | Ga0310040_11815741 | F059711 | MRERTLHTSMNLLLEPDIYQRIKMIARLQKRSMSKFIREGINLRLAQYDKENNSIIGGKDRERTDNQ |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |