 |
Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |
| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300026002 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0111376 | Gp0116060 | Ga0208907 |
| Sample Name | Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_25C_0N_202 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | Y |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 32880423 |
| Sequencing Scaffolds | 25 |
| Novel Protein Genes | 25 |
| Associated Families | 25 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 3 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 2 |
| All Organisms → cellular organisms → Bacteria | 3 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 2 |
| All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium | 1 |
| Not Available | 7 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria | 3 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi | 1 |
| All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Wetlands → Unclassified → Rice Paddy Soil → Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | terrestrial biome → paddy field → paddy field soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Saline → Water (saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: Twitchell Island, California | |||||||
| Coordinates | Lat. (o) | 38.1087 | Long. (o) | -121.653 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F002916 | Metagenome / Metatranscriptome | 521 | Y |
| F005761 | Metagenome / Metatranscriptome | 391 | Y |
| F011025 | Metagenome / Metatranscriptome | 296 | Y |
| F013220 | Metagenome / Metatranscriptome | 273 | Y |
| F016448 | Metagenome / Metatranscriptome | 247 | Y |
| F017546 | Metagenome / Metatranscriptome | 240 | Y |
| F018551 | Metagenome / Metatranscriptome | 234 | Y |
| F018563 | Metagenome | 234 | Y |
| F020202 | Metagenome / Metatranscriptome | 225 | Y |
| F021743 | Metagenome / Metatranscriptome | 217 | Y |
| F024424 | Metagenome / Metatranscriptome | 206 | Y |
| F028866 | Metagenome / Metatranscriptome | 190 | Y |
| F030263 | Metagenome / Metatranscriptome | 186 | Y |
| F033906 | Metagenome / Metatranscriptome | 176 | Y |
| F034837 | Metagenome | 173 | Y |
| F041384 | Metagenome / Metatranscriptome | 160 | Y |
| F042633 | Metagenome / Metatranscriptome | 158 | Y |
| F056483 | Metagenome / Metatranscriptome | 137 | Y |
| F068676 | Metagenome | 124 | Y |
| F071740 | Metagenome / Metatranscriptome | 122 | Y |
| F097075 | Metagenome / Metatranscriptome | 104 | Y |
| F099916 | Metagenome / Metatranscriptome | 103 | Y |
| F099957 | Metagenome / Metatranscriptome | 103 | Y |
| F100826 | Metagenome / Metatranscriptome | 102 | Y |
| F101108 | Metagenome / Metatranscriptome | 102 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0208907_100902 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 951 | Open in IMG/M |
| Ga0208907_100906 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 950 | Open in IMG/M |
| Ga0208907_102070 | All Organisms → cellular organisms → Bacteria | 775 | Open in IMG/M |
| Ga0208907_102346 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 749 | Open in IMG/M |
| Ga0208907_102360 | All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium | 748 | Open in IMG/M |
| Ga0208907_102852 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 711 | Open in IMG/M |
| Ga0208907_102899 | Not Available | 709 | Open in IMG/M |
| Ga0208907_103127 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 693 | Open in IMG/M |
| Ga0208907_103268 | All Organisms → cellular organisms → Bacteria | 685 | Open in IMG/M |
| Ga0208907_103941 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 652 | Open in IMG/M |
| Ga0208907_104044 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 648 | Open in IMG/M |
| Ga0208907_104573 | Not Available | 626 | Open in IMG/M |
| Ga0208907_104582 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 625 | Open in IMG/M |
| Ga0208907_104744 | Not Available | 620 | Open in IMG/M |
| Ga0208907_104952 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium | 613 | Open in IMG/M |
| Ga0208907_104997 | Not Available | 612 | Open in IMG/M |
| Ga0208907_105942 | Not Available | 584 | Open in IMG/M |
| Ga0208907_107274 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 551 | Open in IMG/M |
| Ga0208907_107486 | Not Available | 547 | Open in IMG/M |
| Ga0208907_107526 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi | 546 | Open in IMG/M |
| Ga0208907_108930 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 519 | Open in IMG/M |
| Ga0208907_109141 | All Organisms → cellular organisms → Bacteria | 515 | Open in IMG/M |
| Ga0208907_109842 | All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes | 504 | Open in IMG/M |
| Ga0208907_110014 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 502 | Open in IMG/M |
| Ga0208907_110113 | Not Available | 500 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0208907_100902 | Ga0208907_1009021 | F021743 | MNFSDPVVSAALIGASGTVLTALVQLRISWRREMKERERGQPITKKTRRGPVMAVFALMIAAAVGGFALSQYFQSLREDDRDSLRAELQAKLSEINATAVRLEQTRTTE |
| Ga0208907_100906 | Ga0208907_1009061 | F011025 | MNYSRILRVIGQTLEPLRPETYEVVCYGNCYLVRCRVKQDSQGKKEEEKKVTGLAAFLRLWREQEKRSIHDNPSEQTSMNVEFLYSLDELTRQDEEHKEPRSDANAMADPYSLSNTLRVVGEFLDRKPDAKLLFASNHGQEVVILYETKA |
| Ga0208907_102070 | Ga0208907_1020701 | F068676 | VLDSNLQIGQQLKLPLRSYVESKTLEEELGKKDARLGKLERKSSDLEKKIASAESQLAWHPVWLWGFWISFGIIAFIVSGAYWIFRQTHPRVFKQARDRSIRDLRESQIRARSSFPYDEESASSRTGQWQRSLKRVPAHR |
| Ga0208907_102346 | Ga0208907_1023462 | F033906 | RRRPETDFTTQGRVVHVGDELASGGRMVGVQFIGPRFHRVFRPEA |
| Ga0208907_102360 | Ga0208907_1023601 | F034837 | MIVILGLLLAAPATVVAAQGLPGGRPPDAIDHARGLATRPFDTPAPPGRPAERYVPPRRVYSPAQGREVLVPGHYERDVNGQRVEVPPLVTTTPDGRNPTVTPGGERGPLESRGGAP |
| Ga0208907_102852 | Ga0208907_1028522 | F097075 | LIRHARPAPALTVLLLPIPVVEPAFRALLIAVVGSPVLPAPGCGAARRAAIALSAIAMGTNPEHRLTSLAAANALPENHFSMNRHPPMQADFDNGNGSCQGRTSFDGGLLMKVAEPEPRCSNGGVLLPPSKPQYKFSLECFDADD |
| Ga0208907_102899 | Ga0208907_1028991 | F030263 | MRASYHSVSSARRFSSWLAVALGLVAYVGLIYGLTLLPLQLEVPLPHWGVALVPPVAYALLVLLFVRRPSIVRWLVGTAVLSVLHVLLALAREPLTALIDPALAGHPVAWMLPPPLPELVGVMLLLVPLRDVLRARPRPARERVPGAPRVASSARGR |
| Ga0208907_103127 | Ga0208907_1031272 | F013220 | CAPFAALDGCLAALHASHNLGVDFICLRAAATGVHTSADTSGCKVADGDKAEGLSGAIHQLKPDANAKQATKDAEQQVKDDLKGIGG |
| Ga0208907_103268 | Ga0208907_1032681 | F041384 | MYRILCDRSPARELGSGLTWLKKDGRIVEFSTTEEAGAKAKELNEGHTVAGVKYTAREYNIGADM |
| Ga0208907_103941 | Ga0208907_1039412 | F005761 | DVLPRWEQMPFERRQAIQRRLRVLREMPESARNQHLRDPNFTRGMSREDQALLDDLSHLHVGGAPELPAEH |
| Ga0208907_104044 | Ga0208907_1040441 | F002916 | MQYLPGWTVQCLNPECPARGHWLRVEGLPQEICSNCGAPLHNVPPPLAPRFRMRPRPLASYRPARRPR |
| Ga0208907_104573 | Ga0208907_1045732 | F017546 | GSAMNKPAGGELSLETVMKRGALVCVVALGGVAVGLALWALRQWRDEREYRAWRTSVSADPDRRDRNGYPVGARLGFSRAR |
| Ga0208907_104582 | Ga0208907_1045822 | F101108 | ATASVIVGPCKPEGVPGAREECTEKSAVRIAVCARVPESAKVKEVLLYTRSEDSQQTWADARVQPGQESGQARFADKFVERPDADSTKQICQGFANWSSDRSRLARILVKYTL |
| Ga0208907_104744 | Ga0208907_1047442 | F071740 | MNAFNNRAALALAALAGSLALAALSPGSVVIQSLGSWTLGAPASRDMEQFTNVLAERVSYQFGTNAAGSWFSLTKLVPWAKADPFALVRGGN |
| Ga0208907_104952 | Ga0208907_1049522 | F042633 | MPTIERSCRRIVLTALLGAAAGGLFAACSSLPQGPTYTEAELRAACERHGGWWR |
| Ga0208907_104997 | Ga0208907_1049972 | F018563 | MKILGFLLLLAGWAIVITAVALLVVEVPRAAFVLAGIGVEILGLVLVIRAHPAQRGERE |
| Ga0208907_105942 | Ga0208907_1059421 | F099916 | VADHRLQVTLLGLLGARDEELERGARHGGEGIARIERLEDPAWPSRLLAYGAMTEGALLMNAGQFVEARAAYLRAVKLALTTSERQALAATVNIVELDVASGDTTAALQLGRPMALSLRHLGRRETRFELLVMIFSALLLAGETDEARATGAELYDLALRLDTSKLFLALDAMAFLACVNRNLELAARVARCSD |
| Ga0208907_107274 | Ga0208907_1072742 | F016448 | TIGSDSVMDRHLWIEVIEYIVAAVGVVLMAWVLAQDFGSPLWGELTSIRMR |
| Ga0208907_107486 | Ga0208907_1074861 | F018551 | MSWNGTPVIDLDSHIVERADRFYGDYLDPAYQDAYRQLCEAVKRQAEAGNTYSLFGSRTSIVEPVEAGRP |
| Ga0208907_107526 | Ga0208907_1075261 | F099957 | MRAAAPTWIEPGASATLIWHGAAAPGPGGVRLYPVSGPAFERPPISPLFILAPVETGAFAGRLYRGQATLADLRGFLSHCRIARGALVDEMQSVATSEEAPVLPVLDDWREALGPPRLPYLADIDAFLPAAAPLYVTAEAHAAAQRENNRTPIQLRVDELIVHRAHRVERFELFAFGNFN |
| Ga0208907_108930 | Ga0208907_1089301 | F024424 | MTPISGPVERLVKLLQDETRIDEKIRDAQAAVTVVRKRVSETLAQHYISTRETRIQVPEDLMKEEQSYERLLQALQDMKTEIAKQIRPVEEQIIQANVDHLRQTFNQESRRLNKCLEQMDENILACREYLHDY |
| Ga0208907_109141 | Ga0208907_1091411 | F028866 | MNATLETGAQSFVLLRLGDRQFALPAERIGELVPAS |
| Ga0208907_109842 | Ga0208907_1098421 | F056483 | MRLLLRAGVIVGVAAVMGGCGTDAPTPVDFNDPAAISANLSSVDSTFDSDVFRSFTTASLMLDVATAPAIRPATTVLETLRPQLQRSGTQMFLPGLLRAQKLQALLPNLSVSAAQGRIIPDSMYGRVFEWDTTLHQYTFQDSTV |
| Ga0208907_110014 | Ga0208907_1100141 | F020202 | VNRESVDELPILTDVVELHATGSFARPDHIEEAAGPYASGLLSEDDVSALQAALVSRMMNLTDELLHAAAREIEAVMFERVIDRLRAALPELVAAALREHLAPGED |
| Ga0208907_110113 | Ga0208907_1101131 | F100826 | HYCIIYVLREGMLDLSEAWVHRPIIERFRGYTHQNAIRLNRIAVAYDDCLVFALQLVDPDVAIQEIVDDISDLLRELLPWPPTLEGEHPWREVRICTIGAPEAAEKEIRAYIEAVRRSKPDNGG |
| ⦗Top⦘ |
|
Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |