| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300021293 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225742 | Ga0210358 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.589 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 39942751 |
| Sequencing Scaffolds | 27 |
| Novel Protein Genes | 31 |
| Associated Families | 30 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 17 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Chaetocerotophycidae → Leptocylindrales → Leptocylindraceae → Leptocylindrus → Leptocylindrus aporus | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Bacillariales → Bacillariaceae → Pseudo-nitzschia → Pseudo-nitzschia australis | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira pseudonana | 1 |
| All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 4 |
| 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) | 46.286 | Long. (o) | -124.052 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000073 | Metagenome / Metatranscriptome | 2639 | Y |
| F002996 | Metagenome / Metatranscriptome | 514 | Y |
| F005443 | Metagenome / Metatranscriptome | 400 | Y |
| F012678 | Metagenome / Metatranscriptome | 278 | Y |
| F017072 | Metagenome / Metatranscriptome | 243 | Y |
| F017093 | Metagenome / Metatranscriptome | 242 | Y |
| F017955 | Metagenome / Metatranscriptome | 237 | Y |
| F021217 | Metagenome / Metatranscriptome | 219 | Y |
| F022124 | Metagenome / Metatranscriptome | 215 | Y |
| F025295 | Metagenome / Metatranscriptome | 202 | Y |
| F027700 | Metagenome / Metatranscriptome | 193 | Y |
| F031322 | Metagenome / Metatranscriptome | 182 | Y |
| F033058 | Metagenome / Metatranscriptome | 178 | Y |
| F035541 | Metagenome / Metatranscriptome | 172 | Y |
| F038082 | Metagenome / Metatranscriptome | 166 | Y |
| F042355 | Metagenome / Metatranscriptome | 158 | Y |
| F053809 | Metagenome / Metatranscriptome | 140 | N |
| F055433 | Metagenome / Metatranscriptome | 138 | Y |
| F057770 | Metagenome / Metatranscriptome | 136 | Y |
| F062310 | Metagenome / Metatranscriptome | 130 | Y |
| F063220 | Metagenome / Metatranscriptome | 129 | Y |
| F064269 | Metagenome / Metatranscriptome | 128 | Y |
| F067276 | Metagenome / Metatranscriptome | 125 | Y |
| F068326 | Metagenome / Metatranscriptome | 124 | Y |
| F074319 | Metagenome / Metatranscriptome | 119 | Y |
| F076772 | Metagenome / Metatranscriptome | 117 | Y |
| F077370 | Metatranscriptome | 117 | Y |
| F079410 | Metagenome / Metatranscriptome | 115 | Y |
| F082867 | Metagenome / Metatranscriptome | 113 | Y |
| F084398 | Metagenome / Metatranscriptome | 112 | N |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210358_100486 | Not Available | 562 | Open in IMG/M |
| Ga0210358_108955 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Chaetocerotophycidae → Leptocylindrales → Leptocylindraceae → Leptocylindrus → Leptocylindrus aporus | 654 | Open in IMG/M |
| Ga0210358_109936 | Not Available | 555 | Open in IMG/M |
| Ga0210358_110912 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 552 | Open in IMG/M |
| Ga0210358_115715 | Not Available | 716 | Open in IMG/M |
| Ga0210358_117037 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Bacillariales → Bacillariaceae → Pseudo-nitzschia → Pseudo-nitzschia australis | 663 | Open in IMG/M |
| Ga0210358_117833 | Not Available | 811 | Open in IMG/M |
| Ga0210358_123793 | Not Available | 504 | Open in IMG/M |
| Ga0210358_123820 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 636 | Open in IMG/M |
| Ga0210358_128319 | Not Available | 565 | Open in IMG/M |
| Ga0210358_129167 | Not Available | 719 | Open in IMG/M |
| Ga0210358_134855 | Not Available | 924 | Open in IMG/M |
| Ga0210358_142029 | Not Available | 515 | Open in IMG/M |
| Ga0210358_146741 | Not Available | 639 | Open in IMG/M |
| Ga0210358_147865 | Not Available | 1064 | Open in IMG/M |
| Ga0210358_148345 | Not Available | 707 | Open in IMG/M |
| Ga0210358_148879 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira pseudonana | 580 | Open in IMG/M |
| Ga0210358_151576 | All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes | 1517 | Open in IMG/M |
| Ga0210358_155674 | Not Available | 690 | Open in IMG/M |
| Ga0210358_169023 | Not Available | 695 | Open in IMG/M |
| Ga0210358_172677 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 776 | Open in IMG/M |
| Ga0210358_173868 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 573 | Open in IMG/M |
| Ga0210358_178454 | Not Available | 645 | Open in IMG/M |
| Ga0210358_178538 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 598 | Open in IMG/M |
| Ga0210358_184033 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 676 | Open in IMG/M |
| Ga0210358_185927 | Not Available | 682 | Open in IMG/M |
| Ga0210358_191793 | Not Available | 802 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210358_100486 | Ga0210358_1004861 | F027700 | AKAERLLWHQRLAHCGDEQLCRAHMFSDGIPEITRGKDSALDSCPVCLAANMRSRNRGDGETRTATEPGQGLSLDFSFAGQHSKNATDPKKMRINDYMGVHGETCYLLLYDHATERLDGVCRQSKAPPLAWLKRWLKKDVKDEVKDRYVYMDGGPRRRAIQIQSN |
| Ga0210358_107060 | Ga0210358_1070601 | F064269 | MFMIPVLLAVCMVFACVPEVLYWLFGINTKRSTSRKLKSLIPTTLVNVKRYLGSTLHYFLSSTYNVVNTLLLPTKEQRLQRPSKRKALDRMFFMFLLMNHGRVSAKSARRTSYRGRPGLSEIPQAIPQDLSAEMLAPWDNIPQGWSQRLLNGNKLKQFDPDNVIPVSEKIDPNIGTINPASWLIQGAPSL |
| Ga0210358_108955 | Ga0210358_1089551 | F017955 | MLNASFQADWQFIKEQKQRLIVQNNKRENAKRKPHTYNVGDVVVVKAGVKRKHGSNPYLDPMRITQVNDNGTVKLVKVAENNGGAVSQTWNIRNIEPRMA |
| Ga0210358_109936 | Ga0210358_1099361 | F068326 | MNEARNLGVSNVTLRNWVGLNNSSSIIDYTTLQQNISSDEIDLTESERCRTFSNDIPGYHKTLLESSGVKDNVKDLNYSSAHCLHQNIQTLAHYLIDKIDTLQKTQLDIHHIEIITDRVFHNIEKLKNENRVNNSYVQSLENRTRNLEAKIDVLLMQNEIITQKCTKFELL |
| Ga0210358_110912 | Ga0210358_1109122 | F084398 | MARLELTLNFPKSFHIKTFNVKSEKKLSPLAKLILQNVQFKHFYYVRDDISYLLKSNPIERDFLLQALYSIVISLQNNLSVNFFDM |
| Ga0210358_115715 | Ga0210358_1157151 | F082867 | MPKKRSSRRVHHINDINHNDTNITVQYRVVKPLTFTSNTLVLSVNPSLTDLSNTLATIYRQYRITELSFTFQCSDVAGAYALAMQYVPQIGGNPSTLPTALNEFEGPAVGYCETGRGREYTYKVPGHVLNAMGLNYYSTRISVSPPQDDDLITQGLMVFLTSTPATPIIAYMHVKYEFQTLEDPSFLAKLVNGDEKKENDTLVVPRMTRSPGGELWN |
| Ga0210358_117037 | Ga0210358_1170371 | F076772 | YASHKSTLKNVKGAYLVGINGKKVFSKEDAISMLRQLHDERAENLQLELAIERKLSSAEAWRAVAEHNIMDPSAVPDVDHHHQLTLADIRSISAVRYPHLDFSEASISTEEMEMVVQAIQSQAITPAEQAIGRFTRRKLRSLSTWDQWRAGEHKQLDHFHDLKMYGEPVRKPPGAIVLRPHWQYSIKRDGYRRSRNCCDGSPRSAPLLHGIASTYSSCVE |
| Ga0210358_117833 | Ga0210358_1178331 | F025295 | IMVTGPGEAAELLRRREVLIPKTLKFVTRKSNLQKLI |
| Ga0210358_123793 | Ga0210358_1237931 | F017072 | MRMRDLAVGSDEKPLRTESSSPETFRFRMNRSHPEGEQLLLCISTVRAALAESNQIEAAQRKTPKGGQKERGHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKCNLREKRRDPWFRANASSKAMADPGLVVKTRTRD |
| Ga0210358_123820 | Ga0210358_1238203 | F012678 | MRSQHSLEEIAELYGLLENIKKEYEDGIHSVLRKSNPELFSNPHTIPKLKKLVLIED |
| Ga0210358_128319 | Ga0210358_1283191 | F057770 | DNAEGYVPIKCYYTPGIPNFILSPNSFKALLGKHYNGYKLECDDDKKSFRFSLNHKMRKSGSVLLRGTTRGGLCYTRSAVPPMPTTEGTAEMSLDMADRAAISMVEDHPKNLYRHEMKLHALSAKAERLLWHQRLAHCGDEQLCRAHMFSDGVPEITRGKDSALDNCPVCLAANMRSRNRGDGETRT |
| Ga0210358_128627 | Ga0210358_1286271 | F000073 | DGLSEEDKKNFALTGGKVSTPSENLKLTQTFQAWMDVHSNFRDICEDGKGKLQWERDIPQEALDNLQSLANSDFNANLGKIIHDIYLTGHNLFKDMPQGDHKKRAKYRFASKTLMRILPDGIKEECEALIAKETMTLDLYEILGQCTWGKTPKQAAA |
| Ga0210358_129167 | Ga0210358_1291671 | F035541 | GMYGCPSKICSIYGFKVIFIRELPTIRRSHVKRLVLIVSLAILALLVAAPVYAGATTDLNNIPITDTLDEGTFEWDVTGRYNEDIGRGRKVDTRLFGALFNNFEFGMSWGVSRRPSAGPVEFSVKYKILDEYDGNFPVSLAIGAMGITGNYQRTGFDPTYYGVIGIHDVHLGGWWDWYVGVANNPTGFDDEDSSLFGGFKYWFDEDLQFNADYWGTNENENYILSGGFNYDWVNHIGFQ |
| Ga0210358_134855 | Ga0210358_1348552 | F055433 | MTVVAMSSLFSFQSPSTACITSVGEQAFLVGSLVGRMAGTLLIGGVSESLALITD |
| Ga0210358_138647 | Ga0210358_1386471 | F038082 | MNEPKAKRDLIQSGFDIEFSTRMGAHIKRENFLQSNLPKAFAYIMHDYCTDGLKTRLVALPDFTTSIQDDPLALLKAIKTCVHENAVTQHPPVTIHQHWSRLLRLTQNSDEDPPTYAKRFEQQLDTVKGYVGNTFTDGFAEHMPEHKANAHKHDTSKIAALLAAHATDDSARQALAADLHELFSHHKPKETQAQLDIEAQAQLEFDACLFLQSASKAKCGSLLIL |
| Ga0210358_142029 | Ga0210358_1420291 | F021217 | NKNPCRIRLICADGKTPIVPEGYGTVRIPADNAEGYVPIKCYYTPDIPNFILSPNSFKALLGKHYNGYKLECDDDKKTFRFSLNHKMRKSGSVLLRGTTRGGLCYTRSAVPPMPTTEGTAEMSLDMADKAAISMVEDHPKNSYPHEMKLHALSAKAERLLWHQRLAHCGDE |
| Ga0210358_146741 | Ga0210358_1467411 | F033058 | MNRRRVLIWFAGRWRNHQSKRAEKPHSKSSSGDALDGPATRPETPLAVENSVGKPAAPEAPNAGTGKREWRTPIP |
| Ga0210358_147865 | Ga0210358_1478651 | F062310 | LMEMVLAGIKSALTRQPFSVSQDLRNLAAAQEAIGWTNLFKGRISKQWIERQRHHIGDKATTKNNALNWATTVIDYFFTQWFKVWDQRNLDRHGNDYQGRANKLKDVAFREMTHLYTFEEAVPEDIRWLFQTPLEECLHWPLFRQRAWITNWEHIIKKEYATQMETG |
| Ga0210358_148345 | Ga0210358_1483451 | F067276 | DASSLFDLLHDDPEFDSIRLNSVVVLRVPEEVITIDDLEEDEWTDEESIEDKAYKNVQELQISEVATGSILTANRYEAHLDGGSQASTTNDKAVLWGFKWYTDKNPCRVRLICADGKTPIVPEGYGTVRIPADNAEGYVPIKCYYTPDIPNFILSPNSFKALLGKHYNGYKLECDDDKKSFRFSLNHKMRKSGSVLLRGKTRGGLCYTRPAVPPMPTTEGTAEMSLDMADKAAIS |
| Ga0210358_148879 | Ga0210358_1488791 | F002996 | ANEIAIENSKTGKVTAVVAILKVFGDNTRNWRNANPGKLLNKPNKRLNSKKKHLNRALKRPNELNESVSDISERLIVKQKTIRVLLDTGSSGDLLFVRKGSQKYIPTLKRAVPQSWGTSNGTFKTKKVGEITLSFAEYSLSKSVHLTPDIVEDDAGATAPLYDLIIGKQTLHNIGAVLDFKEKTITIDSILL |
| Ga0210358_151576 | Ga0210358_1515761 | F005443 | MLSYTLNTNEVKNSAGTEIEFQSWKQSDRYRIYAQVNEGPSAPNHLTISHQESGTGLKRRRRSVVRVDKTTQSGIDPTLPITTSAYLVLDHPVGASSDNAEAANVIAQVLSFCASLGASTTILYDGTGNGATALLQGSL |
| Ga0210358_155674 | Ga0210358_1556741 | F053809 | DQLPLLHLHVNYLSQLQLINRCCLHDFDVLSGKRHTRGAGAIRVAKIGAAYAEDRIRAHLGALIVDNNDLLAEWFRLKTYTDGHTPLICSNRPALQMNTMPFDTHGVCTIQGDGIPHPADMRSTIQIIERILLPHAQSAARCCTITDYRNHNAAYMCVREFVRETKRSLDDVRGRLYYLQYDEIDLWRSVQNFEYNIEDSSTIIHELFANTQPTQPFSQVVTPTTNGVAH |
| Ga0210358_169023 | Ga0210358_1690231 | F077370 | QPRIVNNKQSRNRRNNRKRILKNNSHQLAVPRPMSILGKTNDRAIDILVNIFAVNSLGTPFYSFAVSAGSPQVSANLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNYIGGGTTILQNTPSIFLQASTIPYNVGTVSLQRAIAQSDNSIEIDLQTYDPKSYDILLPPHIVSNNRANNQTFAFGSQTWISTRLNNVQNFPDLFLNLGSLATPTFDPSTTSGNSVLIG |
| Ga0210358_170639 | Ga0210358_1706391 | F063220 | VNTSTTNYAPFATVQEKIATHIQKSYDSGHDLAKSIRTGTLVDLSKEQPIRKLASMSEPKAKRDLIQSGFDIEFSTRMGAHIKRENFLQSNLPKAFAYIMNDYCTDGLKTRLSALPDYLTSIQDDPLALLKAIKTCVHENAVTQYPPVTIQQHWSRLLQLKQSSDEDPPTYAKRFEQQLETVKGYVG |
| Ga0210358_172677 | Ga0210358_1726771 | F031322 | NTDKNILWYDTETHAVKIAKHVRFDEGMNDLPPDLVPPNVVHLQRTQNGEPLPAETKETSVDQFTFHLNPFSYTMVKGVPVTDNDPSFGLTLASDKLSHRAYVTDVKENSTADKMYASHKSTLRNVKGAYLVGINGKKVLSKEDAISMLRQLHDERAENLQLELAIERKLSSAKAWRAVAEHNIMDPSAVQDVDHHHQLTLADIRSISAV |
| Ga0210358_173868 | Ga0210358_1738681 | F079410 | RRDATESAHQKLHGEKDNLGLLRTFGCRLWVKILAWQNRAKYIQDTKKGIFLGYRTNTLKNVVWYDPLTDRVKYGYHVRFDEGFNDLPLSKLPPNVVLMDRREERIPAETLTITIPPFTTSEHPFFDKDDVTVKVVCDSDLYGFELREDDCMKRVYISDFKKDGKGTKGRRSCNTICSTEQATRRKYRGAH |
| Ga0210358_178454 | Ga0210358_1784541 | F042355 | MSTDLKQINKAKKNLRRTDTVNEPKFVERLIKISRVSKVTKG |
| Ga0210358_178538 | Ga0210358_1785381 | F074319 | LANIRSISAVWYPHLDFSEASVSTEEMEMVVQAIQSQAITPPEQAIGRFTRRKLQSLSTWDQWRAGEHKQLDHFHDLKMYGEPVRKPPGAFVLRPHWQYSIKRDGTRRSRNCCDGSPRSAPLLHGIASTYSSCVEQPVQRLFFALAARENYRVYGGDAQDAYAHSPPPETPTFVSIDNAYADWYEHRFKKKLDRSLVLP |
| Ga0210358_184033 | Ga0210358_1840331 | F022124 | EPVDVQCDDDNPDAIRAQIDTGAHVSCTDQLHMLHGHRKFTRSRPSPVKLMPATVDSDAVRKGIGYLHVPAKNAQGHLAVPTFHTPCLRTTVIDERDLVKAAKVNVKDIRSDSITKHKDAGTFTYHARHRMKSSKDVIVHGVLIDDKCYTGALISPDLSPSDPKATPSTSSILAMESDPDFAEQCCKATILAVHGYNEAVETQLRDEMTKLPMQFHTLPFHEYIQ |
| Ga0210358_185927 | Ga0210358_1859271 | F017093 | MQPSRKHGSNPYLGPMRITQVYDNGTVKLVKVADNNGGAVSQTWNIRNIEPRMA |
| Ga0210358_191793 | Ga0210358_1917932 | F025295 | GNWPGKATELLRRREVLDPEKLKFITRKSDSQKPI |
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