2140918025: Permafrost microbial communities from permafrost in Bonanza Creek, Alaska - Bog Site B3

Overview

Basic Information

• IMG/M Taxon OID: 2140918025
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0063124 | Gp0051911 | Ga0026288
• Sample Name: Permafrost microbial communities from permafrost in Bonanza Creek, Alaska - Bog Site B3
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 168462295
• Sequencing Scaffolds: 44
• Novel Protein Genes: 48
• Associated Families: 46

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia	1
Not Available	12
All Organisms → cellular organisms → Bacteria	9
All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales → unclassified Bacteroidales → Bacteroidales bacterium	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	6
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanotrichales → Methanotrichaceae → Methanothrix → unclassified Methanothrix → Methanosaeta sp. PtaU1.Bin112	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Archaea → Euryarchaeota	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	3
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Spartobacteria → unclassified Spartobacteria → Spartobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → Pseudolabrys taiwanensis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Sorangiineae → Polyangiaceae → Sorangium → Sorangium cellulosum	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Soil Microbial Communities From Permafrost In Bonanza Creek, Alaska
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Unclassified → Permafrost → Soil → Soil Microbial Communities From Permafrost In Bonanza Creek, Alaska

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): terrestrial biome → solid layer → permafrost
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Soil (non-saline)

Location Information

• Location: Bonanza creek, Alaska, USA
• Coordinates
  • Lat. (^o): 64.7
  • Long. (^o): -148.3
  • Alt. (m): N/A
  • Depth (m): .3 to .7

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001213	Metagenome / Metatranscriptome	746	Y
F001962	Metagenome / Metatranscriptome	611	Y
F002889	Metagenome / Metatranscriptome	523	Y
F004844	Metagenome / Metatranscriptome	421	Y
F005423	Metagenome / Metatranscriptome	401	Y
F006577	Metagenome	370	Y
F008108	Metagenome / Metatranscriptome	339	Y
F008963	Metagenome / Metatranscriptome	325	Y
F009862	Metagenome / Metatranscriptome	312	Y
F010068	Metagenome / Metatranscriptome	309	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
NODE_102798_length_1091_cov_6.799267	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia	1141
NODE_108312_length_822_cov_8.434306	Not Available	872
NODE_119661_length_3420_cov_5.914620	All Organisms → cellular organisms → Bacteria	3470
NODE_121058_length_706_cov_14.504250	Not Available	756
NODE_148397_length_1214_cov_9.708402	All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium	1264
NODE_150515_length_1106_cov_14.988246	Not Available	1156
NODE_171902_length_1338_cov_15.592675	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium	1388
NODE_179581_length_737_cov_14.826323	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales → unclassified Bacteroidales → Bacteroidales bacterium	787
NODE_182535_length_1650_cov_16.822424	Not Available	1700
NODE_213257_length_1112_cov_12.989208	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1162

Sequences

Scaffold ID	Protein ID	Family	Sequence
NODE_102798_length_1091_cov_6.799267	b3_nosca_v_02270700	F002889	MNRNAYIFGFLVLTLAGLVGCSSAPPAKDSTKAGTALDKIQGKSQIVQTETTQIDSALNAGGPSVYIWEGARRYRLFFKTAVEVAPGKEYIVEGVNAQRVIDEIGDPDQGKNGYPLPESCDRVVKTAWSGLAFDVSDGQATVLRNRVKRYPARPVFLVNRITPVPEGGAASADAKKAAEEKDIPEVTVAADKQRALLIDGPAVLPAPLWQPAGGTVRCKVYIDKEGKISELGTGEQLCEAVPWSQYRYQPPVQGGHPVTVSTVVEVRFEPRK
NODE_108312_length_822_cov_8.434306	b3_nosca_v_00760590	F030615	SFYETKVKTWLGWVSFTVFYKTNILHIVSVPSVQKSMAYERIYQYCEIKGYKKKNIEISEINKNESKKWIFFQRIYSD
NODE_119661_length_3420_cov_5.914620	b3_nosca_v_00410170	F076659	VAVLLYRREIGSERQVEMGDESTRYTWHDSPYLPQTVNALVRGIFWSPTSDPVHPPYAITHYLQHESMHAPSIDAFVRAVRAECRPGERIFGEYSLGPFAAAIGPCVLGANLADTNPHRFKVHESTPEDWVRALEQDHLDLAIIVPGMTMLKERALHEYLTGNFPRIVATWDDPYAGHVELRRRPN
NODE_119876_length_1035_cov_10.643478	b3_nosca_v_00578270	F071801	ASLVCAQAGPDGHWEGFYKVNNSEIEYGISLDLAKNEKSEWIASMGRPSQNVTGLVVTHVAVNGKSVKFNAVELQGRRCDLTLGPDGTMKGTMSAPQDPMATQISMPVELKRTGEAKVELIPLSPAVSKELEGDWEGLLQAPNGMSFPLVFHFKNQPDKTVAATWTVPAGTPWLCR
NODE_121058_length_706_cov_14.504250	b3_nosca_v_01324200	F006577	LELNGARSNPRAGVELSRVGALHDELLRKALANPREPRPVPAKVSPVLETVTLVLERSERPMRAREIHAAACELVGEPLLWESVKAALSADVASEHSRFRRVRHGVYQIARDVKRCTS
NODE_148397_length_1214_cov_9.708402	b3_nosca_v_02419470	F072571	EVQVDEALRELLEGEAEAVITEASIRELLAKLDTIAPVTMVEVAPVDLASFDQLCLDMEVPQ
NODE_150515_length_1106_cov_14.988246	b3_nosca_v_01023780	F103711	VNRQPSSDKTDGGFFMSKRKSGGQAAELPSPPEMVCILVVDAVIDEIEVEICCQRTDGVDRVFSTSRGMDWLRTERPSVSTLTYSIDTLLFSMIAMCLRYVGYPVDVRAGLLSKKHVEAIINSVCFELEEIKKENEVWREAEIVTKAANLGLALEASNFSRGTWIACCPGTNHTLDLQPKRN
NODE_171902_length_1338_cov_15.592675	b3_nosca_v_00517150	F009862	MKDEKPLLIRCPNCKQVHEPDFNETTRRYVCPLCAAPVDAQVVIEKKKRGLK
NODE_179581_length_737_cov_14.826323	b3_nosca_v_02291220	F098320	CHPVASFLSFTSVAVQSCVGAGHLSPYTGLIESSGAVTVMSPYTISLESRDGLQKP
NODE_182535_length_1650_cov_16.822424	b3_nosca_v_01272310	F046098	AIVLLVVGILGLFPSMGWAHVQLWRAILEIVVGGLVLIISWRR
NODE_213257_length_1112_cov_12.989208	b3_nosca_v_02276230	F015236	DQPVTETELRALIEQTDGLVRTLGAHLAGSERRISELNEHEDSSLTEIAAELQRVEELRPRFEEASSLLADLELRARELRTSWLLGKAEQSRSR
NODE_218432_length_754_cov_12.051724	b3_nosca_v_02291380	F106197	AQIDSFDFPSGDWYRGLDQGGANVWIKNTGDISHTFWVSYEVMDRRGKWYTAPPESVYAEPGSDTYFVSPRWHIPDDAEIGGYQADFYLYGYYDPYTGELSDQLDQVAQVSAFSVVG
NODE_248733_length_1464_cov_17.907787	b3_nosca_v_02057900	F069500	MGTLERTETLAHRLGTSGRMSIKTIGGLLRVRGVDGEEARMTVAYKIRATDHASAERALETGRVLIDRGPGSLEVETPERRLSSGLAWLFGGARVSADIAI
NODE_253123_length_943_cov_14.342524	b3_nosca_v_01557660	F055310	GNLRQWGRLGMVGESRASNVVYGMTDHLGVGEGQMYRRSRVTPVEGRALASGVLEKEERSGDWR
NODE_254349_length_1610_cov_15.545962	b3_nosca_v_02164590	F092954	VTGLPGKLPARDFEEIRLAEALERGRCPVCDARQEASYAALRGLAREGATDRGLRDQMDGGLGFCQPHSVGLSRMELQQTSSQLATAVLLDAVLRRRLATLKKLAGNDAATQARGLAELADPRCPVCARIAESSLATVRRLLDLSADPAWSAALGSAEICLDDLYSLWALAAAGPKESRQRWSIIVSAQLRRLEALQKTLADYAHNSTHDRRYLITPEQQEAGAASIRFFGGSPDRDRQR
NODE_264298_length_1040_cov_23.298077	b3_nosca_v_01812200	F074194	MKVRYSVIVVVAAFMATASGLACYEGPQSFQPATYGAKPWNPDYIPVYDPDYDPNNPWNPQPTCASGYYVAIDSCPGCTGISYALCVGINFTQCVCGGPFWPGAECPKSLVCCSNDFPPFNWLELVKYAGPGWAGYNYGAGAPTRTCP
NODE_275366_length_3919_cov_18.958662	b3_nosca_v_01854040	F001213	GSVIRFDPETTRQAVAGPNGMTFVSVGARRGSYEPRGPF
NODE_281067_length_959_cov_17.157455	b3_nosca_v_01992570	F097844	MSSPLDLLNKIIGAVIAYGPRNKTKKARKARKAAHRKKIAAIKRD
NODE_286741_length_2475_cov_22.068687	b3_nosca_v_01913300	F078013	MTRGIESDDCNIDNVDELHAMRDEALTNVKAPPPSEYDIAQFKEAFADNEEDSDYDRQERNAKQRALIWYSDTLYSASELLVIMPKVVPDYNEFDGSKTIQLLTSMYPEAYFLPSREYGVAIFIYPPNGTTALKKPNEIEMERLKANSYTIHVTQREGELIHVIELWFD
NODE_2933_length_1966_cov_9.398271	b3_nosca_v_02046730	F010068	MNAKGTIFVITKTNMIAGFGDERWNSFMTKLVEKDNYFSKMIMSITLIPVEKLIIFFDEMSKEFFSNDRTTYLMFGKAGAKYALSSEGPYKAYMLTKDIKQFVDLVLPKLWSTFFDGGAVTTRFENNIVHFKVTGIKIKNLYFENLIMGYNQQALKIFGKKSVVKRVRSISSGDDDIY
NODE_297648_length_710_cov_13.766197	b3_nosca_v_01644020	F017216	HICVMTNVKVTCNCGAIYEVIETKGPPRDPKSFKCVLCEKELFAWEGTNVGQFRLVARPEADRE
NODE_303496_length_2786_cov_11.491027	b3_nosca_v_01609680	F104110	MYLGKDVTTEDSMELGKVSDVSISSSGEVYYLVEKGKDPNIRYYFTQEDVLASNERVVTRSVGEFTDDIAKRSHFLCALYGVEVRDTTNNRVGVLDNFVASPQGALVVIEDVKGNALVGRYRDLDLTRLSKFAILKQLPAQDSFDEYLKDINRDTLLTKGISCDLSSVAKDEGLLSRIRKKLSQSEEDRIITDQALID
NODE_35003_length_3520_cov_11.417046	b3_nosca_v_01130090	F053674	MKKVLLVLVLVMAVLAVNAQVTKPTVTKEKPVRAAVMVADLQKTITDNIAKDY
NODE_362399_length_573_cov_5.492146	b3_nosca_v_01817670	F069499	MAIDPMASAPRFPGLPLLKAFDGALKEGLLLDEALGGILTAALHFFDAPVVALLPGAGVAPMTRLGPSGIGAAAEARLLQHLSEILAHGRPKKISGGKLSFFGAPVKVKDQVQAVLGVVLATLPGEEEETEAEEAVRIFARTVGHVLERERTVGTLMKRREEAVALFELASGAFLSLNPDEVIRLTVASLSREL
NODE_365837_length_1003_cov_19.671984	b3_nosca_v_00413560	F008963	VLADIFTLLIPVWILLGLVGLLGVVAVLGRIQNGRYLRPVITLISKVPIFKRGLEKASNAALERSNPELASAMKKMQRSGALRDPNRAQAAMSQLTAQERRALIQVQEEQGMLAPEATNREMRRKLEKAKRDGQRRR
NODE_37703_length_1361_cov_14.185893	b3_nosca_v_00539280	F055309	MATRSCAFSKKWCLLTRDTLDLNRANPVAKARLRQADSPVGPLSDFHSLQYANNIGLPQTVNPLQTLALPRNQRINPQTRSAQEAV
NODE_408183_length_1158_cov_17.609673	b3_nosca_v_01923180	F016316	MPERLRVWLERGESGYWLRDAATGEALRWNDGPLRVVKLAGS
NODE_409489_length_2008_cov_7.839143	b3_nosca_v_02330060	F004844	MHTMTRPGERITVLLFALFLLVLFVALAFAAGYGLGRILL
NODE_412229_length_633_cov_9.350711	b3_nosca_v_00543100	F030296	MHVGCRLSEKEYALVSAAATDANLAPADWFRRTILDSLAPKDEPTTTLLLEEIEALKLIFASTVPPILAGTRMQKDQSAALMRDCDAAKTDAAKKVLRAFTDRKDRP
NODE_419632_length_832_cov_16.991587	b3_nosca_v_00374920	F026449	KKANTNSKSKMISRRQRGSDEAYYTYVEEADDDANKDSSLI
NODE_432646_length_1096_cov_15.935219	b3_nosca_v_01861770	F089596	MFTQHQIAATVPPLAYVPARLAIGWRYERWTHAGALRIFFANKAGREIAFIASLFHGSCRAGMEKSFQLDGVKVWWSDTVDEQQAWRCVNGVKLIAMTFLGPDRFADVGLGRIAASGHRI
NODE_444989_length_1064_cov_13.534775	b3_nosca_v_00370050	F001962	FHRLDLTRQAGFIVTIYDEDGLKLAATMPCSMPADAFAEARKIVDNKVEGPKK
NODE_449457_length_1088_cov_20.794117	b3_nosca_v_01723490	F015236	VAETPDLALLERLREVLDDQPVTETELRGLIEQADGLVRTLGAHIAGSELRISELNEHADSSLTDIAAELQRVEELRPRFEEASSLLADLELRAR
NODE_462720_length_889_cov_19.092239	b3_nosca_v_00206310	F040280	ESVPDSTVRAISRAFNPGVPMYGIVLLVAVFSPLASVVLTFAIAAFYLPSGALFAER
NODE_49430_length_1019_cov_10.429833	b3_nosca_v_01746140	F094344	MKTRHVVALSMLVGLALGALAVQGLHAEDTYIRNLPLDAWTVPVPVPIIPPGSTLDLRPTRSPDATDQMTGYTPATKDSTIPSIGLSIKAPLDDRK
NODE_501705_length_2733_cov_17.132820	b3_nosca_v_02287360	F054454	MEKTGDSAASSSKRKRRPRAAWVKEVRSLRDSDLSPEEYAAKRGIVLSTLKFWMRVLRNEVEARTKSAVPAFLPVSVLHTTEAPAARASVMVEVDLANGRRVRMQVRANTDFKQVSELVDALESGL
NODE_509203_length_849_cov_10.906949	b3_nosca_v_01415380	F014092	LVLIMAVLAVNAQATKPTVTKEKPVRAAVLVADLQKTITDNIAKDYVGYTIKEATSVTANGIVTYEVVVVKDTMTETLVYDNNGVFVKKLPPPTPKKK
NODE_528733_length_1339_cov_7.297984	b3_nosca_v_00684250	F005423	MKEASAIKEFLALVSPGFCMEGDLPAVQVEGIEVRKDGRAIAMVQADGRTLPLRFTFDEGKIARVEVL
NODE_541379_length_595_cov_7.872269	b3_nosca_v_00929290	F021887	MLAEMEEAVETGPVSAFPRRRGLVDTLPALALRPLIAEYTVTFGSTWAPVTQRKHRDDFVRLIDWLEAHDLPVTTASLDFMTLVDYVTDLRSRPKVAGVWRGSPDALGRSLAAGPVQTLSANSVNAYVRPLRSLAIWLVDEGLLALNPFR
NODE_556705_length_4994_cov_12.205647	b3_nosca_v_01561070	F092956	MHDSDDRMLARYQHLYNKALKVKAFQLEKIQRAETRELCISALFKAVVICNTTLKEMDVKQYEAGPEQFLLEK
NODE_575270_length_1893_cov_16.328579	b3_nosca_v_00296380	F012538	RDLLAVLVSEEAAEIGRSVAQIVRGEGWHEAKASAVLVDALVTWLGPAAVHPLGFYANGTGPVEVVARVGNYYITGHGIEDEQDLTINCCQRHRARFSQSRLADLDLMVPNTRFTMGNPLAKRAAERVGALLTEEIDPEIARVVLGA
NODE_589_length_1683_cov_12.374926	b3_nosca_v_00176970	F037996	DPAQIKAIEPEKGEKLGTLGASLTKVLQGDHRGAHMAVKRGVIYVSLGPIPGARRASGPR
NODE_591976_length_1061_cov_7.115928	b3_nosca_v_00888950	F010859	MSVGGRGRVRERVLRRAALVAGVLVLFALLFLVSGHWVLGIIVGVAAAAAVWVFLLARTV
NODE_605635_length_555_cov_11.740541	b3_nosca_v_01061790	F006577	LLELNGARSNPRAGVELSRLGAIHDELLRKAQANPRKPRPVPPRVSPVLETVTLVLERAGKPMPAREIRAAACELAGEPLLSKSVKAALSANVAGEHPRFRRVRHGVYQLARDVRRCTS
NODE_608738_length_4647_cov_22.409081	b3_nosca_v_01786880	F106196	GGTMAEDDEQNEIIKCTVTCPECGGEIVCSHEDAKHEGKHRCEKGHEWT
NODE_609010_length_930_cov_26.569893	b3_nosca_v_01840850	F008108	VVAGCNGGTVDRHALTNDAATLDSIACEGALLAGDVARGRTTTYFAREQAEELRIESSNLADALSRRKALPSIERRVREKAKHAAVLAVTLQRLHDHPSDRAVGAAVASALKKLGSCT
NODE_72467_length_612_cov_10.687908	b3_nosca_v_00010410	F042097	VKATPMRLNDVYFLPGDDPSGWKVTSSVNNNDSNNLGSFVTVTLRGKRLGHLDFEYQISASKTGNDILVSLGRSNNTGKPVDVDDMDYFVSRDARLGGTTDKWITLGTQSRNRDYYELWSVMNLITPKTYAVNHVVRDSDTGNSLLMGHVTALKGASRFEVRSGWTGQVPDRMQVRGYCSYKIVVPPGKSFAGEKLLIDFNQDALSAMQHQADLIAIAHD
NODE_88220_length_708_cov_17.783897	b3_nosca_v_00709950	F012999	MDYELAKSLMDAGFPQIGKGSLIGSLNKLVWRSGDRVYVPTLEELIEACGENFVSLHKQHDGWLAYANYDQSCFAKTPAEAVARLWLTLQKR