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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 | 3300021297 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225753 | Ga0210369 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.669 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 44968496 |
| Sequencing Scaffolds | 22 |
| Novel Protein Genes | 24 |
| Associated Families | 18 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Eukaryota → Sar | 2 |
| Not Available | 11 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 5 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 1 |
| All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Cnidaria → Anthozoa → Hexacorallia → Scleractinia | 1 |
| All Organisms → cellular organisms → Bacteria | 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) | 46.313 | Long. (o) | -123.997 | 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 |
| F001105 | Metagenome / Metatranscriptome | 776 | Y |
| F001506 | Metagenome / Metatranscriptome | 681 | Y |
| F006508 | Metagenome / Metatranscriptome | 371 | Y |
| F012678 | Metagenome / Metatranscriptome | 278 | Y |
| F012874 | Metagenome / Metatranscriptome | 276 | Y |
| F021307 | Metagenome / Metatranscriptome | 219 | Y |
| F034767 | Metagenome / Metatranscriptome | 174 | Y |
| F037756 | Metagenome / Metatranscriptome | 167 | Y |
| F045132 | Metagenome / Metatranscriptome | 153 | Y |
| F046726 | Metagenome / Metatranscriptome | 151 | Y |
| F053305 | Metagenome / Metatranscriptome | 141 | Y |
| F059979 | Metagenome / Metatranscriptome | 133 | Y |
| F061147 | Metagenome / Metatranscriptome | 132 | Y |
| F065810 | Metagenome / Metatranscriptome | 127 | Y |
| F075465 | Metagenome / Metatranscriptome | 119 | Y |
| F077370 | Metatranscriptome | 117 | Y |
| F087250 | Metagenome / Metatranscriptome | 110 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210369_1007560 | All Organisms → cellular organisms → Eukaryota → Sar | 601 | Open in IMG/M |
| Ga0210369_1013717 | Not Available | 548 | Open in IMG/M |
| Ga0210369_1022064 | Not Available | 889 | Open in IMG/M |
| Ga0210369_1024223 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 915 | Open in IMG/M |
| Ga0210369_1027106 | Not Available | 1009 | Open in IMG/M |
| Ga0210369_1034014 | Not Available | 511 | Open in IMG/M |
| Ga0210369_1037246 | Not Available | 594 | Open in IMG/M |
| Ga0210369_1040730 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 967 | Open in IMG/M |
| Ga0210369_1041440 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 679 | Open in IMG/M |
| Ga0210369_1047042 | Not Available | 539 | Open in IMG/M |
| Ga0210369_1048526 | All Organisms → cellular organisms → Eukaryota → Sar | 578 | Open in IMG/M |
| Ga0210369_1048853 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 939 | Open in IMG/M |
| Ga0210369_1049074 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 586 | Open in IMG/M |
| Ga0210369_1055278 | Not Available | 610 | Open in IMG/M |
| Ga0210369_1056761 | Not Available | 800 | Open in IMG/M |
| Ga0210369_1056965 | Not Available | 556 | Open in IMG/M |
| Ga0210369_1062238 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 522 | Open in IMG/M |
| Ga0210369_1063773 | Not Available | 734 | Open in IMG/M |
| Ga0210369_1069270 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 643 | Open in IMG/M |
| Ga0210369_1074815 | All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Cnidaria → Anthozoa → Hexacorallia → Scleractinia | 1180 | Open in IMG/M |
| Ga0210369_1076258 | Not Available | 800 | Open in IMG/M |
| Ga0210369_1089757 | All Organisms → cellular organisms → Bacteria | 534 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210369_1007560 | Ga0210369_10075601 | F012678 | MLNQHSLEEIAEIHNLLGDIKKEYEKGIKPILIKNSPKLFKNPHTVPKLKKIQINRGLRLAAQNTNVLKKNIEEFEKIT |
| Ga0210369_1013717 | Ga0210369_10137172 | F053305 | MLKKSVSMALMALFVFSFIAVATVSADETQKITGTVMSVNVETGEMIVKDDAGEMKSLMTDPKAGVDLKMLKEGDPVSVESDSDGVIKSIAVSK |
| Ga0210369_1022064 | Ga0210369_10220642 | F046726 | LGKIPEQEKIEIIKTGFQLQNQGKISLKKYYESTDSDSLFQYNNGYNIKYQTIRKTTLYQNLKE |
| Ga0210369_1024223 | Ga0210369_10242231 | F001506 | MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQIKYQKNLSTTAKCILNSFQNKYIYYAIDDILYLLKSKPSERENLLAVLYSPILSLQNNFSVNFFDIWIGEVYIDEISKNNKFLKNDLTTLKQFNYITIKFFYKTRVPVKKQESFW |
| Ga0210369_1027106 | Ga0210369_10271061 | F046726 | KIEIIKTGFQRQSEGTISLRKYYESTDPNSLFQLKGYSIKYESIRKNKLYQQLKA |
| Ga0210369_1034014 | Ga0210369_10340141 | F077370 | RNRRNNRKRILKNNSHQLAVPRPMSILGKTNDRAIDILVNIFAVNSLGTPFYSFAVSAGSPQVSANLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNYIGGGTTILQNTPSIFLQASTIPYNVGTVSRQRAIAQSDNSIEIDLQTYDPKSYDILLPPHIVSNNRA |
| Ga0210369_1037246 | Ga0210369_10372461 | F012874 | MPAKAGIQNSLKTLDCRIRGNDAKGRFKTFYENIKIPLAIGFIQR |
| Ga0210369_1040730 | Ga0210369_10407301 | F001506 | IKTRSEGKPLQYPKSIEITSKTFQMKYQKSLSTTAKCILNSFQNKYIYYAIDDILYSLKSKPIERDNLLAVLYSPILSLQNNFSVNFFDIWIREVYIDEISKNNKFLKNDSTTLKQFNYITIKFFYKTRVPVKKQASLW |
| Ga0210369_1041440 | Ga0210369_10414401 | F034767 | KGVNATIWGGVQEADKVGKIVKTGISGADVVIGTSHALEDFGCNDYVCGSLDVIGSVSSAVGLVLGNIPSTKPLTLITGSVTIGCRSVRYYCKNYGTFWGCTVAAGQGIKESVKFIINK |
| Ga0210369_1047042 | Ga0210369_10470422 | F006508 | VALANAPSKAVAVQCQTVKTRKRNRRRVLTWFASRWRNHQPKRAEK |
| Ga0210369_1048526 | Ga0210369_10485262 | F021307 | MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQMKYQTSLSPTAKCLLNNFQNKYIYYAIDDILYLL |
| Ga0210369_1048853 | Ga0210369_10488531 | F001506 | GKPLQYPKANEMTSQTFQIKYEKKLSSTAKAIFNSFHNKYIYYAIDDILYSLKGNLIERDSLLAILYSTILSLQNNFSVNFFDIWIREVYIQEISKMNPFLNQDSQTLTQFSYITIKLFYKTRVPAKKQESLW |
| Ga0210369_1049074 | Ga0210369_10490742 | F065810 | MKYQTSLSPTAKCLLNNFQNKYIYYAIDDILYLLKAKPVERDNLLAVLYSPILSLQNNFSVNFFDIWIRDVYIDEISKTNRFLKNDSTTFKEFNYITIKFFYKTRVPVKKQESLW |
| Ga0210369_1055278 | Ga0210369_10552781 | F053305 | MLKKSLSLVLVALFALSFIAVATLSADETQKITGTVMSVNAETGEVILKDDAGEMKTLMADPKAEGAVDIKMLKEGDSVDVESDSNGVIKSLKAGE |
| Ga0210369_1056761 | Ga0210369_10567611 | F053305 | MLKKSLSIVLTALFVLSFIAVGTVSAAEVKGEVVSVNAETGEMVIKDDAGEMKSLMADPKAVDLKMLKEGDMVSVESDDAGAVQSIKASE |
| Ga0210369_1056965 | Ga0210369_10569651 | F046726 | KIEIIKTGFQLQAEGKISLKKYYQSTDPDSLFQWKGYSIKYETIRRTKLYQSLKD |
| Ga0210369_1062238 | Ga0210369_10622381 | F059979 | MKSFLLVLAQLSLVTLVYAFAYRAGYRSAQSKAISVVKKFADPVTCLLDSLKDTIDELVKDEDENG |
| Ga0210369_1063773 | Ga0210369_10637731 | F000203 | MGVRHSLFPVPTLGASGAAGFPTLFSTASGVSGLVAGPSSASPLLDFE |
| Ga0210369_1063773 | Ga0210369_10637732 | F045132 | VLMHSSNHYPLGNCDSPGSETNPDYLTQFGTVSNRSSLPSSFFAFTDGARTPPEELVNSASFAKCVSTSLKRGLVNQPDL |
| Ga0210369_1069270 | Ga0210369_10692701 | F075465 | LRQCTRLLQDRMKQDADWLTVSTRYNPLSLYRLIEKTVLAQTEDQYPFATVYDQEHAFYSFRQELMTNAMWYEKFNTRVDVGEAIGITRQHTVLLEFVAQEVHTKAFTALTAAEQQVIRLDAEERYQSYVFLRQSGAQHSHLKQSLQNDFTTGDNHYPKNRQQTLHLLDKFSKTVAPKVAPIQSEGTAFAQGSGDQKQPFDKKFWKDKECFKCH |
| Ga0210369_1072259 | Ga0210369_10722592 | F087250 | SKTGLQGAAAEAGFTSSSGGVRAPSVNAKKELGDEER |
| Ga0210369_1074815 | Ga0210369_10748151 | F001105 | MSTTQQSKITKTITDAAVITGLVAGIGWVGRKVLREDFTKDPSANAMNYAKMTAAVAGAVALKGYLEDQKILPM |
| Ga0210369_1076258 | Ga0210369_10762581 | F037756 | QALFPVPTFGAHLAAAAGFPTPFSAANGVSGLVAGPSNLLQG |
| Ga0210369_1089757 | Ga0210369_10897572 | F061147 | MNSRTRTTTTPSHSLAALLEQIGLHALAGEVDDFVARATKQRW |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |