3300025814: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - Muzzi_PWC_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025814
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101364 | Ga0210101
• Sample Name: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - Muzzi_PWC_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 300931930
• Sequencing Scaffolds: 48
• Novel Protein Genes: 52
• Associated Families: 40

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	6
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales	2
All Organisms → cellular organisms → Bacteria → PVC group	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia	4
All Organisms → cellular organisms → Bacteria → Proteobacteria	6
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales → Chromatiaceae → unclassified Chromatiaceae → Chromatiaceae bacterium 2141T.STBD.0c.01a	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	3
Not Available	12
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	3
All Organisms → cellular organisms → Bacteria	6
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Dehalococcoidia → unclassified Dehalococcoidia → Dehalococcoidia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Methyloceanibacter → Methyloceanibacter marginalis	1

Ecosystem and Geography

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

Associated Families

Family	Category	Number of Sequences	3D Structure?
F003627	Metagenome / Metatranscriptome	476	Y
F004052	Metagenome / Metatranscriptome	455	Y
F004928	Metagenome / Metatranscriptome	418	Y
F005789	Metagenome / Metatranscriptome	390	Y
F007779	Metagenome / Metatranscriptome	345	Y
F008223	Metagenome / Metatranscriptome	337	Y
F016304	Metagenome / Metatranscriptome	248	Y
F016664	Metagenome / Metatranscriptome	245	Y
F016971	Metagenome / Metatranscriptome	243	Y
F018371	Metagenome / Metatranscriptome	235	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210101_1000020	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	61429
Ga0210101_1000065	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales	35351
Ga0210101_1000102	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	29431
Ga0210101_1000157	All Organisms → cellular organisms → Bacteria → PVC group	23970
Ga0210101_1000169	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	23315
Ga0210101_1000196	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia	22236
Ga0210101_1000207	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales	21638
Ga0210101_1000255	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	19094
Ga0210101_1000285	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia	18172
Ga0210101_1000339	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia	16253

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210101_1000020	Ga0210101_100002018	F005789	MATAVTLDTSPLNVLRSMRGSIVGARIAYPEVLHVEIKDSAGELWRLATQDAEWSPPDPLELVGRSVKDADIDEKTGELRCQLSGDLLLDVKPTAREAEDDPPNWELITPGGIVLEFGPGVRWQIGSADSRASSRA
Ga0210101_1000020	Ga0210101_100002019	F032367	VSRKRDIKQFRQACKEAGLTVQERYEASEGLHAEKGSGTVQRDMSYRELLAWLRQWKG
Ga0210101_1000020	Ga0210101_100002022	F005789	MATAVTLDASPLNVLRSMRGSIVDARIGYKDVLHVEIEDSAGELWRLATQDAEWSPSDPAELVGRSVDDADIDEQTGELRCKLSDGSLLNVRPANRETEDDPPNWELITPGGVVLEFGPGVRWQIGNADSRAYSRA
Ga0210101_1000065	Ga0210101_10000653	F019205	MFDTKKNFSGHLADAVDLTIEFATLGEYGLEPVDPRPRACEARQRGARRSTGAWTAAIDRFAARS
Ga0210101_1000102	Ga0210101_100010212	F027211	MVRTYWLVPVFNEASGHLGLQPFARTDQVEACRPRAMSLPIVRCRL
Ga0210101_1000157	Ga0210101_100015717	F029294	MTQETGETRDAIIEDDNKRIQDIVDFYKSRTDPYWIVVFAKPLKQQVDGKPTLIKHIKPYFTRPSSQVGAIIGEVDNKSGEIKWEVNMPQRPFDFDALKGLGAQECNEVFTETTSIPNAYLTK
Ga0210101_1000169	Ga0210101_100016912	F016304	MIGWSAIRPVLVGLLLIADAFTVGALLVVRPQGWLPPLVAFGALLVGLVAFEGWAIRHRHDD
Ga0210101_1000196	Ga0210101_100019611	F003627	VDRETSRRDIGAGLTAGAFAAAVFALCFVAAMLYIAS
Ga0210101_1000207	Ga0210101_100020711	F063671	MMNSTTPHPWMTRVALRISASSGLPLQPAKAAPCVLDLLGHAPPQAHAAMKSTI
Ga0210101_1000255	Ga0210101_10002554	F054019	MPTIIVMSKSAAERNTLETLREDVQPVHLESEHHAAQLIERIGWAVADAEADEGTRT
Ga0210101_1000285	Ga0210101_10002853	F063671	MPDLTTPHTWMAAVALRISASSGLPLQPAKAAPCVLDLLGHARPQAHAAVRSGI
Ga0210101_1000339	Ga0210101_100033913	F003627	MDRETAKRDLTAGLVVGGIAAGVFALCFVTAMLYIAS
Ga0210101_1000365	Ga0210101_10003651	F029006	YFLGDPDLQYLAWLGDLKLYIVAAAIALVSMPWIAEQLDG
Ga0210101_1000864	Ga0210101_10008649	F033045	MKISELELPQHLFTDEITSPGGALTRLIAPDKLVSWAEAGRGDAISGLCHALYERKLASIDAWERDRILQLEAEWMAAGNDEDMPGFKYANVRHYPMTREAVAREAELKRARVKKRMHQHQTAIEQLVQEAREFLSAYVAQQDEGDMLAYLMGFAVLIAAGYALFY
Ga0210101_1001349	Ga0210101_10013497	F055469	MLKRTVVIFAAAAFFGGAVPTQTAQAGDDIWDLMNPSWWADEVFDNNDDDWRYYRRHYYNPYWGAHYGGNRPQYVIV
Ga0210101_1001454	Ga0210101_10014547	F055469	MLKRTVVILAAAAFFWGTVPTQTAQARDDIWDLMNPSWWADQIFDDDHDDWWYYRHHAYSPYLGAPYVQRPRVIVIQPPETEAQNPETRPPE
Ga0210101_1001749	Ga0210101_10017491	F104552	MMVCRASTLFLSRLAYYQLWTLLLLGLLVPAQAAEALKPDALPQAQATLERLEQQLATARTANAQELKTLRKEVATVRSTAQDCLQQAEPKIEILDSELAILQPDKPKDTQKKTAQETQPAEQPEAPVSPAIAGQLQELLSSKASLEGRIAICKLLLLKSNYLESNVDDYLRSVQTRQLLARGPTLVSVLQENLDERKQWLDFTSQLAMTSTGWDAIRPIHLAGASAVGLLGFILGRIVPRRLRVRAARMKVGEEEVSAGLVQAVMACGASYA
Ga0210101_1002149	Ga0210101_10021495	F029294	MQQTGETRDAILEDRQKRIDAIIDANKSRQDPYWIVIFAKPASKYVDGKPALVEHIKPYPIRPPAQVGMIIAEVNNKTGKVEWEVNMPQRPFDFDALQQFGAKSCNEVVTETTSIPWAYETK
Ga0210101_1003271	Ga0210101_10032715	F090405	MKIAIATATLLALLLAGVASADPPDCARQLRQINHFEDMVARAEQLGNEEWADKTQMHLDLLEDRLASRCPNYTDRDERQEAARQFARLLKVAADAAVTFFTMGAF
Ga0210101_1003398	Ga0210101_10033986	F084486	MRLARFFETINKHRRALDLAIEQNFDGLLDAAGWRQAFEPPEPEDANRTMVVTGDHSAILNAYIEILKASAGSRLVGLLPHRRPHADQAIEAVRADKGLTNVQATLLNELYVLEGRLEHASPDVSAEEVRVAVEKLRASLPTLVESLRAWLARHGIEFG
Ga0210101_1003809	Ga0210101_10038091	F074893	MISSRLEASADNGALTIRINGPMDLLLTSALREFCHDTGTAYRRYIVDFQDVSIVRDSGLALLLMLKRGLSHTGATLHVT
Ga0210101_1004554	Ga0210101_10045542	F004928	MVQALHSKETEPEHTIEIVVHIAEKLEEQQRGNLVASLGNNDGIVAAEFCPLRYHLMLVRYDRDLYSSQDVLAKVNSQNVNARLIGPV
Ga0210101_1013001	Ga0210101_10130013	F032661	MTERRKVERRRYEAHTEFPAIDHQGDFIMSERRHLSTRRAFDIFVDDVDLPTVFIDINKQMY
Ga0210101_1018627	Ga0210101_10186271	F039145	MNNFLMSLLLPLILLTGCSQEGVQAPLELSAFIEELQGNGVDGTLTIRGPVNEDMEYVAEYAISRYASTRIISLFKCKDAEKAAANLAEALKNPKLSGQASNGTFIMAATFYPPDDEAVEKIKVLFLAHEFE
Ga0210101_1020441	Ga0210101_10204413	F057346	MEAQGKRVGNWTPDGEVERARLRRDYLELAPAQRMKQVCDLSRFMSRVAEAGRRHRGA
Ga0210101_1030243	Ga0210101_10302432	F063671	MTTPATRHTWMARVALRSSASSDLPLAPPKAASCVLALLGHAHPQAHLAAEEAI
Ga0210101_1032983	Ga0210101_10329832	F104552	MMICRGSTLFLSRLAYYQLCSLLLLGLLVPAQAAEALKPDALPQAQATLERLEEQLATARTANAQELKTLRKKIATVRSTAQDCLQQAEPRVEILDSELAILQPAKSKDTQKKTADEAQPAEQPEAPVSPAIAGQLQELLGSKSSLEGRIAICKLLLLKSNYLDSNVDDYLRTVQTRQLLARGPTLVSVLQENLDERKGWLDFTSQLAVTSTGWDATRPIHLAGAAAVGLLGFILGRIVPRRLRVRAARMKVGEEEVSAGLVQAVMACGASYAPILLA
Ga0210101_1039321	Ga0210101_10393212	F016971	MNQVAQHLPAEEKCAVEVVVYIKKSLGEEQQDLVISALEQTNGIMGAEFCVMRNHLVLAKYDKDVMSSQDVLKSFNSLNLEARLIGPI
Ga0210101_1041662	Ga0210101_10416623	F019205	MFDSRKSFSSKAADAADLVIDFATLGEYGLEPVEQPTRTCEGRRRIGRPRSTGAWTAAIDRFATQP
Ga0210101_1043345	Ga0210101_10433452	F023595	MVDFGSGQGLSDFETGGIACYFEDFKRAKTPPRAER
Ga0210101_1043379	Ga0210101_10433791	F074897	DPTIRRIAEQLAGEALVSISVLADELRQYVKELNSHHENAEFVDYDVAKRVGSLCWRLLAALPDEPDERQHRLTQLAINYFVLAEDAQDDNHSLAGFEDDLQVVTAVIHELGLGHLLEK
Ga0210101_1044599	Ga0210101_10445991	F081350	EPIHPACIHALTMHQGDRAPVTTAVSLEGCASSARSKPKVHYEPGDLAVIEDDELLGGGTFGYRVINQLDNGIFGLIVRRVLPDGQERVSLAAVEIVVRPMIRQGKIVRVRQIELLGELWLPGMELTSFRSMGNRVHFAAGTGPNRIERDVDFTRLGNLRH
Ga0210101_1049093	Ga0210101_10490932	F008223	MNLFTRLFGKREPPPSPQDEVAGILHRFTTATIMGIDREDLGRYPAKQRKVMAFHYGAIRCLAQEYGLDETESMAVFVMFVNKYFNLPVSETGSISERLEGFRENAEERRYLEAGADVFRRWHEQEERRAPLELGEMLRG
Ga0210101_1051146	Ga0210101_10511463	F019205	MFDSKKTSSERVADAADLIIDFATLGEYGFEPVEPAVTACEGRRRSYNRRSTGTWRSAIDRFATQH
Ga0210101_1056271	Ga0210101_10562711	F018371	MDYSNIIKPKRLTDMQEMEVHVTGPEGANRLFMHSGMAEVEIRGGLPHPRWTLEVVCFEVGRTYDLSEESIIKINASAALAGGRMDGVASFAGWQIFGAAGELDNESRRVRMNIAAGARDTQAFLEQISFQVNILARVKE
Ga0210101_1056504	Ga0210101_10565041	F004052	MRILTLPVQLTLTALLCSCDQQNSVSDVDPMLGLECFNSHHLPPGTQYEGIEKLAENVLTIRIMNGVEVVTLDCGLNPDGSLRSTGE
Ga0210101_1059391	Ga0210101_10593911	F048676	YSRLCETASDAVDAVKLEIQQGFKFLKFRMSECLKNMIK
Ga0210101_1074786	Ga0210101_10747861	F055297	KEIGPDAAMRFKQSPLRLHPGEQRRFSILFDPMRVAEGTDVALKADPGITARFRGAGRVPRPGSRGWSRIGGRVRAQASAEPGSRLTVTAEAAGHLAELEVLIVRHRASGWVREIARKDVDSQIEAEFDPESGVVTVYEGRREFRALERAARRAGLPRRRVREYLPYRMLEVEVAANAVYAWAAERVLERRFTESLPSDPARYAAAVRLEAQALRHRAHEKLMRAFLDPAVFEGASVPSGRAGR
Ga0210101_1082713	Ga0210101_10827131	F055469	VPTQTAQAGDDMWDLMDPSWWADKMFDDDHDDWLYYRHHRYSPYWGAPYGQRPRVVVVLQQPEMKAQNPETRLPE
Ga0210101_1087007	Ga0210101_10870071	F070135	GQHMYSCDLLGSYALNIPLDSNGQYKLQVYADGFAPMIQKFDEFKTLNDVRMTRAVEC
Ga0210101_1091006	Ga0210101_10910062	F031074	MASAIRKLDIVVGEIVEIDGRRYEVVPDRMGGVTIEPPITPVAELEKRWGTMPASDEDFERLTAADPSDGEG
Ga0210101_1096056	Ga0210101_10960561	F099325	MRDALFRFWRWSQKSPAERRAAKARARFWVEMREGQLEAEAHSRP
Ga0210101_1104764	Ga0210101_11047642	F003627	VDRELAKRNMSGGLIVGGLAAAVFALSFVAAMLYIAS
Ga0210101_1112778	Ga0210101_11127781	F051143	MTTLEAVAYANRLSNRLKSDNCTDEERQNGVDILGRLTERVSFLKITLEPPTFCRIGWNYFVEPGGRSSN
Ga0210101_1119523	Ga0210101_11195231	F074893	MVSSQLNAVAGDGSLTISINGPMDLLLTRALREHCQDNGATYHRYIVDFRDVSIVRDSGLALLLMLKRWANRAGATLCVINGNRDLMRRCFSLGIGPA
Ga0210101_1129802	Ga0210101_11298021	F072362	MHKLFAIGVTIYLVGDPSLSMLSSFSESRDLIIASVLALIAVPWVVSQFDN
Ga0210101_1134503	Ga0210101_11345032	F064729	MGELNEWIRYWRKTFAKCFKMHKDSRAHKQAYAELSDYLNKVEASAEQQELDATVLWAVKFMQRMHELERDMGLFVLDKKVPSARPSGGEHKTGD
Ga0210101_1138733	Ga0210101_11387331	F023596	MSSKLLQTLLYAGAGVIALLFAKLMFDMSRSMSEMTGYVGAMSQDVREMQNSMRTMNDSLLRMEKSVHGLGQAFNQGSKQFQQMNPAGMMQQVLPDSGQRTR
Ga0210101_1148568	Ga0210101_11485681	F007779	RVPITRFAKTACVLQGDGAMFEALLEKRAIQREEHRAYQERVDDCLAVLFCGFPEGVLPVLRHRVGNAGLVRRAQAEGTDARSCSVQLAVLLIRKLIASLSDQERQDLARAFLQNDATNPTYKGFKSMFWVVERLEVSPALVSYLNTEVAGQLRGMSQQAIFGSWVEGQVSGVMGRLRERCLEEAEFKADLWR
Ga0210101_1154803	Ga0210101_11548031	F063710	MKKPRQRSLRVRVEHEPNRFSDDYLERIYEQLHPTKSRKVTPDKNNKQGEVELQKG
Ga0210101_1173697	Ga0210101_11736971	F016664	MDQVVKEMPVLDEVKDTVEIVVHIAEDLDDGQRHNLVVALEQSEGITSAEFCPLRYHLMLVRYDREHYSSQDVLGAVNDHKLEARLIGPI
Ga0210101_1185296	Ga0210101_11852962	F087388	LAREIIRRLDQGEPLESAISMVLTGEGVEDDVLVELQVAGLRDAVIHEAFHELLDWHANFGGLAEFLEIDEAIHRTAERIGHDFDQDLPDHPSEPGARLVH