3300004021: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - China_Galinas_PWB_D1

Overview

Basic Information

• IMG/M Taxon OID: 3300004021
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101334 | Ga0055449
• Sample Name: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - China_Galinas_PWB_D1
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 804550212
• Sequencing Scaffolds: 54
• Novel Protein Genes: 55
• Associated Families: 51

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → Desulfosarcina → Desulfosarcina ovata	2
Not Available	21
All Organisms → cellular organisms → Bacteria	5
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → unclassified Myxococcales → Myxococcales bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Actinomycetales	2
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. WSM3983	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Nevskiales → Sinobacteraceae → Nevskia → Nevskia soli	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Methyloceanibacter → Methyloceanibacter marginalis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	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): 38.015041
  • Long. (^o): -122.501831
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000816	Metagenome / Metatranscriptome	879	Y
F000842	Metagenome / Metatranscriptome	865	Y
F002359	Metagenome / Metatranscriptome	567	Y
F004052	Metagenome / Metatranscriptome	455	Y
F004591	Metagenome / Metatranscriptome	432	Y
F007779	Metagenome / Metatranscriptome	345	Y
F008223	Metagenome / Metatranscriptome	337	Y
F008361	Metagenome / Metatranscriptome	334	Y
F010065	Metagenome	309	Y
F011352	Metagenome / Metatranscriptome	292	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0055449_10003308	All Organisms → cellular organisms → Bacteria → Proteobacteria	4664
Ga0055449_10005947	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	3506
Ga0055449_10012146	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → Desulfosarcina → Desulfosarcina ovata	2491
Ga0055449_10024590	Not Available	1791
Ga0055449_10024862	All Organisms → cellular organisms → Bacteria	1783
Ga0055449_10037239	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → unclassified Myxococcales → Myxococcales bacterium	1485
Ga0055449_10041532	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Actinomycetales	1414
Ga0055449_10054541	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1251
Ga0055449_10060229	All Organisms → cellular organisms → Bacteria	1195
Ga0055449_10067483	Not Available	1134

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0055449_10003308	Ga0055449_100033082	F049003	MGDYPEAMSQATVGSVSTDIERRAALKAWLRRRLIEGERPREEWRQLLEATWDHVLATPLRELIHEDSAKALADALIDGAWLTELARPTVVNVARAVIAELREDQAPIDHFLPAEAQERLDAVLARPGLVHPDWVRAMFRGEAAEAVLNDALYRALKDFSTLLPRLMVKVSPVGRFGMLGSAGMFAEKLIEELEKRIEPEIRSFLAESSDRILQRAGEFTISKIDDPASIEFRTNFVRFVLAKSPAFFLEATDDELVADIGTIVELSARHVAEMPELLAEVHHWIDRGFGHAAGKTLAEALEIESMEIHPPIGAIADATWPAFIVVLGSPQAQAWTDRLVDELFDEYERI*
Ga0055449_10005947	Ga0055449_100059472	F054249	MTRTRTRWLVPAVELILGLLIAGSLLGQSASPAQVAISFGVVLGYAIVLVVLQSRSAVASLLSGMPRDERWDTINLRALSLASQVLAVALVAAFLGTQLHGGEAIPYALMGGLFAIACLGGVAWYRAWS*
Ga0055449_10012146	Ga0055449_100121464	F045104	VLIDPVTQRQLSLSLANTEQAHSALLAWLAERSAHLVIPNTLLAEPFLNQTSHTPVVVWIAPNALLEAIRLATGLTTRAPKQTAALLARWPTAPALRPFLRRLNTSCSPDQLSLL*
Ga0055449_10024590	Ga0055449_100245902	F071802	MGAKTSKLMHANLITKILIVLVILNIAGDVLAAAFFLWDPSLGELSVYGGLIASFAGKNGAVMITAAILLGYAVVYAVSVFGLLSKLKWALPLFIAVSVVNRALALGVIFEPNVAWLIWSAWKLVIIALAFYLWRKT*
Ga0055449_10024862	Ga0055449_100248621	F025772	MWFTFVTARLFPSLSFQPHLTAALLSSGSVANSPTRRVGLSPTLRSASLAQTACPVVW
Ga0055449_10037239	Ga0055449_100372392	F081351	VTRSVARAPSSAARVHNECTTNDKQRQVAPTTREPVSGRRNCRWFFACEKKCSARATFRGAKPITRVMDERERSDLTGRLRKAAEKMPYPYFLLRLEDIEAWLKAGYSVKSAWRIYCEKSVPFPGSYRSFLRYCREHCESAPPVRRRAPKAPKAAPHRPVSVLGQTRFPPPLDRPPGLTREQIDRLMDPDRHLDPKR*
Ga0055449_10041532	Ga0055449_100415321	F004591	MRNPPILISVIGFFAALAGFAHLFFGLRDLGFDWFGALGDLPAFESVGIWGWMAIGMAVLWLLIAFGLWALQPWAWLTAVIIAGFSLFEAFIAFFQFPGSGVGF
Ga0055449_10054541	Ga0055449_100545412	F010065	MRGESGISLTGLYVCGAIALVMLVLKLSVIDTWSWWRVMLPLGIIVGFNVTNMVVAFIYLSFAHIPERPDGDEAEVLEPHTLDAHYVAAMIFFVVFGDNLVRWIEGSETSHWFWLFSGKIEALTVFGGLSVVALFSYWSRLRRVLKASG*
Ga0055449_10060229	Ga0055449_100602292	F000842	GTLGKNIAEQERPSLAAMSGKDRSYKAGRLKSGGARRESERSIVPGKACSKTRWREGALL
Ga0055449_10067483	Ga0055449_100674832	F070131	MKGKMLKKIGIIGVLTFCFLLQVDLAQGESKIITQYKKKSNVPMDIELNFSSVPMLNERAVLDIEIRALKDAPNTLIDIDLPRDGFKLISGNTQLNEDLSSGSTAKYQLEVLPVALGQYKIAASATSGVTDYIFGKREVLYVNIGDGFSELSKTSFNSELASHRSGAIKIGDLSETPTHVSTDQKSIENEEAFYFAAPGPGQIAVKGYWFYQDKDGVDRPLRDAKVEIWDSDTSGDTLLETTHTDNSGYYASGNISNNDSEGGGQDIYVKV
Ga0055449_10075484	Ga0055449_100754841	F008361	ELEKATLAIEKAETSKDRLDASVELKKATARLEAINYLS*
Ga0055449_10082140	Ga0055449_100821402	F077317	LVMEELITKSSDETSWYENEQPIREFLESFRKAEILEADDQAEELSWINVVKKS
Ga0055449_10087515	Ga0055449_100875151	F041204	PSMPNPLLEPTQEGRYALPMAVIVNWNGVDVPEELKALEKGRYVLVPIDEPPELTEEQEAGLEAAMASIRAGEGLSRDEAFAKLKASLE*
Ga0055449_10088566	Ga0055449_100885661	F035989	MTPEDLHHLRRIGRAALGSTDYFGRFAEVRGAHYRRGYDDELLYNLAAEVIEAVNRASGNAQRLPWTNLNGLTVNRPGKDT
Ga0055449_10099338	Ga0055449_100993382	F049002	MAKADYDKAQTELINAIEKDAPCTFDNPIPVLVTLDNGVKYEGLAYEVQAKSDNFPDGLVMVRSGSTDIGVPVSYIRGK*
Ga0055449_10105449	Ga0055449_101054492	F045771	MTRRIFLDTEWTRPPWSKRSELMWIGLADEAGRSWYGISSEVDIDPSTNDFISGVFRLITPDEPRLANEEIAAAVIDFCGDVDEFWAWIPTMERFSEWFGLGEEAAEVYARCWDWDLQMVRS
Ga0055449_10109459	Ga0055449_101094591	F033045	MKISELELPQHLYAETTSPCGATDKLIAPDKLVSWAEEGCGDAIFKLCQAVYERKLASISAWENERVQQLEDEWMVSGSEEDMSGGKYVHVKHYHTTREDVVREAELKRANSKERMTEHQTALEDLVAEARAFLSAHEVYPEEDDMLAYLLVLSVIVIACYALFN*
Ga0055449_10111623	Ga0055449_101116231	F048318	MATVENVRLTITDSNGKPGFSRIAYSYELHPSELDCSEQREYTVKTDLWGEDLVDDDVLAWGKDEHKVKFDSARPGEPITVERVFEIETKVLDEDVFGDDEVYAMVEASSGLGSDAGGEDPVMGRSNTVIGDF*
Ga0055449_10119614	Ga0055449_101196142	F074891	MSAVTHDVIVKRSRGKKRRKSMSALRKLRAAMARRKLEEMHEEEILKEQIYDVFADSEESS*
Ga0055449_10123984	Ga0055449_101239841	F011352	NQVLNNHEGLDLPGRAAARENAVALAANLRNGDMMPGFKWGGWFVSVVDEHGHKIEEVPIADEVGER*
Ga0055449_10132145	Ga0055449_101321451	F045104	VLIDTLTQHQRALSLANTALAHTTLLDWLAQHNAHLVIPDTLLAAPCLNQASQIPVAVWIAPSPLLEAIRLAAGLTTRPPKQTAALLARWPTAP
Ga0055449_10138811	Ga0055449_101388111	F031307	MSNMHTYFGFKNGKLISVLHTLDEDIKKAVDCTYFITEPQEVDKQIEQWKKENV*
Ga0055449_10140268	Ga0055449_101402682	F016664	MDQAINRVPAAHESVNAVEIVVHVSENLEDQQRRDLVAALEQEDGIVSAEFCPLRYHLLLVRYDRNRYSSQDVLQAVGTQKIQAR
Ga0055449_10144286	Ga0055449_101442862	F105198	MKNVFLALCLVLFAGQASAYFTWGVGSQTCNFYVSAKAEYDHARDQRTHLAHLNWIKGFITGINWSRESDIARNLSIETVDQWIDAYCRANLDASIGEA
Ga0055449_10148674	Ga0055449_101486741	F102142	ESNETVRDLLKASLVGILAVVITVIPFEQFVAQFAGLSYDEFRGGMPTLYLLPLFLIYAATGLVLARMKQNLNIGRRGAFLILFAFYYFIVSILPDIEGLIYLPDFTFLSAMTSGLILAGAVVGLIIYLWKQDENPDAKPGEQIKSHFSSRSVLSWVWRFFLVWILFYIATMIVGILAMPFNGSYLDDPLNPLGMVVPSMGTLFAITQFRSLIYILVILPFIIFWNSSKRALFLYLALILIILYPLLGDGLAYFWPAMYRL
Ga0055449_10172274	Ga0055449_101722741	F002359	VENIGSPVPGLPSGPFFLSYPSLLLRTNMSHYDIADMVTGVRNMIEAADIRPGDQVLLLADRRSDPPSMEAITACLKMIGAEPMALITEPISRYGHVPQAVLQAMHASDVVIWVWPVFITFTPDHRAMGRKREESGSQLQEKRMKPYFVYFEGAPGLLARDYAKFPNKVLWKLAEKVRDVVAAGKVVRIEDDLGTHLTATYDGSRLYGMQFRAGDPPGRCHFPWGRCGVFNGSGKADGEVYLS
Ga0055449_10175178	Ga0055449_101751781	F046383	FTGLVLGVLLGWALVPASALACEPEQDGCLGCDDDELPVCLQAFVLQICQESGNPANCDTGRAYDDVERYVLISTGSHMSRIRSMVRSARKYQIH*
Ga0055449_10182614	Ga0055449_101826141	F048318	MATVENVRLAITASTTKTGYSDLAYSYELHPSELDSAWNREYTVRVDLWGEDLIDDDVLAWGKDEHKVKFDGSGPCEPKKVDRVFEVETKVLDEDLFGDDEVYLTVEASTGLGSDAAGEDPVIG
Ga0055449_10188656	Ga0055449_101886561	F074799	MDDTATRNKIQQHVDAVVRGDMDAAAADFSEDLRPQLPQIAKALPQPVTSAEVLSVEVGEEEAVATIRWTGETGVVTIRSRWQDIGGHPLLVHAEPVD*
Ga0055449_10192292	Ga0055449_101922921	F055469	KMLKRTVVILAAAAFFWGAVPTQTAQARDDIWDLMNPSWWADQIFDDNHDDWWYYRHHAYSPYLGAPYVQRPRVIVIQPPETLAQNPETRAPE*
Ga0055449_10194436	Ga0055449_101944362	F000816	MSYKKNTRPNTMRKPGKRVLIGETREEEAARLEREIAAHPVTKCEPGEYKPTSSRPGWSNKPFVPQKDQAIAEGIAKKMMRKPKA*
Ga0055449_10197528	Ga0055449_101975281	F056029	KRTAPMDLFMSWARSTVANAERALGRSDEWFDRILVGILVLLAVAVVFLFAQ*
Ga0055449_10200912	Ga0055449_102009121	F004052	MRILTTIITLALTSLLCSCDQQNSVSDVDPMLGLECFKSHRLPPGTQYEGIEKLTENVLTIRIMNGVEVVTLDCGLKPDGILKGIDR*
Ga0055449_10202611	Ga0055449_102026111	F034932	MRRVRIESDSHDLIAGFVAGVEWVNDSAIAVVDLDCRSQTAFVVVEDLDGSGEDEVLRLTSDGIAGKE*
Ga0055449_10203266	Ga0055449_102032663	F044506	MMEQLDSGVMGSGILQYWIYGPATGWIDDKIKVAIILLKTNIPSFHHSIIPISGKIRKPQNATIFSVGCRNSETLITGRPNPAGRFDKT*
Ga0055449_10204513	Ga0055449_102045131	F077315	MAICKASTHFFSRFACCQVWVLLLLGLLIPVQAAEALKTDVLPQAQDTLERLEQQLATARTATAQELKSIKKEIATVRSSAQDCVQQAEPEIELLDSQLAILQPEPPKDSQAKTAEETQPAEQTDAPVSPAIARQLQDLQGRKASLEGRIATCKLMLLSS
Ga0055449_10205939	Ga0055449_102059391	F021307	MNRIFYERRCRCKEKKKISRTPKRKLSARSEGKALQYPDEMISKTFQIRYDKKLSSLAKFILNSFKNKYIYYAIDDILYLFKSNPVERESLLGLLYSPVLSLHNNL
Ga0055449_10207060	Ga0055449_102070601	F029006	MKEATMNKIIITLMAIYFVGDPHLQYLAWLGDLKLYIVAA
Ga0055449_10208757	Ga0055449_102087572	F057781	MKLPDLQMLAHWLDPALVAAVETRRREKKEWHRCRKLATLQTLWLMLAVSLD
Ga0055449_10219437	Ga0055449_102194371	F055469	MLKRTVVILAAAAFFWGTVPTQTAQAGDDMWDLMDPSWWADKMFDDDHDDWLYYRHHRYSPYWGAPYGQRPRVVVVLQQPEMKAQNPETRLPE*
Ga0055449_10230405	Ga0055449_102304051	F084436	GYTWSVPQKIFEDITLNADGSSSEEFWGFWRFKRGRGIGCTKPVLYATGYNDGDSKVGLFASTDGIEWHKRGIILDSYLDVPSEAELNFFGSRAVALVRLDNQGILTDGQTAICTADPPYDAWECGRRLEQRFDGPTWIVRRRRGKVRNFVVARKHLPCTRKRTAVYELRGDLADPAAEIEVCEVAELPSSGDTAYASVVRLNHGRNLLSW
Ga0055449_10244522	Ga0055449_102445222	F062769	WIGSATRPALLVARARVYQARRQAPEERPVANAILKRITQELAARGAFAKPRTV*
Ga0055449_10255097	Ga0055449_102550971	F064729	MQDRHGRWVMGELSEWIRYWRKTFAKCSKMHKDSRAHKQAYAELSDFLNKVEVSAEQQELDATVLWAVKFMQRMHELERDMGLFVLDRKVHSARPAGDEHKTGK*
Ga0055449_10268476	Ga0055449_102684761	F069741	MENIFFDVDQFSSLDKIEQARRLEEAERQIDEVQRAAADDPDSMNWVDQQRQYLVDMQHLIFEC*
Ga0055449_10273056	Ga0055449_102730561	F063710	MNKPRERSLRVRVEHEPNRFSDDCLERIYEQLHPTKSRKVTPDKNNKQGEVELQKGSGGRQ*
Ga0055449_10274766	Ga0055449_102747661	F078730	VDYSNVIEPNRLTNMQEMEIHVDGPDGANRLFIYSGMAEVELRGGLPHPRWSLEVVCFDIGRRYDCDNGEDIIKVVTT
Ga0055449_10276822	Ga0055449_102768221	F007779	LWHGNISCKSCLGCSYSGDGAMFEGLLEKRATHRAYQSAVDDCLAVLFCGFPDSLLPALKPRLGTSGLVRRGQAEGTDARACSVQVAVLLIRKLIGHLSEQERQDLAQAFLRNDLSNPTYKGFKYMFRVVEQLNVAPALVSYLNTEVAGQLRGMSQKAIFNSWVEAQIGGVMGQLRERCLAEAERKTSLWQ*
Ga0055449_10292384	Ga0055449_102923841	F008223	PIEEINRIMARFTTATIMGVDRDDLGRYPAKQFKVMAFHYGAIEYLARRYGLDETQTLGLFVAFIDRYFNMPINETGSISERLQGFQDNADEHRFLEAGVDVFRRWHEQDERRAPLQLGQMLKDA*
Ga0055449_10300658	Ga0055449_103006581	F012442	MNKNIAVVLLLVLAAGCSSNPRDEAYAPPPMDPTRTVSEQVCTRTITVEGGNLLCHEVTEAERRAKIAEEQRLARARKEAAARAERERLE
Ga0055449_10301441	Ga0055449_103014412	F051517	EVDGLDALIEQTREAGYRFLSVDAKPIQRPFGRFVFAIDPDSVLVEFAEPNGDRNGRRGRR*
Ga0055449_10318269	Ga0055449_103182692	F094484	MGDPMKRLALALLVTGLMAATAHAAESQGRRMIVFALYGAAGTSGSTATTTVIDFTTQVACREARDELRRHAKAPGFGLFATCVEP*
Ga0055449_10340773	Ga0055449_103407731	F016971	MNQVAQHLPAEGKCAVEVVVYIKKDLGEEQQNLVISALQQTDGIMGAEFCVMRNHLVLAKYDKEIMSSQDVLKSFNSLNLEAKLIGPI
Ga0055449_10359656	Ga0055449_103596562	F062769	SGDTPMTDLDAFSAWIGSATRPALLVARARVYQARRQAPEERPAANALLKRIAQELAARGAFAKPRTA*
Ga0055449_10360329	Ga0055449_103603291	F099226	MANIAKIFTVAVTLVVGTGAISGIALANTNPLYPDRLKNPHVSLPSARVGSGIPSPYRIGGRIDEPRVSLPSARVGSVIPAPYRIGN*
Ga0055449_10364689	Ga0055449_103646891	F090229	MLRAMPTEGHYARQAALYKLSPREIKAAWIAGAVTFVAMIAIVLATIGDSNPPTPLGCIRAEVAGIVGAETISGCGTEAEMKCAHAANFDSPRAKTVVA