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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 | 3300021257 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225713 | Ga0210329 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Oregon, United States ? S.272 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 27217085 |
| Sequencing Scaffolds | 41 |
| Novel Protein Genes | 52 |
| Associated Families | 38 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales | 2 |
| Not Available | 35 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 1 |
| All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Solspiviridae | 1 |
| All Organisms → cellular organisms → Archaea → Asgard group → Candidatus Lokiarchaeota → unclassified Lokiarchaeota → Candidatus Lokiarchaeota archaeon | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series |
| Type | Environmental |
| Taxonomy | Environmental → Aquatic → Marine → Intertidal Zone → Estuary → Estuarine → Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | estuarine biome → estuary → sediment |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Saline → Water (saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: Washington | |||||||
| Coordinates | Lat. (o) | 46.178 | Long. (o) | -123.853 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000203 | Metagenome / Metatranscriptome | 1619 | Y |
| F000344 | Metagenome / Metatranscriptome | 1257 | Y |
| F000748 | Metagenome / Metatranscriptome | 908 | Y |
| F001024 | Metagenome / Metatranscriptome | 803 | Y |
| F001346 | Metagenome / Metatranscriptome | 718 | Y |
| F001418 | Metagenome / Metatranscriptome | 698 | Y |
| F001758 | Metagenome / Metatranscriptome | 640 | Y |
| F002020 | Metagenome / Metatranscriptome | 603 | Y |
| F002557 | Metagenome / Metatranscriptome | 548 | Y |
| F004323 | Metagenome / Metatranscriptome | 443 | Y |
| F004925 | Metagenome / Metatranscriptome | 418 | Y |
| F006508 | Metagenome / Metatranscriptome | 371 | Y |
| F007695 | Metagenome / Metatranscriptome | 346 | Y |
| F010305 | Metagenome / Metatranscriptome | 305 | Y |
| F010436 | Metagenome / Metatranscriptome | 304 | Y |
| F011154 | Metagenome / Metatranscriptome | 294 | Y |
| F014854 | Metagenome / Metatranscriptome | 259 | Y |
| F016502 | Metagenome / Metatranscriptome | 246 | Y |
| F020183 | Metagenome / Metatranscriptome | 225 | Y |
| F023505 | Metagenome / Metatranscriptome | 209 | Y |
| F024439 | Metagenome / Metatranscriptome | 206 | Y |
| F025295 | Metagenome / Metatranscriptome | 202 | Y |
| F033058 | Metagenome / Metatranscriptome | 178 | Y |
| F034947 | Metagenome / Metatranscriptome | 173 | Y |
| F037756 | Metagenome / Metatranscriptome | 167 | Y |
| F037987 | Metagenome / Metatranscriptome | 167 | Y |
| F041496 | Metagenome / Metatranscriptome | 160 | Y |
| F041780 | Metagenome / Metatranscriptome | 159 | Y |
| F045132 | Metagenome / Metatranscriptome | 153 | Y |
| F049440 | Metagenome / Metatranscriptome | 146 | Y |
| F053305 | Metagenome / Metatranscriptome | 141 | Y |
| F060937 | Metagenome / Metatranscriptome | 132 | Y |
| F077370 | Metatranscriptome | 117 | Y |
| F082737 | Metagenome / Metatranscriptome | 113 | Y |
| F092888 | Metagenome / Metatranscriptome | 107 | Y |
| F094695 | Metagenome / Metatranscriptome | 105 | Y |
| F102092 | Metagenome / Metatranscriptome | 102 | Y |
| F102644 | Metagenome / Metatranscriptome | 101 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210329_104783 | All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales | 977 | Open in IMG/M |
| Ga0210329_106486 | Not Available | 545 | Open in IMG/M |
| Ga0210329_106664 | Not Available | 671 | Open in IMG/M |
| Ga0210329_108529 | Not Available | 571 | Open in IMG/M |
| Ga0210329_110240 | Not Available | 606 | Open in IMG/M |
| Ga0210329_110538 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 813 | Open in IMG/M |
| Ga0210329_115072 | All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales | 1287 | Open in IMG/M |
| Ga0210329_115324 | Not Available | 794 | Open in IMG/M |
| Ga0210329_115713 | Not Available | 562 | Open in IMG/M |
| Ga0210329_116545 | Not Available | 661 | Open in IMG/M |
| Ga0210329_117339 | Not Available | 523 | Open in IMG/M |
| Ga0210329_117365 | Not Available | 654 | Open in IMG/M |
| Ga0210329_118174 | Not Available | 532 | Open in IMG/M |
| Ga0210329_118479 | Not Available | 783 | Open in IMG/M |
| Ga0210329_121418 | Not Available | 566 | Open in IMG/M |
| Ga0210329_122149 | Not Available | 1065 | Open in IMG/M |
| Ga0210329_125019 | Not Available | 672 | Open in IMG/M |
| Ga0210329_127210 | Not Available | 748 | Open in IMG/M |
| Ga0210329_127645 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 506 | Open in IMG/M |
| Ga0210329_127793 | Not Available | 803 | Open in IMG/M |
| Ga0210329_128000 | Not Available | 752 | Open in IMG/M |
| Ga0210329_128729 | Not Available | 804 | Open in IMG/M |
| Ga0210329_128784 | Not Available | 1049 | Open in IMG/M |
| Ga0210329_129362 | Not Available | 713 | Open in IMG/M |
| Ga0210329_130936 | Not Available | 558 | Open in IMG/M |
| Ga0210329_132967 | Not Available | 717 | Open in IMG/M |
| Ga0210329_140301 | Not Available | 586 | Open in IMG/M |
| Ga0210329_140398 | Not Available | 655 | Open in IMG/M |
| Ga0210329_141496 | Not Available | 809 | Open in IMG/M |
| Ga0210329_142972 | Not Available | 1696 | Open in IMG/M |
| Ga0210329_143727 | All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Solspiviridae | 4108 | Open in IMG/M |
| Ga0210329_145069 | Not Available | 591 | Open in IMG/M |
| Ga0210329_147511 | Not Available | 534 | Open in IMG/M |
| Ga0210329_147646 | Not Available | 807 | Open in IMG/M |
| Ga0210329_147731 | Not Available | 821 | Open in IMG/M |
| Ga0210329_156787 | Not Available | 570 | Open in IMG/M |
| Ga0210329_157524 | Not Available | 702 | Open in IMG/M |
| Ga0210329_157617 | Not Available | 808 | Open in IMG/M |
| Ga0210329_159132 | Not Available | 726 | Open in IMG/M |
| Ga0210329_159406 | Not Available | 795 | Open in IMG/M |
| Ga0210329_160110 | All Organisms → cellular organisms → Archaea → Asgard group → Candidatus Lokiarchaeota → unclassified Lokiarchaeota → Candidatus Lokiarchaeota archaeon | 879 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210329_104783 | Ga0210329_1047832 | F020183 | MSLTINAKTYNADRFGQDAIGYVGPAHTLSVLDDVQLSRVAPKPTVTFSGVGRASAKMTRTLTLTGALTPTGNAICQINVSVPVGAATADVDSLLNDMGAFLSSASAKTLVEGLQISF |
| Ga0210329_106486 | Ga0210329_1064862 | F025295 | DHGNWPGKATELLRRREVLIPEKLKFITRKRSLQKPI |
| Ga0210329_106664 | Ga0210329_1066641 | F011154 | MRSDEKPLRIESSRPGRFRAWANRSYPEGIRLLLCISTGGRLWRPPEGGLPNERRRKAGQSERPNREGHAASAGPVKTFQAVGDVKNDTADLWTKGNLRVKRRDPWHRANALSKAAADPALSGEDADQKTQTCLDLVRKPVAQPPAQAS |
| Ga0210329_108529 | Ga0210329_1085291 | F102092 | MHGIEHCEQKRRTICPPAPQWPFSPAAGSMRYDSPLAAFCPEPVARNGFSLSHNSCRLSATSIPGSKFPACYFASFQVASVPVRPFGSTTAFPGLRRLRPLHCLWPVALPLPGSACRACRLHSPPGLLPPSGSKRSTAFAARRSTWRIRPISSRSPLPALVKVGASDHRSRSATFPPACC |
| Ga0210329_110240 | Ga0210329_1102401 | F006508 | VALANAPSKAVADQSQVVKTRRRNCRRVLTWFASRWRNHQPKRAEKPHSKFSGASRWTALLRG |
| Ga0210329_110538 | Ga0210329_1105381 | F000344 | MRPKHPHAAESGVGKHTARESERAQACVTGKERVANAH |
| Ga0210329_111620 | Ga0210329_1116202 | F000203 | GMGVFQALFPMPTLGAPLSGAAGFPTPFSTASGVIGLVAGPSSALRTLNFE |
| Ga0210329_112975 | Ga0210329_1129751 | F001758 | SGQAGWRDSSQAGAQVPGAEAEFTSSSGEVRASSVHAKKELGDEER |
| Ga0210329_114030 | Ga0210329_1140303 | F037987 | VPAFGARFAAAAGFPTPFSTASGVIGLVAGPSGTLQRADFE |
| Ga0210329_115072 | Ga0210329_1150722 | F020183 | MSLTFNTKTYTADSFQKDSVGYYGAAKTVSVKDDLKLSRVAAKPSATFSGMSRTEAKLTRTVTLTGALTPTGDEILGINVAIPIGTSATDVDALLNDMGAFLSSASFKTHVKQQLISY |
| Ga0210329_115324 | Ga0210329_1153241 | F034947 | LLLCIGTGRETLAGSINRLKPPKENHRKVDKQRARTGENTQTRQIA |
| Ga0210329_115713 | Ga0210329_1157131 | F011154 | KPLRIESSSSGEFRARANRSYPEGMRLLLCISTGGRLWRSPEGGQPNERRRKAGQTERSNREGHAASAGPVKTFREVGDVKNDTADLWTKGNLRVKRRDPWHRANALPEAAADLALSGEDADRKT |
| Ga0210329_115713 | Ga0210329_1157132 | F000203 | LALGAELAASFPTLFSTASGVFGLVAGPSSILRSLDY |
| Ga0210329_116545 | Ga0210329_1165452 | F037756 | LFPVPTLGAHLAAAAGFPTPFSVTSGVFGLVAGPFNLLRD |
| Ga0210329_117339 | Ga0210329_1173391 | F041780 | AFRMTGLDSLCSPRPLFGGCASTLRAQPASHSNRNRNLETAFLLLCGDFPYPELRDRLKRSQPASSISLPRPIRGRSALNSLPDAFGFRRGHGHKTRFPLAARQLRPILEPPLPFGVSSPPDHNAQSDSGRKVYLGKTPDHLLLPERINE |
| Ga0210329_117365 | Ga0210329_1173651 | F000203 | LFPVPALGASGAASFPTLFSTASGVSGLVAGPSSAFPPLDFE |
| Ga0210329_117365 | Ga0210329_1173652 | F002557 | VLMHSSNHYPLGNCDSPKPETGLGYLTQLGAASHRSSLPSSFFAFTDSARTLPEELVNPA |
| Ga0210329_118174 | Ga0210329_1181741 | F000748 | MTRSPDSLIPSGAGQLAMEKRDDKVLNCRQEGEANLRAATQVNVVSASSIPPAITPIQLELFPGRACPLEAKPATHRRTARRKPRRRDGVQDGGTQRQSIKLTGETLFGPAEETPTGREVHKGQTRKRSNEAGQGVGGGYSTDELRDNRREGRAATFIKRTK |
| Ga0210329_118479 | Ga0210329_1184791 | F060937 | GNGRKIEECTAGIIPGDWGTVGPGWLVQPLGSRIARFGERRQYSPAPLTGVATRHNAIEELGGEER |
| Ga0210329_121418 | Ga0210329_1214181 | F077370 | RKRILKNNSQQLAVPRPMSILGKTNDRAIDILVNIFAVNSLGTPFYSFAVSAGSPQVSANLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNYIGGGTTILQNTPSIFLQASTIPYNVGTVSLQRAIAQSDNSIEIDLQTYDPKSYDILLPPHIVSNNRANNQTFAFGSQTWISTRLNNVQNFP |
| Ga0210329_122149 | Ga0210329_1221492 | F016502 | MSPLRRTERSGKQFNPARVVPGMATSPWNSCGAAETPGGASTDLSVQPPGKNESLCA |
| Ga0210329_125019 | Ga0210329_1250191 | F010436 | MELEVYSQSINRGVVKMPSQGFPGLVIQGETLSTLLKLATSIHEKSQGTSDTELIASSVEMKESLEKLVAHFESTLSRHKIPMPYSTVPSKQAEE |
| Ga0210329_127210 | Ga0210329_1272101 | F007695 | VKRRDPWFEVNALPKAAAALGLDGQDAEISHGSVLIWFAGRWRNHQSERAEKPHSKSSGGNALDGPATRPETPLAVENSVGKLAAPEA |
| Ga0210329_127645 | Ga0210329_1276451 | F004323 | MPRYDLRRLEGRATPAVAIHSPVTRDYPSRALSDVFQAAALRLF |
| Ga0210329_127793 | Ga0210329_1277931 | F004925 | RWTAVIERKSQVVSRIIPGNWGKAESGWLAWPLLNQIAGSGDGGRIHQFLWPRSHAVSNAKKEPGDEE |
| Ga0210329_128000 | Ga0210329_1280001 | F034947 | VKRSYPEGIRLLLCISTGRTTLADSINRLNPPKENHRKVDKRSGRIGKVTLTRQVV |
| Ga0210329_128729 | Ga0210329_1287293 | F025295 | VTGPGKATELLGRREVLDPEKLKFVTRKSNLRKRI |
| Ga0210329_128784 | Ga0210329_1287841 | F024439 | RPVVGTDKSVEAPPGVSASPQLVDRDVAVPGTTLSGLTGLSERSARRSGAIGSPPPPRRLYDHEEFRRSAIRAVRRPPGSSRRLRRPLRVRAEVPSPAMPGQVAPPGVSCPFSGISGGIRITRVCLTRHVPSSGFLAPSTVSSPSGLADSLGPLPLMGFPLVQLFRAAGP |
| Ga0210329_129362 | Ga0210329_1293621 | F045132 | VLIHSSNHYPLGNCDSPRPETGLNYLTQLEAVSHRSALPSSLFAFTDGARTPPEELVNSACLVRCISTRLERGLINQPDPTFPR |
| Ga0210329_130936 | Ga0210329_1309361 | F041496 | GAFIRPEPPGLVSCRIRSWGHPPELSSSRAAVRCLQRRSPRGVCSAFRVLLRARVRHPAQLFKLKTERVALLGLLPSRVFALSTLARPSPVLPSCGCRCGRERTRRLHFRVSHVESPAHLSRDCRPSWGLWPHGRHARLSLAGILESPPKAPGVRHRPLVSPSSHPCVTLPEPSITNLSASPPLRL |
| Ga0210329_132967 | Ga0210329_1329671 | F033058 | MNRRRVLAWFAGRWRNHQFKRAEKPHSKSSGGDALDGPATRPETPLAVENSVGKPAAPEAPNAGTGKREWR |
| Ga0210329_134749 | Ga0210329_1347491 | F000203 | GAHLAAAAGFPTPFSVTSGVFGLVAGPSSALRPLDFE |
| Ga0210329_137910 | Ga0210329_1379102 | F000203 | LFPVPALGASGAAGFPTLFSTASGVSGLVAGPSSASPLLDFE |
| Ga0210329_140301 | Ga0210329_1403011 | F082737 | FQVTLGCSSLPNLHARFEPVTSGTPDAFRLASRLRSFSVGASLLSGTPASLPVRSRSLEADFHSPTKASLLPDDRGGVRAPALLLPLHDTSPVSPVRSGLHPRPVSRTAWDFNNQNPLLSGPAPLLPASLNRRSPSGLFAPPDQCTRSRWPTENLLSGTPDLPSLPTGGRIRYQHQRIIVPAPLRPFQLAVP |
| Ga0210329_140398 | Ga0210329_1403981 | F001418 | NMRVAEAGFTSSSGDVRTSSVHAKKELCGKGRLEAVPSRLK |
| Ga0210329_141496 | Ga0210329_1414961 | F094695 | MGESQSAVSVTRTSAKLGLPFRGSATNSIGPSWVRPIPVQRLPFPAASFGFSLSAVVRGLSHPRHSSLRLTCLLEALPPINRPRMRTREHLSCDFVPYSAQQKQASVSPGDSNLRHCPSSGFLTLSTSYSACNPDQLVSSGLRSWGSTGSVYSPSPFGHGRVRRFRVSSSKLSPFPR |
| Ga0210329_142972 | Ga0210329_1429721 | F102644 | VGHPRCESGESEPGTHEVRVHAVRLGGRNRLDALRVFSTGRLQGLL |
| Ga0210329_142972 | Ga0210329_1429723 | F049440 | MPPSSTSSTVDEDRLPRSHRCRLQRLNGFYDRESVAR |
| Ga0210329_143727 | Ga0210329_1437272 | F020183 | MSLTINAKTFTADKFGVDAVGYIGPAHTLSILDDVQLSRVAPKPTVVFSGVGRTSAKLTRTLTLTGALTVSGNAIVQINVSVPVGAASADIDALLNDMGSFLSSASYKSHVKGLQISY |
| Ga0210329_144324 | Ga0210329_1443241 | F000203 | GVRHALFPRPTLGAFEAAGFPTLFSTANGVFGLVAGPLSALPSLSY |
| Ga0210329_145069 | Ga0210329_1450692 | F006508 | VALANAPSQAAADQRQVVKTQERIHGCVSTWFASRWRNHQPKRAEKPHSKSSAARRWTAL |
| Ga0210329_147511 | Ga0210329_1475111 | F004925 | KRFRIIPGDWGKAGSGWLARPLESRIARFGGGGRIHQFLWQRSRVVSNAKKELGGQE |
| Ga0210329_147646 | Ga0210329_1476461 | F010305 | LKRAEKPHSKFRRRKALDGPATRPKTPLAVENGVGKLTAPEKGAPNVSPGKRAWRTPIP |
| Ga0210329_147731 | Ga0210329_1477311 | F023505 | SWDAGDGRKKVASVPRIIPGDWGKIEPGWLAQSLEDRFARNGNWRQDSPVPLPAFARRQ |
| Ga0210329_153819 | Ga0210329_1538191 | F014854 | RFGGGGRIHQFLWSRSHAVSYAKRNLAARGDKKPLRVGSSSPGRFRAWANRSYPEGKWLLLCIGTGRVTLADSINRLKPPNESHRKVDKGSARTGKITQARQAA |
| Ga0210329_156787 | Ga0210329_1567871 | F002020 | DFQPGSLPACTAWSTCRQKRRTIRRFAPRKLCFSAPGSMRPGSPLAALCPEPSARNDLSLACNDCRLSAATIPGSKLPACYFASSRVFLVSVPPFGSAATLPVAPVAAASMPRARYTSSTRSGLPRPQSPLPSGNLTSLGIKAFNRVCCLPVHLTNSPDSLSLPAARSY |
| Ga0210329_157524 | Ga0210329_1575241 | F053305 | MLKKSLSIVLTALFVFSFIAVGTVAAAEVKGEVVSVNAETGEMVIKDDAGEMKSLMADPKAVDLKMLKEGDMVSVESDDAGAVKSIKASE |
| Ga0210329_157617 | Ga0210329_1576172 | F001024 | MRPVTPLAVENSVGKLAAAERQMSAWERERGELPP |
| Ga0210329_159132 | Ga0210329_1591322 | F001346 | VKTFQEVGDVKNDTADLWTKGNLRVKRRDPWHRANALSKAAADPALSGEDADQKTQTCLDLVRKPVAQPPAQAS |
| Ga0210329_159406 | Ga0210329_1594061 | F077370 | GKTNDRAIDILVNIFAVNSLGTPFYSFSTSAGSPQLSSNLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNFIGGGTTILQNTPSIFLQASTIPYSTGSVVLQRAIAQSDNSIELDLQTYDPKSYEIFLPPHIVSNNRANNQTFAFGSQTWISTRLNNVQNLPDLFLNLGSLATPTFDPSTTSGNSVLIGQIHGRMQLSFAGPIVG |
| Ga0210329_160110 | Ga0210329_1601101 | F092888 | VHEQGKLEQNQNLFTLRVRRTSGTIYFLIIGVSFTIFSLILIQAMVSGHPALRFTLSEPCSSLVLAAVGYVGFLASWKELTITVNNLDKRFTANTRNLITRKSKKREAIFSEIQAMYGKVDEITNEVKVTIARDNQETIQFQLDSNSYGPLEKYLKTLLPKIPIITRETRNYEADILPGHINAMY |
| Ga0210329_160777 | Ga0210329_1607771 | F020183 | MSLTINTKTFTADRYGQDAIGYVGPAHTLSLLDDVQLSRVAPKPTSVFSGVGRTSAKLTRTLTLTDALTPTGNAIVSISVSVPVGAASADVD |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |