 |
Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |
| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300025798 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0111376 | Gp0101359 | Ga0210063 |
| Sample Name | Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - Muzzi_PWA_D1 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 230742206 |
| Sequencing Scaffolds | 28 |
| Novel Protein Genes | 31 |
| Associated Families | 29 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia | 3 |
| All Organisms → cellular organisms → Bacteria | 3 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Betaproteobacteria incertae sedis → Candidatus Accumulibacter → Candidatus Accumulibacter phosphatis | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 4 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 3 |
| Not Available | 6 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1 |
| All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Halobacteria → unclassified Halobacteria → Halobacteria archaeon | 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 → Aquatic → Marine → Wetlands → Unclassified → Natural And Restored Wetlands → 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) | Unclassified |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Saline → Water (saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: San Francisco Bay, California | |||||||
| Coordinates | Lat. (o) | 37.926434 | Long. (o) | -122.509186 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F002483 | Metagenome / Metatranscriptome | 555 | Y |
| F003627 | Metagenome / Metatranscriptome | 476 | Y |
| F004436 | Metagenome / Metatranscriptome | 438 | Y |
| F005789 | Metagenome / Metatranscriptome | 390 | Y |
| F005815 | Metagenome / Metatranscriptome | 389 | Y |
| F008223 | Metagenome / Metatranscriptome | 337 | Y |
| F010065 | Metagenome | 309 | Y |
| F016664 | Metagenome / Metatranscriptome | 245 | Y |
| F016971 | Metagenome / Metatranscriptome | 243 | Y |
| F018371 | Metagenome / Metatranscriptome | 235 | Y |
| F018541 | Metagenome / Metatranscriptome | 234 | Y |
| F019205 | Metagenome / Metatranscriptome | 231 | Y |
| F024115 | Metagenome / Metatranscriptome | 207 | Y |
| F024437 | Metagenome | 206 | Y |
| F027211 | Metagenome / Metatranscriptome | 195 | Y |
| F032367 | Metagenome / Metatranscriptome | 180 | Y |
| F046383 | Metagenome / Metatranscriptome | 151 | Y |
| F048318 | Metagenome / Metatranscriptome | 148 | Y |
| F049002 | Metagenome / Metatranscriptome | 147 | Y |
| F051143 | Metagenome / Metatranscriptome | 144 | Y |
| F051533 | Metagenome | 144 | Y |
| F053306 | Metagenome / Metatranscriptome | 141 | Y |
| F055469 | Metagenome / Metatranscriptome | 138 | Y |
| F074891 | Metagenome / Metatranscriptome | 119 | Y |
| F074893 | Metagenome / Metatranscriptome | 119 | Y |
| F076055 | Metagenome / Metatranscriptome | 118 | Y |
| F094484 | Metagenome | 106 | Y |
| F099226 | Metagenome / Metatranscriptome | 103 | Y |
| F104552 | Metagenome / Metatranscriptome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210063_1000001 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 428371 | Open in IMG/M |
| Ga0210063_1000002 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia | 270612 | Open in IMG/M |
| Ga0210063_1000006 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia | 216102 | Open in IMG/M |
| Ga0210063_1000007 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 176171 | Open in IMG/M |
| Ga0210063_1000059 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia | 35806 | Open in IMG/M |
| Ga0210063_1003137 | All Organisms → cellular organisms → Bacteria | 3564 | Open in IMG/M |
| Ga0210063_1006847 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 2258 | Open in IMG/M |
| Ga0210063_1008889 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 1961 | Open in IMG/M |
| Ga0210063_1011083 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Betaproteobacteria incertae sedis → Candidatus Accumulibacter → Candidatus Accumulibacter phosphatis | 1753 | Open in IMG/M |
| Ga0210063_1025456 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 1168 | Open in IMG/M |
| Ga0210063_1028193 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria | 1112 | Open in IMG/M |
| Ga0210063_1031546 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 1054 | Open in IMG/M |
| Ga0210063_1032477 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 1040 | Open in IMG/M |
| Ga0210063_1050282 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 852 | Open in IMG/M |
| Ga0210063_1050329 | All Organisms → cellular organisms → Bacteria | 851 | Open in IMG/M |
| Ga0210063_1056077 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 810 | Open in IMG/M |
| Ga0210063_1074169 | Not Available | 712 | Open in IMG/M |
| Ga0210063_1086416 | Not Available | 664 | Open in IMG/M |
| Ga0210063_1089937 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 652 | Open in IMG/M |
| Ga0210063_1091279 | Not Available | 647 | Open in IMG/M |
| Ga0210063_1097679 | All Organisms → cellular organisms → Bacteria | 628 | Open in IMG/M |
| Ga0210063_1109366 | Not Available | 596 | Open in IMG/M |
| Ga0210063_1117807 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 575 | Open in IMG/M |
| Ga0210063_1121303 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 568 | Open in IMG/M |
| Ga0210063_1121947 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Halobacteria → unclassified Halobacteria → Halobacteria archaeon | 566 | Open in IMG/M |
| Ga0210063_1133495 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 542 | Open in IMG/M |
| Ga0210063_1140775 | Not Available | 529 | Open in IMG/M |
| Ga0210063_1150298 | Not Available | 512 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210063_1000001 | Ga0210063_1000001320 | F076055 | MTRTTVDVDERALAAARRELGTKGLSDTVNVALREATRRHVLQGFDVRRDIDGTPEEIREGRERL |
| Ga0210063_1000002 | Ga0210063_1000002121 | F005789 | MATAVGLDSSPLNFLRSMRGAIIDARIAYPEVLHVDIKDSAGELWRLTTQDADWSPLDPEQLIGRSVEDADIDGETGELRCKLSDGSLLDVKPAEREAEDDPPYWELITPGGVLLEFGPGVRWQIGSADSRASSRA |
| Ga0210063_1000002 | Ga0210063_1000002122 | F032367 | VSRKRDIKQFRQACKEAGLTAGERREASDAFHAEKKSGSVQRDMSYGELLAWLRQWRA |
| Ga0210063_1000002 | Ga0210063_10000022 | F019205 | MFDSKKSFSHKAADAADLVIDFATLGEYGLEPVEQPARSCEGRSRIGSPRSTGAWSAAIARFATQA |
| Ga0210063_1000006 | Ga0210063_100000661 | F027211 | MVRTYWLVPVFYEASGNLDLRPFARTDQIEACRPHAMCIRLYAAG |
| Ga0210063_1000007 | Ga0210063_100000750 | F002483 | MAIGFLRRRPKKRPQRAAAPWPSTPLPPRRPASYYLVAGVALDRELERLRGLPVFAAGPLATQRPQLKVRRASKRPNKLGFAVPAEFRLQVTAYPGIGPGDVLETLLHELTHLHVGRAAEAHAWHGRTFKRALAQAMEQAYGVEIPPPSHTRHGVYAAAIDASRSPAQFGGEG |
| Ga0210063_1000059 | Ga0210063_100005912 | F003627 | VDRETARKNMSSALVAGGFAAAVFALAFVAAFLYIAQA |
| Ga0210063_1003137 | Ga0210063_10031373 | F055469 | MLKRTVVILAAAAFFWGTVPTQTAQARDDIWDLMNPSWWADQIFDDDHDDWWYYRHHAYSPYLGAPYVQRPRVIVVQPPETQAQNPETRAPE |
| Ga0210063_1006119 | Ga0210063_10061194 | F051533 | MVYAFKITIMEDKTRPMQEKIIVVTDSLKDLAIYLSGVKDGKGNLLPLGTVVLDDLWNAIKYLQGDTRYTCPKRDDK |
| Ga0210063_1006847 | Ga0210063_10068472 | F099226 | MANIAKIFTVAVTLVVGTGAISGIALANTNPLYPDRLKNPHVSLPSARVGSGIPSPYRIGGRIDEPSVSLPSARVGSVIPAPYRIGN |
| Ga0210063_1008889 | Ga0210063_10088894 | F024437 | RAYDASLTGSSARQLPVDGIRKSLVAHGQAGQFYRHLQFHIGCRFLGWPGMLASWLMHRVDVRQAARGRMESAVEVKGNEAAFACAEVLSDRLHRRISRAEAAERLRDILTD |
| Ga0210063_1011083 | Ga0210063_10110831 | F104552 | MVICKASTHFLSRIACSQVWALLLLGLLIPAQAAEALIPDTLPQAQAALERLEQQLASARTATAQELKSLKKEIATVRSSAQDCVQQAEPEIASLDSQLAILQPAPPKGTQAKTAEETQPAEQPQAPLSPAIARQLQDLQSRKASLEGRIVTCKLVLLGSNNLDSKVDDYLRSLQTRQLLARGPDLVSVVQANLDERERWLDFTRQLAVTSTGWDAIRPIHLAGAAAVGLLGFILGRIVPRRLRARAARMKVGEEEVSAGLVQAVMACGASYAPI |
| Ga0210063_1025456 | Ga0210063_10254562 | F074891 | MSTVTHDVVLKPRARKKRNKGVAALRMLRRALARRKLEQMRDEELLREQIYDVFEDKGGP |
| Ga0210063_1028193 | Ga0210063_10281933 | F049002 | MPKTDYDKAQTELTRAIQEDAPFTFEEPIPVRVFLDNGVKYDGVAYEVQPASTTFPDGLVMVRTNNSDIGVPVSYIRGK |
| Ga0210063_1031546 | Ga0210063_10315462 | F053306 | MQLLAKVKKEFLIAAATLLSLSACGQPEPITYESLVWVNQYYVDHPVASLSATAGGWLFRGAREFGTEIRIGFLVPGPINPDPAKRQAVLETICPDRSEPIWQTLPKDNKLVINVWTEDRKFKDMKTC |
| Ga0210063_1032477 | Ga0210063_10324771 | F016664 | MDQVVHQMPTLDVANNTVEIVVHISESLDDVERNNLVAALEQNYGIVSAEFCPLRYHLMLVRYDRDLYSSQDVLHDVSDRKLQARLIGPI |
| Ga0210063_1050282 | Ga0210063_10502822 | F008223 | MTVFGKLFRKKDRPPSPVEELGKILDRFTTATIMGIDREDLGRYPAKQYKVMAFHFGAIQYLADQYELDETRTLGVFVAFIDKYFNMPISETGSISERLQGFLENEEERAYLDAGLDVFRRWHEHNERRAPLELG |
| Ga0210063_1050329 | Ga0210063_10503291 | F094484 | MKQLALALLISGGVLSVADAAHAEGRRMIIFTLYAADGTTDSTATTTVIDFTTQVACREARDELRRNAKAPGFGLYATCVEP |
| Ga0210063_1056077 | Ga0210063_10560772 | F018541 | VDFPLTDEQYSKLDLRWRRRQNFYEVKNEPPSGIRLRSFCTFGGEDYKILSLEARGDIDAYNDTIKIMDKWINETLGEY |
| Ga0210063_1074169 | Ga0210063_10741692 | F018371 | MDYSNIIKPKRLTDMQEMEVHVNGPEGANRLFMHSGMAEVEIRGGLPHPRWTLEVVCFEVGRTYDLSEESIININASAALAGGRMDGVASFAGWQIFGAAGELDNESRRVRMNIAAGARDTQAFLEQISFQINILARVKE |
| Ga0210063_1086416 | Ga0210063_10864161 | F046383 | MKKYLSLFVVFLFVPASQIALACGPEQDGCLGCNDEELPVCLHTLVQDVCQSSVKPTNCDTARVYDDAERYILTSTGSHMSRIRAMFRSSHKYQLH |
| Ga0210063_1089937 | Ga0210063_10899371 | F004436 | GVNGHANDSNNVYSRKPSDAAKFSPLSQRRLVHRRRRPMQLRTAVGLIELQVLHGQDPKDKHWGCPIRECWGLSCHQQLSLALEDKLAFTATATGSYEEAAAVARKWGAAVSPSALHALTQRLGARAEANTQAQLGRTPSERQPERAPTKLAVLMLDGWQVRQRGPGWGKSRTQQPRVEWHEWKTGVYYRQEQAGHSAGGRGMLEEKIVIGWQGEPM |
| Ga0210063_1091279 | Ga0210063_10912791 | F055469 | MLKTTVVIFAAAAFFGGAIPTQIAQAGDDIWDLMDPSWWADEVFDNDDDDDWWYYQQYRYNPYWGAPYGRRPQVIVIQQEPETVPQIPETRLPE |
| Ga0210063_1097679 | Ga0210063_10976791 | F074893 | GTTEELKMMVSSQLNAVAGDGSLTISINGPMDLLLTRALREHCQDNGATYHRYIVDFRDVSIVRDSGLALLLMLKRWANRAGATLCVINGNRDLMRRCFSLGIGPA |
| Ga0210063_1109366 | Ga0210063_11093661 | F074893 | MMVSSGLQAIAKNGALTIRIKGPMDLLLTSALRDFCHGTGAVYRRYIVDLRDVSVVRDSGLALLLMLKRLAGRTGATLHVTNGDTDLMQRCRRLGIKPA |
| Ga0210063_1117807 | Ga0210063_11178071 | F024115 | VQLTLPRILWFVAALAMAWGLNTWRREAASHGLEAAQRGDRNAAESWVDRALREGECELHEAREYVQSPATRQYVRRPDYVESFVEKLYAGGAPKLEICDSDLVGFRFAHYLLVTLPEDPTEQEQVIADAQSFVRRDAVVYRGVSSSEVEAIVRDSTLVGEHRVLLDLPAEAD |
| Ga0210063_1121303 | Ga0210063_11213031 | F048318 | MASVENVRLAITASTIKPGHSDIAYSYELHPSELDCGWKREYTISAVLYGEDMIEDDVLAWGKDEHKVRFEDSRPGEPIKVERVFEVETKVLDEDLFGDDEVYLMVEARSGLRADA |
| Ga0210063_1121947 | Ga0210063_11219471 | F010065 | VLPSRGRLKRVTMRGESGISLTGLYVCGAIALVMLVLKLSVIDTWSWWRVMLPLGIIVGFNVTNMVVAFIYLSFAHIPERPDGDEAEVLEPHTLDAHYVAAMIFFVVFGDNLVRWIEGSETSHWFWLFSGKIEALAVFGTLSVVALFSYWSRLGRVLKASG |
| Ga0210063_1133495 | Ga0210063_11334952 | F016971 | MNQVAQDLPVEESCAVEVVVYIKKDLGEDQQGLVISALQQTNGIIGAEFCVMRNHLVLAKYDKDIMTSQDVLKSFNSLNLDAKLVGPI |
| Ga0210063_1140775 | Ga0210063_11407751 | F005815 | MNTTRLTLYWSTDEAATAIEFLDTLRDALWETYGEQITRMRCEACQDHMPDTSQREFEFDDDIPF |
| Ga0210063_1150298 | Ga0210063_11502981 | F051143 | MMHKFAQEEGLEKVATMTTLEAVAYANRLTKRLKRDDCTDAERTNALELLRQLTERVPFLKITLEQPSFCRIGSSYFDKHARSREWT |
| ⦗Top⦘ |
|
Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |