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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 | 3300022389 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225701 | Ga0210318 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.24 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 288743431 |
| Sequencing Scaffolds | 35 |
| Novel Protein Genes | 36 |
| Associated Families | 36 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 1 |
| Not Available | 15 |
| All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Porifera → Demospongiae → Heteroscleromorpha → Haplosclerida → Niphatidae → Amphimedon → Amphimedon queenslandica | 1 |
| All Organisms → cellular organisms → Bacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria | 3 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium | 1 |
| All Organisms → cellular organisms → Eukaryota | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Rubrobacteria → Gaiellales → Gaiellaceae → Gaiella → Gaiella occulta | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales → unclassified Chromatiales → Chromatiales bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group | 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) | 46.302 | Long. (o) | -123.036 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F001196 | Metagenome / Metatranscriptome | 749 | Y |
| F001314 | Metagenome / Metatranscriptome | 725 | Y |
| F002436 | Metagenome / Metatranscriptome | 559 | Y |
| F002557 | Metagenome / Metatranscriptome | 548 | Y |
| F007629 | Metagenome / Metatranscriptome | 347 | Y |
| F011154 | Metagenome / Metatranscriptome | 294 | Y |
| F012678 | Metagenome / Metatranscriptome | 278 | Y |
| F012874 | Metagenome / Metatranscriptome | 276 | Y |
| F017093 | Metagenome / Metatranscriptome | 242 | Y |
| F022407 | Metagenome / Metatranscriptome | 214 | Y |
| F023254 | Metagenome / Metatranscriptome | 210 | Y |
| F029446 | Metagenome / Metatranscriptome | 188 | Y |
| F031525 | Metagenome / Metatranscriptome | 182 | Y |
| F031603 | Metagenome / Metatranscriptome | 182 | Y |
| F036746 | Metagenome / Metatranscriptome | 169 | Y |
| F042355 | Metagenome / Metatranscriptome | 158 | Y |
| F042669 | Metagenome / Metatranscriptome | 157 | Y |
| F044534 | Metagenome / Metatranscriptome | 154 | Y |
| F046726 | Metagenome / Metatranscriptome | 151 | Y |
| F048170 | Metagenome / Metatranscriptome | 148 | N |
| F048198 | Metagenome / Metatranscriptome | 148 | Y |
| F050371 | Metagenome / Metatranscriptome | 145 | N |
| F051162 | Metagenome / Metatranscriptome | 144 | Y |
| F055103 | Metagenome / Metatranscriptome | 139 | Y |
| F057781 | Metagenome / Metatranscriptome | 136 | Y |
| F062310 | Metagenome / Metatranscriptome | 130 | Y |
| F070125 | Metagenome / Metatranscriptome | 123 | N |
| F070130 | Metagenome / Metatranscriptome | 123 | Y |
| F076808 | Metagenome / Metatranscriptome | 117 | Y |
| F080000 | Metagenome / Metatranscriptome | 115 | N |
| F087210 | Metagenome / Metatranscriptome | 110 | Y |
| F087396 | Metagenome / Metatranscriptome | 110 | Y |
| F088283 | Metagenome / Metatranscriptome | 109 | Y |
| F093890 | Metagenome / Metatranscriptome | 106 | Y |
| F099325 | Metagenome / Metatranscriptome | 103 | Y |
| F105482 | Metagenome / Metatranscriptome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210318_1005497 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae | 1507 | Open in IMG/M |
| Ga0210318_1009893 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 1268 | Open in IMG/M |
| Ga0210318_1017850 | Not Available | 1053 | Open in IMG/M |
| Ga0210318_1018951 | All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Porifera → Demospongiae → Heteroscleromorpha → Haplosclerida → Niphatidae → Amphimedon → Amphimedon queenslandica | 1033 | Open in IMG/M |
| Ga0210318_1020155 | All Organisms → cellular organisms → Bacteria | 1012 | Open in IMG/M |
| Ga0210318_1021355 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 993 | Open in IMG/M |
| Ga0210318_1023314 | Not Available | 965 | Open in IMG/M |
| Ga0210318_1024574 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium | 949 | Open in IMG/M |
| Ga0210318_1025412 | Not Available | 939 | Open in IMG/M |
| Ga0210318_1029053 | All Organisms → cellular organisms → Eukaryota | 899 | Open in IMG/M |
| Ga0210318_1041855 | Not Available | 797 | Open in IMG/M |
| Ga0210318_1047253 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 765 | Open in IMG/M |
| Ga0210318_1047572 | All Organisms → cellular organisms → Eukaryota | 764 | Open in IMG/M |
| Ga0210318_1055472 | Not Available | 725 | Open in IMG/M |
| Ga0210318_1055759 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Rubrobacteria → Gaiellales → Gaiellaceae → Gaiella → Gaiella occulta | 724 | Open in IMG/M |
| Ga0210318_1059338 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 709 | Open in IMG/M |
| Ga0210318_1063726 | Not Available | 692 | Open in IMG/M |
| Ga0210318_1065145 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 686 | Open in IMG/M |
| Ga0210318_1075885 | Not Available | 652 | Open in IMG/M |
| Ga0210318_1077255 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 648 | Open in IMG/M |
| Ga0210318_1082006 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 635 | Open in IMG/M |
| Ga0210318_1082937 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi | 632 | Open in IMG/M |
| Ga0210318_1088891 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont | 618 | Open in IMG/M |
| Ga0210318_1090039 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 615 | Open in IMG/M |
| Ga0210318_1090640 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales → unclassified Chromatiales → Chromatiales bacterium | 614 | Open in IMG/M |
| Ga0210318_1092474 | Not Available | 610 | Open in IMG/M |
| Ga0210318_1097427 | Not Available | 599 | Open in IMG/M |
| Ga0210318_1101002 | Not Available | 592 | Open in IMG/M |
| Ga0210318_1111579 | All Organisms → cellular organisms → Bacteria → Terrabacteria group | 572 | Open in IMG/M |
| Ga0210318_1132040 | Not Available | 540 | Open in IMG/M |
| Ga0210318_1132335 | All Organisms → cellular organisms → Bacteria | 540 | Open in IMG/M |
| Ga0210318_1147765 | Not Available | 520 | Open in IMG/M |
| Ga0210318_1149168 | Not Available | 519 | Open in IMG/M |
| Ga0210318_1158020 | Not Available | 509 | Open in IMG/M |
| Ga0210318_1159846 | Not Available | 507 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210318_1005497 | Ga0210318_10054973 | F087396 | VLNEPTLVNSGVLSYLASVASLIERRAIGREELLHWLRSSMRQRSIGQSARREYVLRYLHQHPP |
| Ga0210318_1009893 | Ga0210318_10098931 | F012678 | MLNQHSLEEIAEIHNLLGDIKKEYKEGIKPILIKNSPKLFKNPRTVPKLKKIQINR |
| Ga0210318_1017850 | Ga0210318_10178502 | F105482 | MDLIHPNSRDEVVRAIRDANSTNKRVLVIGGRRHIDK |
| Ga0210318_1018951 | Ga0210318_10189511 | F042669 | VGFKNTTHEKNIYTGTFCGEKVLLVRQVDDFALGCCQESTAKSVYATIRAKLTLHNEAEAHFEYLGLVDSFDGYDVLQTRDYIKLSAESYIRRLLKAHGWENPSPRESSNKPKPPLHESDVANLFNLAAGPVENTPEHKALEAEHGFGYRSVLGEILFAYVLCRPDIGYAVTTLAKFSTAPNALHYKSLKHLAIYLRQTQDWGIMYWRDEPIASLPEVPYFPMRFDDSLPVIPPPSHLRQLITHVDAAHANELRQRQSTTGYGCCLAGGVVAYRSRT |
| Ga0210318_1020155 | Ga0210318_10201553 | F031525 | GLGVGTFTRRPLPTSTVVVGAFVALLIAQTHEPFAAFAAFSLIALAGLVADSVRETVGLLLGR |
| Ga0210318_1021355 | Ga0210318_10213552 | F029446 | MLIIYILVTGTAVGMLPGLLKFDRMFSITNIVVGFAGALVGAFLGFGDAPLFLEYPFLNEITLMVTVSFLFVIIKVSVSRKRTDP |
| Ga0210318_1023314 | Ga0210318_10233142 | F046726 | LGKISEEEKIEIIKLGFQLQAEGTISLKKYYEGIETHSLFQSKGYSIKYETIRRTKLYQQLKPLNN |
| Ga0210318_1024574 | Ga0210318_10245743 | F070130 | MTSVHEVPDTPARQPDVFVGWWEAVFHIKDGEQTDVTGIIEHIDAAGNFTVFRDGERIGAGHHVEFTVDPDGFTNVQEVAGTHTQTGRGLAVYRFSGDVLEVCKASEHQGRPTSFVSPRGSGWIHVAIRRISDDDPRIPAQR |
| Ga0210318_1025412 | Ga0210318_10254122 | F007629 | MAPEAAGKEGSNIETKDVAELVSKFDAKYNVKVTAQGKGQKNDHVLIEGSDNGSISPVIQAGNQGSRPENTVRPKGKDTNPRTEQSKGIKK |
| Ga0210318_1029053 | Ga0210318_10290531 | F017093 | HTYRVGDEVVIKAGATNKHGYDPYLGPMPITQVHDNGTVKLIKVSDENGGAVTQTWNIRNMQPRMA |
| Ga0210318_1041855 | Ga0210318_10418551 | F080000 | SIQDTGRMWKEFHILEVQFDNNDGGTALAKSPTPAYKVGDEVQYEKNERGGVKIQRDQSNFSSNSNYSNNSPRMKQDNSEQIARSVVFKGAIDLVSSGKMQITDIPSFVDKYLSVVTGASAQGESYQAHFQESSMPF |
| Ga0210318_1047253 | Ga0210318_10472531 | F012874 | MPAKAGIQNYLKTLDSRLRGNDAKGLFETFYGTIRVKYYKFMHF |
| Ga0210318_1047572 | Ga0210318_10475721 | F062310 | MSGLRKKLNSLDTELGLMEMVLAGIKSALTRQPFSVSQDLRNLAAAQEAIGWTNLFKGRISKQWIERQRHHIGDKATTKNNALNWATTVIDYFFTQWFKVWDQRNLDRHGNDYQGRANKLKDVAFREMTHLYTFEEAVPEDIRWLFQTPLEECLHWPLFRQRAWITNWEHIIKKEYATQMETG |
| Ga0210318_1055472 | Ga0210318_10554722 | F076808 | MLLASPENFSENGARPVQILGRHGRLIGWARSFSDTMTVTDNTIVGGRPQGRLTRIAGRDVSGPDGHTVGKTFSRKELLECPWKPSPARSAESASNHIPAPSQDRPQSVDPAGPLMHKSSYPQNGARETGLGHWLPGFLRSNQSFTPIDSLQPAVSSLLPAMPQEN |
| Ga0210318_1055759 | Ga0210318_10557593 | F031603 | GLLSQHEPTLRDDERADLSQIEQRCSWRPGSRPTRPEPMVVAFLNLFDRAEQEEFTDRTLAAGTVDDLRRTFREQLSRETPLS |
| Ga0210318_1059338 | Ga0210318_10593382 | F036746 | VGGAPLPRWTYAVPPLAGALLWPVLTVALQWTQRPQHSSAEL |
| Ga0210318_1063726 | Ga0210318_10637261 | F002557 | VLMHSSNHYPLGNCDSPKPETSLGYLIRLGAVSYRASPPSSLFAFTDGARTPPEELVNPASAIEPFDPTLEGSRQPA |
| Ga0210318_1065145 | Ga0210318_10651451 | F099325 | MSETGPGIWDRLRRALERLRSQSQESAQDRRAALARARFWAEVREGEREAEAMSRP |
| Ga0210318_1075885 | Ga0210318_10758851 | F093890 | VRFRLRLFLLLLSCMLSVSLFSTELLANPTFLNRQAFPLPLGLTEIGRFHNNDLKTFEVWTQWNNASNEKLVVKVTFTFFDRDSADSQLGEDGEDDSLMAVTETVTIPEQVSNWGKYFQLTAIGHKLNQGYDHPAAGAGWELYLD |
| Ga0210318_1077255 | Ga0210318_10772551 | F044534 | VTGEWIATAGVAFPSERRKSPRGIYHQFLWPESCPVSSHTNQELCGEARLETVPNRVRLTGSFDPCADAVTPEGFGCYCADQNAVTVPGGPTPPKGLVRRTNEARKGTGTAGRERIWQSP |
| Ga0210318_1082006 | Ga0210318_10820063 | F050371 | MTFKIKGAIFKNTAEKLQQRLGDRYDASKKYPEVDGVFGIKEEDRMAFASYIMNAAVNDKGEVPLRVNGYNNTSQSSGVKYLGLTIEPDFKTLKAIEEARLAALVQPEVVPASQDDLF |
| Ga0210318_1082937 | Ga0210318_10829372 | F002436 | MRSCIVGLFSGRDRRPVAVVVTTDGRRAHLPIETGPFDASLLSLLRSLFVGLESLLGLITGSRRENGG |
| Ga0210318_1088891 | Ga0210318_10888912 | F057781 | MKKPDLQMLAQWLDPTIVTALENRRRMKKEWHRRRKMATLQTVWLMLAVSLDTHRSSL |
| Ga0210318_1090039 | Ga0210318_10900392 | F051162 | MPLVKLFARNTLSKAVPLKALQTELCKIWGTKPETTKLMLFRCEDWTDCDTFTPEDVYVDIRAYGKSERTRDFVLEGMESVQRAFAGHNLVANVRLETYEGDRYFHVPPPAPS |
| Ga0210318_1090640 | Ga0210318_10906401 | F088283 | GSDVTGTYSPSCVAFEGNTIELSENRFTWDKFTDEVTVDDTGNEVDPFPGFPVRGTYAIEDDVASLTTDVGELAAELYIVRRPGQVYLLTEAEFEAWQKDSTVPDCALLLGSGE |
| Ga0210318_1092474 | Ga0210318_10924741 | F048198 | SDQNRESSGPWLPGRLCCPARSSLTMATSAPLSAPERLMDYSVRLRVQPANRRGSPIYSASPFTPCRRPYSGGPGECAQQCLPRRFCLRRICTGSATTGPTIPDRVGRVTKLQRSLYATACECRLPCSGQDVYDRACVGRVTPIPHVGYHWMVHCHLPSPVFHRLDWQPYGLRADRRGPAQMGGGQVVVSPPANQGTLRAISA |
| Ga0210318_1097427 | Ga0210318_10974271 | F055103 | MIAEQDTLALGLRGLRPVLDGHLGHARLANRMIYWPRRSSPTWLAQNNPQIRVLMKYPG |
| Ga0210318_1101002 | Ga0210318_11010023 | F048170 | MYNNYKGNSALLRQQARQQRRELSIKIAGWCVIGCGAIVGAGVFYAFAVVVLAMG |
| Ga0210318_1111579 | Ga0210318_11115792 | F001314 | MWILFQVPCPTTDGQSAKDLYDKRVTGITEAMQASAEQHGCQFHRAWHASDGSAFYAIAKWESREGASAFFEEWQIEDEPGEIAVILEGDVGLVPQP |
| Ga0210318_1122617 | Ga0210318_11226171 | F087210 | MRFLMGVLALAGAEAALAHTPDTGFLRNFGHQLTSLHHSPAAMLLGVLVLALLLVA |
| Ga0210318_1132040 | Ga0210318_11320401 | F001196 | GIFGLPWNAGKAAIEAKYPGGAWDQDDQGRARYCAASQQPLLKLPPQHQTRELCFLIGSDGTLASAMARMDASLPALLAIVNRSRTIFGDFDSVRRDEAAIQSRSTAMLWTREAPYVVQVSSANDNDGRPMEVTFTVADEANIHTVGSERVSHRPPGT |
| Ga0210318_1132335 | Ga0210318_11323351 | F070125 | VTTAEERRQWIEALHAYRDDSERLFALVASLANLLDEEMVVETMESVLGIVAVHDNDCVIFDDLAIRFGSDGRVKSVFRTIDGSGNGT |
| Ga0210318_1147765 | Ga0210318_11477651 | F023254 | CNSDLYGFELREDDCMKRVYISDFKRDGKGVKSRRSCNTICSTERATRRKYRGAYITAIDDEEIVTLNQAKEKLKELRNKNVDTFTMILAREPRPSKSMTRRAYDELELPEFDLDENLGEDFFTSDGNLEGDSSMTASHETNTFGTDYVPTIGTKISKDFGTKGFFAGTVTSG |
| Ga0210318_1149168 | Ga0210318_11491681 | F011154 | RLLLCISTGGWLWRSPEGGQPNERRRKAGQTERPDRGGHVVWAGPVKTFRKVGDVKNDTADLWTKGNLRVKRRDPWHRANALSKAAADPALSGEDADQKTQTCLDLVRKPVAQPPAQAS |
| Ga0210318_1158020 | Ga0210318_11580201 | F042355 | MTSDLKKINKKPNSRRKQNIQEPKLVERLIKISRVSKVTK |
| Ga0210318_1159846 | Ga0210318_11598461 | F022407 | MTDSVDRTASSGRGYTYGGPAFVGGILVGIGLGILLGDFAAWFLIGLGSGFILLAFIAALGK |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |