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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 | 3300027102 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0085736 | Gp0057309 | Ga0208728 |
| Sample Name | Forest soil microbial communities from Harvard Forest Long Term Ecological Research site in Petersham, Massachusetts, USA - MetaG HF028 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 17778847 |
| Sequencing Scaffolds | 35 |
| Novel Protein Genes | 42 |
| Associated Families | 42 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium lablabi | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 2 |
| All Organisms → cellular organisms → Bacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Beijerinckiaceae → Methylocapsa → Methylocapsa palsarum | 1 |
| Not Available | 17 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Rhizobiales bacterium GAS113 | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria | 3 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 5 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Forest Soil Microbial Communities From Harvard Forest Long Term Ecological Research (Lter) Site In Petersham, Ma, For Long-Term Soil Warming Studies |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Loam → Forest Soil → Forest Soil → Forest Soil Microbial Communities From Harvard Forest Long Term Ecological Research (Lter) Site In Petersham, Ma, For Long-Term Soil Warming Studies |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | forest biome → solid layer → forest soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Soil (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | Harvard Forest LTER, Petersham, MA, USA | |||||||
| Coordinates | Lat. (o) | 42.471116 | Long. (o) | -72.17263 | Alt. (m) | N/A | Depth (m) | 0 to .1 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000079 | Metagenome / Metatranscriptome | 2532 | Y |
| F000136 | Metagenome / Metatranscriptome | 1961 | Y |
| F000989 | Metagenome / Metatranscriptome | 811 | Y |
| F001274 | Metagenome / Metatranscriptome | 733 | Y |
| F002784 | Metagenome / Metatranscriptome | 530 | Y |
| F004415 | Metagenome / Metatranscriptome | 439 | Y |
| F004686 | Metagenome / Metatranscriptome | 428 | Y |
| F004810 | Metagenome / Metatranscriptome | 423 | Y |
| F005126 | Metagenome / Metatranscriptome | 411 | Y |
| F007186 | Metagenome / Metatranscriptome | 356 | Y |
| F007656 | Metagenome / Metatranscriptome | 347 | Y |
| F008725 | Metagenome / Metatranscriptome | 329 | Y |
| F012806 | Metagenome / Metatranscriptome | 277 | Y |
| F013347 | Metagenome / Metatranscriptome | 272 | Y |
| F014678 | Metagenome / Metatranscriptome | 261 | Y |
| F015667 | Metagenome / Metatranscriptome | 253 | Y |
| F017926 | Metagenome / Metatranscriptome | 238 | Y |
| F018093 | Metagenome / Metatranscriptome | 237 | Y |
| F020247 | Metagenome / Metatranscriptome | 225 | Y |
| F023944 | Metagenome / Metatranscriptome | 208 | N |
| F025158 | Metagenome / Metatranscriptome | 203 | N |
| F026433 | Metagenome / Metatranscriptome | 198 | Y |
| F028270 | Metagenome / Metatranscriptome | 192 | Y |
| F028290 | Metagenome / Metatranscriptome | 192 | Y |
| F029262 | Metagenome / Metatranscriptome | 189 | Y |
| F038357 | Metagenome / Metatranscriptome | 166 | Y |
| F041178 | Metagenome / Metatranscriptome | 160 | N |
| F056188 | Metagenome / Metatranscriptome | 138 | Y |
| F058546 | Metagenome / Metatranscriptome | 135 | N |
| F062051 | Metagenome / Metatranscriptome | 131 | Y |
| F067022 | Metagenome / Metatranscriptome | 126 | Y |
| F067250 | Metagenome / Metatranscriptome | 126 | Y |
| F069205 | Metagenome / Metatranscriptome | 124 | Y |
| F073977 | Metagenome / Metatranscriptome | 120 | Y |
| F078200 | Metagenome / Metatranscriptome | 116 | Y |
| F084549 | Metagenome / Metatranscriptome | 112 | N |
| F090799 | Metagenome | 108 | Y |
| F092807 | Metagenome / Metatranscriptome | 107 | Y |
| F096149 | Metagenome / Metatranscriptome | 105 | Y |
| F096804 | Metagenome / Metatranscriptome | 104 | Y |
| F099687 | Metagenome / Metatranscriptome | 103 | Y |
| F103810 | Metagenome / Metatranscriptome | 101 | N |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0208728_100041 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium lablabi | 2357 | Open in IMG/M |
| Ga0208728_100185 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 1587 | Open in IMG/M |
| Ga0208728_100374 | All Organisms → cellular organisms → Bacteria | 1253 | Open in IMG/M |
| Ga0208728_100565 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Beijerinckiaceae → Methylocapsa → Methylocapsa palsarum | 1050 | Open in IMG/M |
| Ga0208728_100710 | Not Available | 957 | Open in IMG/M |
| Ga0208728_100772 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Rhizobiales bacterium GAS113 | 928 | Open in IMG/M |
| Ga0208728_100795 | Not Available | 919 | Open in IMG/M |
| Ga0208728_100839 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 901 | Open in IMG/M |
| Ga0208728_100864 | Not Available | 889 | Open in IMG/M |
| Ga0208728_100902 | Not Available | 869 | Open in IMG/M |
| Ga0208728_100982 | All Organisms → cellular organisms → Bacteria | 841 | Open in IMG/M |
| Ga0208728_101001 | Not Available | 834 | Open in IMG/M |
| Ga0208728_101163 | Not Available | 781 | Open in IMG/M |
| Ga0208728_101179 | Not Available | 777 | Open in IMG/M |
| Ga0208728_101254 | Not Available | 757 | Open in IMG/M |
| Ga0208728_101270 | Not Available | 754 | Open in IMG/M |
| Ga0208728_101381 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 734 | Open in IMG/M |
| Ga0208728_101448 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 720 | Open in IMG/M |
| Ga0208728_101719 | Not Available | 678 | Open in IMG/M |
| Ga0208728_101720 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 678 | Open in IMG/M |
| Ga0208728_101762 | Not Available | 673 | Open in IMG/M |
| Ga0208728_102021 | Not Available | 639 | Open in IMG/M |
| Ga0208728_102145 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 628 | Open in IMG/M |
| Ga0208728_102270 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium | 616 | Open in IMG/M |
| Ga0208728_102606 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 585 | Open in IMG/M |
| Ga0208728_102773 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 575 | Open in IMG/M |
| Ga0208728_102954 | Not Available | 562 | Open in IMG/M |
| Ga0208728_103219 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 547 | Open in IMG/M |
| Ga0208728_103381 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 539 | Open in IMG/M |
| Ga0208728_103447 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 535 | Open in IMG/M |
| Ga0208728_103661 | Not Available | 525 | Open in IMG/M |
| Ga0208728_103936 | Not Available | 514 | Open in IMG/M |
| Ga0208728_103997 | Not Available | 512 | Open in IMG/M |
| Ga0208728_104043 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 510 | Open in IMG/M |
| Ga0208728_104108 | Not Available | 507 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0208728_100041 | Ga0208728_1000411 | F058546 | SGGTGMVKEGDIRAYDAERDAKRARQPRRAKAAGRRAASRSRYALDPAVIAAGKLPDKAPVVTSAANPHYQKRFDELHKLAAAGDWAAVRDYKVSGSNSYSKLVARYQQDLLALHAASGDAQ |
| Ga0208728_100185 | Ga0208728_1001852 | F041178 | VNAEQASHDEGLVKGSHHGGIETSPVASVSKVQAHLRDAARFRARSTSHAVAARSSCTKIPLSAGRAQEDENHSRKRHFRPWLATVRLPGSARTDQVLGDDGITLVYSLGNLHRNAFDNDTGGHVFPERDQ |
| Ga0208728_100189 | Ga0208728_1001892 | F000079 | MRIYIIGNDGITLCRKAPATVNDGEIAVASNEELHAARLSGKRLLALWNALPGVEKRK |
| Ga0208728_100374 | Ga0208728_1003742 | F038357 | MCPGDPLGNHRQRPIAVSLVFEPVLAHEDGMGVPAPLPHQGRAGLQRSAGVERTSAFLELSRQNLQAALQGGGRAAMGTLLQLIGEPPDDQIATEAQRRADVMQSPPRTPQLLCRLTDQLSDFAINLCQCQTSQPVLPAVVCTERLARVLASRSVVEWGFHGLAGSAMRYTRPRSSLAEARGSPSFFFKVPEKTPRTV |
| Ga0208728_100565 | Ga0208728_1005651 | F000989 | NPVTARRHRVVSLVTHADIQDIVWADDETGCYAVWGKDAKGNRIVVERAGPIRIVGARR |
| Ga0208728_100710 | Ga0208728_1007101 | F013347 | ADIMDACEMAWNRFATNTGLVRSLCAVAWAPASPDP |
| Ga0208728_100772 | Ga0208728_1007722 | F014678 | MSGSLRVGRRGATSKIGFDHVGEDDARLGDVEACDGRIHLVETLATAQKLGVDRTDLVEHLL |
| Ga0208728_100795 | Ga0208728_1007952 | F084549 | MKSVYVSAAAITLTAAVNLSPALAQGPTAFGREGSQPLTTPSSAAVTSAGHYEYRYGYDKHARWRGHWIFIR |
| Ga0208728_100839 | Ga0208728_1008391 | F067022 | VRFPHIGLVAEGAGLYRRGETEYDIAGGPRLSTNMGKWRPFIHAMAGLRDLHSSGLTYRPLLIDVGGGADYKLWFKNFSWRLQGDYMHSHYASAYQNDYRASTGIVWRF |
| Ga0208728_100864 | Ga0208728_1008641 | F025158 | MLQSEVLQPLETTRNKIKEQLSTVQEYRLLVALEKCIAQIPDISNDTMTTLERVRERLTECLQEVRDYRALRTIEETIVEVRSILAEAPSAVQPPAAESTVPDGEPLAGVPDADTERVA |
| Ga0208728_100902 | Ga0208728_1009021 | F023944 | VDPHQKTMMVQSFVAGFAKAARVSDVPEEAIMSDTREPSYMFLAAEWNRSSVSERAYLLAMLFGREFEVEANDLSLQIASLAMTMVEPDGSAALIARVDLGAAD |
| Ga0208728_100902 | Ga0208728_1009022 | F012806 | MTDAPIITNEDAAIDSAFFGSHAGRTCYARAHHSGWVLVVRQIVAQREPPVMLRVWGRLERVPDDDASCLALWERCA |
| Ga0208728_100982 | Ga0208728_1009821 | F099687 | GQADFPHPALGKDSRCYVRRRLQLLNTNCGVARLIVNPHVLRRCLRPSLTGVPSLHRSYPASSVLRTSPPPHTARPVSRELPVDPYRDHRWGFPCCVWSPMRTCHRHYPGRSDAACPLVPLHRQRPSLCNSQVGSCNCFFGACSAFTHVTACTLAESPSDPFHRKLRQLRCLRCRFDCYRVERTSSWAGLAPAEVQRLFTAHFFAN |
| Ga0208728_101001 | Ga0208728_1010012 | F078200 | YANSSNQLAALKELYTDDKDYMKNVVYSKNPWLAMVPKNESPDGFAG |
| Ga0208728_101163 | Ga0208728_1011632 | F103810 | MTEDDVRREIFQAIIQCRGHNGPLINQRDTCEVLAAGVFETLKAKGLLKLDDDN |
| Ga0208728_101179 | Ga0208728_1011792 | F007656 | MSLYRCRYLDRTFSVFEIQGVACENDAEAIVMARRMSANTGAVGFALLQDERCVHMETMPSATARDHRSRA |
| Ga0208728_101254 | Ga0208728_1012542 | F028290 | MYAIAVVLLNALSFASLAYVANRKGYHAMAALLAAGAWLFGVTGGVLIWVWR |
| Ga0208728_101270 | Ga0208728_1012701 | F015667 | MKSETEAAVVSIRENTNERTARVNLRWEGKHEISDFALNKLGSVLNSEGETEHSGWAIVELPVKATVGRA |
| Ga0208728_101381 | Ga0208728_1013811 | F007186 | MKKLVLLFLIVSVTLAYADDSKISPELRNQPATQQTQVIVQYAPGTQVNCSGLLGLVGCLVNDILKIGGTILSEVPIINGVVALLDGNGIQSLSSQSNVVYISPDRPLKPTLNNAASAVNAE |
| Ga0208728_101448 | Ga0208728_1014481 | F008725 | SLEQKGCQKRGISMTTAINSAISPFAQPKTEPNVNAIRFLDTKLSSVSASDIPEEFRTLSRYLLLLVLVPKSALHDKTTQKKPGPNKSVTRLIETSDVCLSLDAAKAWLRNPNATDTFEFGGK |
| Ga0208728_101702 | Ga0208728_1017021 | F000136 | MAKAKLRILYGEGDGDVLSQQAAAFEKAGHVVQKAEGRKNVDEALKKSTFDLVILGSTLSRNDRHHLPYMVKKVNAETSVLVMHADGSRHPYVDACVDTGSSMESVLNRIETMKIAGMMPQAAAAGAGR |
| Ga0208728_101719 | Ga0208728_1017191 | F004810 | ASGVGLVAAIAALWVQGWQRADHRFFAALISIAVTLSLFSVVAWAAAAIAPLPLTWVLVGTLALLFALRLYRELQEPPSGERSP |
| Ga0208728_101720 | Ga0208728_1017202 | F004686 | LTAGETLGYSPTAGDLRRSAEAEKKAAQSMTIRGSAPTLATTKTSPVLRDHFVPNTSVAMEVDSAGFFELLIGRLTGK |
| Ga0208728_101762 | Ga0208728_1017621 | F002784 | MNEFTDKNEQAFLDACGAIGVEPDAMVNTQKERYLVSEFLKNPVSWLETEILYHSYTTRREAKDVAHGIDRMISEGAPVDQSKLFPRPKHSNAPS |
| Ga0208728_101874 | Ga0208728_1018741 | F096804 | MRLMQMIGPAARNVFKATAAMTDDVLRVAALLVPCLLGLRTAVACRRAHYHGLPGADALVWAGLSAVFFLLSLMKTARGLGLLRGFGDFLRGIFKQRGWYEDRRSLQITASIAVAVVVAVLVVWGLLWAWHRIKRYRLAIGFAG |
| Ga0208728_102021 | Ga0208728_1020212 | F067250 | MGKSMNPKMSGFRKWAEIHEPTKIDKARTGANEGGVIAAADVDQDRKTPEATTARP |
| Ga0208728_102145 | Ga0208728_1021451 | F026433 | MQVSQARNQSMWKQVYQDALFELDQTRFKPKLEAALKAVQDRLLEVRSDPADRRELMELEDAKRTIGFLRKHEMEEI |
| Ga0208728_102270 | Ga0208728_1022702 | F020247 | MTFVGSVHNPKIMLGMLVKVLCGDAIATRPRLPREGNVTFEDLMRGTSDFDVRTVTLEILTSMRYLLPIMVGIVAVIATMRSSSLSWSHDTCWIDGEVGSLSNKSVLERLRYR |
| Ga0208728_102606 | Ga0208728_1026061 | F062051 | YRAQADLARRLAEITAQPNLERELRHVAEELDHLANEIASDDTDFLRSEVLEPRD |
| Ga0208728_102773 | Ga0208728_1027731 | F096149 | FLNHEIFNNGPGDCHVQTLLAKSQPLRPQYADPELLELQAAQG |
| Ga0208728_102830 | Ga0208728_1028301 | F090799 | MKISLFFAFLLTVASAFTADAMKFVSPDTSTTLVVDKSGRRDIIELQSGKRVHRLFYEDLDSIFKPKVAEAFNASLNRLAKLYSPRLPALAGSL |
| Ga0208728_102954 | Ga0208728_1029542 | F017926 | MKKTLITGLIAVVFLGLSTAAQDWYHDRDARYRGDQWRSHVFAEIRRDLDHIWSANQAADKERKRLERTKQELRDLQAKLERGEWDNGHVNDVIDSLQKSANDNRLSERDRAVLNDDVTRIKDLQNEHN |
| Ga0208728_103180 | Ga0208728_1031801 | F005126 | MEIGRTEFSNGNKGMSGSNDPHVVEVVRQAHEELRQLMRQRADVMKRIGTVKQTIVGLANLFGDEVLNDELLELVDRKSNGRQPGFTKA |
| Ga0208728_103219 | Ga0208728_1032192 | F018093 | MAYKESFWMACDSTDQLRAEYGPFHTRAEAEAEARKLGFGYLLRYEHLIGPNEEIEEVRCIF |
| Ga0208728_103381 | Ga0208728_1033812 | F092807 | NAIEKQNYAVLGNRPAISKSRKLALVAHAAVAKIFGLSGGPR |
| Ga0208728_103447 | Ga0208728_1034471 | F028270 | VTFPHHAQPRILELMGKSAAVLCHDKRSLQTLTSTLEQLGIELRNCRSNQEALELVMAGECSTLIVDFDLPGAEEAIRMAALLPAEQKPALLAVASRAWPGT |
| Ga0208728_103661 | Ga0208728_1036611 | F073977 | MWSIFPAVAILLAQAQSDPAEKWCFERGQNGAQLCEDTENSCNALLKINPEIATGPCLRVEPRLEQSGSTAS |
| Ga0208728_103661 | Ga0208728_1036612 | F001274 | LRGEPATFEGGAAVTIYQITLRDRETRTVLGYYNGAWTTDRHRAIALPKREVAEDHAARMRDLCPRNAELINVEEIAAAD |
| Ga0208728_103936 | Ga0208728_1039361 | F056188 | VRDANASSELRFKAAQTTLPFVHAKPGSARPGDPAGPAKLIDGTGAFTIDNAVAKALRDDYHRLGELVRKKCGDPLSAAEVEEESRLRARIGDRARAIGCPAGYGLKQAQKESNRLHQLYCKRISPPSCGGGALPDAEDAEEVQLRARVAAFDESPEGCARRRIRDLEMQD |
| Ga0208728_103997 | Ga0208728_1039971 | F069205 | LTAFSLSQEAPPVAPLPFDPLELATGPTVVPDTPQKRAVGLDLLERARQNSAMHTPGTAPFSLKVSFNSVGRGSRNSGYGELEETWLNGQTWRWSARLGDYSQLRIFYAGEAYDDKPRGHMPLRLQMVRNSVFWPVLGNFSSALLRMATAKWEGTDLACILISGALNDVT |
| Ga0208728_104043 | Ga0208728_1040432 | F004415 | MDDTIEARFVAETELLGLELLPGQKETLLAAYTALREMVELVGADYPFETEPAHVF |
| Ga0208728_104108 | Ga0208728_1041082 | F029262 | VRTDPGIPAARQRPPLTKRLSPRHWAALDYVVGAVFGLILLTTIRRGVVETIESPYGWVPYRPMVLTWPLAIVLVLVTVV |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |