3300004056: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - Muzzi_PWB_D1

Overview

Basic Information

• IMG/M Taxon OID: 3300004056
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101363 | Ga0055478
• Sample Name: Wetland microbial communities from San Francisco Bay, California, USA, that impact long-term carbon sequestration - Muzzi_PWB_D1
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 745987756
• Sequencing Scaffolds: 40
• Novel Protein Genes: 41
• Associated Families: 38

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales → Ignavibacteriaceae → Ignavibacterium → Ignavibacterium album	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Synechococcales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales	2
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
All Organisms → cellular organisms → Bacteria → FCB group	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Marinobacteraceae → Marinobacter → Marinobacter santoriniensis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
Not Available	8
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium ADurb.Bin063	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Sorangiineae → Polyangiaceae → Chondromyces → Chondromyces apiculatus	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → unclassified Myxococcales → Myxococcales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Oceanospirillales → Oceanospirillaceae → Amphritea → Amphritea atlantica	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Desulfuromonadaceae → Desulfuromonas → unclassified Desulfuromonas → Desulfuromonas sp. TF	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?
F001506	Metagenome / Metatranscriptome	681	Y
F002483	Metagenome / Metatranscriptome	555	Y
F004052	Metagenome / Metatranscriptome	455	Y
F017764	Metagenome / Metatranscriptome	239	Y
F018541	Metagenome / Metatranscriptome	234	Y
F026568	Metagenome / Metatranscriptome	197	Y
F030933	Metagenome / Metatranscriptome	184	Y
F031139	Metagenome / Metatranscriptome	183	Y
F034003	Metagenome	176	Y
F035835	Metagenome / Metatranscriptome	171	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0055478_10001162	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales → Ignavibacteriaceae → Ignavibacterium → Ignavibacterium album	4087
Ga0055478_10001355	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Synechococcales	3895
Ga0055478_10003214	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	2903
Ga0055478_10003339	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales	2861
Ga0055478_10011470	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales	1864
Ga0055478_10015476	All Organisms → cellular organisms → Bacteria	1673
Ga0055478_10025478	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1395
Ga0055478_10042675	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1146
Ga0055478_10043669	All Organisms → cellular organisms → Bacteria	1136
Ga0055478_10051575	All Organisms → cellular organisms → Bacteria → FCB group	1064

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0055478_10001162	Ga0055478_100011622	F066277	MDRKKFIALFSTSILGATFLKVNPYNFFRAKNSSTLGSEVKVKINPHAVNREKSGKKNG*
Ga0055478_10001355	Ga0055478_100013553	F001506	MNRILYESRCRCNEEFLITKKRSSSNRSEGKPLQYPKPSEITSKTFQIKYEKELSSIAKFVLNSFQNKYIYYAIDDILYLLKSNPIERDHLLAIIYSPVLSLQNNFSINFFDIWINEIYINEVPKVNKFITNDFQNFEQFSYITIKLLYKTRVPIKKQDSLW*
Ga0055478_10003214	Ga0055478_100032143	F053306	MQGSVIMKTKLLSTIASTLILSACGQPEPITYESLVWVNNYYVEHPVASLSATAGGWLFRGAREFGTEIRIGFLLPSPMNPDPAKRQAVLNTICPAKSETIWKALPEENKLVITVWTQDNKFKDSVTC*
Ga0055478_10003339	Ga0055478_100033392	F030933	MINDHQTDELRHKRAQAVKTAWILGIIALAIFATFIGSAIIGR*
Ga0055478_10011470	Ga0055478_100114703	F030933	MNDYPDSEELRRKRAQAVRTAWILGIIAMSIFATFIGSAIIGH*
Ga0055478_10015476	Ga0055478_100154762	F052687	MIKFLTIVLFLTALGGGTYYLLSMETVEDVKVTGKLQISEQYGSYVMASQSEGANYYAVIEGKVKNNLGKSIKNVFIKYVISGQETSATIFDLAPGQELHFNTSGVATTGSSPEYDFVGIYYD*
Ga0055478_10025478	Ga0055478_100254782	F017764	VSVTLTVNLDADILQSAEQEARARHTTLPELVSQQLRLMARNWQDSNAGKTPVTDALRGAVELPVDFNERDALTAELENRHGVRE*
Ga0055478_10042675	Ga0055478_100426752	F084255	MESSRRYLLQAEIEFWHEMLRLNKSRVSKNREDEMRTCLKRAVRALNSNRVPEFRAAA*
Ga0055478_10043669	Ga0055478_100436691	F045765	VTYHSSKGENTTRIKIDDKLYDLLRKFCDKEGRRLKDFVEDALENAIYTDESIKILNAEIKSLKKKEAKYDYAFRRGFQKGFYISFCALHGQILLGPDDEEYEILKNDPFRVSKGVQLDLFR*
Ga0055478_10051575	Ga0055478_100515752	F076224	FKYSVANSNSHSFNVVVDSNVCRVDFQIPPIPESAFSEIGVMDPIIEEATNNIHFYAYKIPKMEKSKSEIKIEYYNDDSVYSVVVDYNVLNIDSIVQATAGTDMLNLDRFKPVRPQDDTMLIKYEFDKNYYRYYSDDEFKKQMEELQKELQQLGNELKNQKIRVHTEVTKGQKK*
Ga0055478_10062884	Ga0055478_100628842	F097365	MVNESDWKAMKQQAFDAFALDGKMSVYELEQIVNIALADGEFDEMEKAVMVNIISNLTGADMTDAMWLKVDELINKFDLHGD
Ga0055478_10066020	Ga0055478_100660202	F073180	MKKEFTQLQLTRLVYGETTKAESDMLLELAATVPQIANTLETLKMGKETLGKDRFTPSDKVINFLLGYSASSAPVSAS*
Ga0055478_10066267	Ga0055478_100662671	F002483	MLNTLPMPIGFLRRRSKKRPQRAAAPWPSSPLPPRRPPSYYLVAGVALDRELERLRALPVFAAGPLAARRPQLKVRRASKRPNKLGFAVPDEFRLQVTAYPGIGSGDILETLLHELTHLHVGRAAEAHAWHGRTFKAALAQAMREAYGVAIPPPSHTRHGIYAAAIDATASAAQSGDEG*
Ga0055478_10067451	Ga0055478_100674511	F105200	PVQDRHRRRNVPDSFERKLEQLLEYSEAPQAEAFTINVMRSIRREQRRRKIILWSFGLVGALFGLSGALMLTGPVSELLTFSLEMPVMKTMQVTLFVVGATAFYLWFMNDDFSLGS*
Ga0055478_10071247	Ga0055478_100712471	F064415	MSSLEEFAESDEHPLLTMREATTILRIGRTLGYQLAHEYLNSGGTSGLPVIRFGKECYRVPRWALIELVTTGRVVR
Ga0055478_10092534	Ga0055478_100925341	F074893	MMVSSQLNAVAGDGSLTISINGPMDLLLTRALREHCQDNGATYHRYIVDFRDVSIVRDSGLALLLMLKRWANRAGATLCVINGNRDLMRRCFSLGIGPA*
Ga0055478_10095260	Ga0055478_100952601	F075466	MSDEKVMCSHVLTIRFDQLEDNRVNWYVEPDDKIGQAGGLSLIDLAECRAPLAAMGIRALWKICVDGLVYHALEQANDIQVEVGRRLATEPAEAPLELVPEGVTIN*
Ga0055478_10101884	Ga0055478_101018842	F026568	MHKPSPLKEMYDPYYHYTRGVLYYDENHFTFTAYRMPYLELDSKSWETEKAFKADYRRVV
Ga0055478_10106624	Ga0055478_101066242	F082775	MSEPDILYPAIFVFSMLLTGLLLTMWEFSRLQKRQQQKTDRDEPVSDPGFRASRGNVRKVSNF*
Ga0055478_10123861	Ga0055478_101238611	F068850	MMHGEKTEMQQLKKCMTGIIAIAALWLSSAIAEQQLEQETISIKGNQALPKTLYIAPWKRVGAPLEGGRIDAEITEESKPLERDMFQRQLELQRKGYSID*
Ga0055478_10140175	Ga0055478_101401751	F031139	MTEVVELTTHASAQSDRWLFVASLIVCGLFAVGVMRYFVRQHEQLLADSKQARDSYQESLRGIVAEQSAANAKLVTCLEHNTKVLEECRDELRDSRMQRRTA*
Ga0055478_10141882	Ga0055478_101418822	F087249	MQDTDEPTSKSVRARMDAYIAAACENADIELLNPNVVDEIAKEFLETLTPMEMGFLMHDDPQPVSLQELDSDTQQKYRSKYGTKSLKRGQFFRLKSGSVTFFSHQHNLKFKVDN*
Ga0055478_10160591	Ga0055478_101605911	F095491	AEKLIEELEKRIEPEIKSFLAESSGRILERAAEFTISKIDDPASIDFRAKFVDFVLSKSPAFLLEVANDELIDDMGVIVELSARHVAEMPELKADLHDWIARALEYSSGKTLAEALGFENLALRPPMQALADAAWPAFTTLILSPQAQTWMDQLVDELLDEYEDTKPAR*
Ga0055478_10167302	Ga0055478_101673022	F034003	MKKRRKRNPATTKSDQLSFDFNPNYPIEIHTPKSDISDLRKELAWHHRPIIEIVKS*
Ga0055478_10172346	Ga0055478_101723462	F018541	MYSPKMKSFWVDFPLTDEQYAKLDLRWRRRRNYYEIKNEPLPAVRISSFCTFGGDDYKILSLEARGDIDAYHEALEVMKQWIVDNL
Ga0055478_10172482	Ga0055478_101724821	F095491	STILPRLMVKISPVGRFGMLGSAGMFAEKLIEELEKRIEPEIRSFLAESSDRILRRAADFTISRIDDPASIEFRANFVRFVLSRSPAFLLGAADDELIADVGAVVELSAHHVAEMPELLAEVHRWIDRGFGHAAGKTLAESLEIESRELRPPIDAIADATWPAFAAVLASPQAQMWMDRLVDELIDEYERA*
Ga0055478_10185738	Ga0055478_101857382	F095691	CPYHGPMLQQDGSIRIAWQADGFEAIFVRARFRPAPDLDEYARTVADVALLERTLPDLRTALRKAYPGQFDLVTDEPVSRPGRVIVSFHPPPGQPNPDPW*
Ga0055478_10187163	Ga0055478_101871631	F082711	LDGRTFRGRVPCSLSKKRPELGPLIDYHELGVFEGKVVQSIFARKLLGPESFGFCRKFCAMSMQAVADLLQVDRRTVQRWESEESPVPPWAMLLVAKMADERSKGRAVMRKWLQELADEEERPTEIDLDVA*
Ga0055478_10189181	Ga0055478_101891812	F004052	MRILTLPVQLTLTALLCSCDQQNSVSDVDPMLGLECFNSHHLPPGTQYEGIENLTENRLTIRIMNGVEVVTLDCVLNPDGTLKGIDR*
Ga0055478_10192774	Ga0055478_101927742	F092074	YLSLVLATGMLLAASLPARADETTTLLCDFRHGQLEININYTRGTANDATAIISDQEIIWSPSGNQGGMAVINRYTGIMQLSRGNKEFNGLCNKKPE*
Ga0055478_10205155	Ga0055478_102051552	F063710	MKKPRQRSLRVRVEHEPNRFSDDYLERIYEQLHPTKSRKVTPDKNNKQGEVELQKGSGGRQ*
Ga0055478_10223690	Ga0055478_102236901	F064234	MNSEQARPLSLREIEMEVEAEGREWTRQRLQQRLQQEAERRGEVFPPEPAAAGASAPAADAT
Ga0055478_10235428	Ga0055478_102354282	F087352	MYHPNEVIEDIRERLDRMVLDFKALLEENKQLETENKSLAHSLEEALNKQEILSKRLDTISQETLRDTKGITHWKTETRKEIRSIMKEVEKCIPQAESLLEK*
Ga0055478_10245467	Ga0055478_102454671	F105198	MKNVFLALCLVLFAGQASAYFTWGVGSQTCNFYVSAKAEYDHARDQRTHLAHLNWIKGFITGINWSRESDIARNLSIETVDQWIDAYCRANLDASIGEASAALVVDLEKQGKPQ*
Ga0055478_10249732	Ga0055478_102497322	F085725	VFLALRKHKRSPVLGLVHASMAVAGIALLFSQIYSGPTDKLNNGAALFLVFALVGGGIVFVLHEKNKPPSMAAVAFHAVMGLIGISLLTINLF*
Ga0055478_10257279	Ga0055478_102572791	F035835	PIWRRTSRKKFIESVRRRDTNPKTGRAWFVVDCVDCGRVMGIGEKERRPLAKGGMSKKARSVFEIDHVEGITPLTDIKETLGQHFYELLYGRQEVVCYACHKHRTAKQVAERKENKSK*
Ga0055478_10274845	Ga0055478_102748451	F077315	KASTHFLSRIACSQVWALLLLGLLVPAQAAEVLKPDTLPQAQATLERLEQQLASARATTAQELKAFKKEIAKVRSSALDCVQQAEPEIESLDSQLAILQPAPPKDTQAKTAEEPQPAEQPEAPVSSAIARQLQDLQSRKASLEGRIANCKLLLLGSNNLDSKVDDYLRSLQTRQL
Ga0055478_10283008	Ga0055478_102830081	F054877	MKKHRNLRVLARFRPMFINDLDAKLVLLIGKEAAFRYHKYLDEDDTPYSGQWVLTAEDPQFGDYWFPEC
Ga0055478_10284968	Ga0055478_102849681	F070130	FDRARAAPMTEVHEVPDTPARQPDVFVGWWEAVFYIRDGEQTDVTGIIEHIDAAGTFRVFRDGERIGAGRHVEFIVDPDGFTNVQEVAGAHTKTGRELVVYRFSGDVFEVCKASERHGRPTSFASPRGSGWIHAAIRRISDDDPRIPAQG*
Ga0055478_10300236	Ga0055478_103002361	F048318	EEIVFMATLENVHLAITASTEKPGYSHIAYSYELHPSELDCKEQREYTVKTDLWGEDLIDDDVLAWGKDEHKVKFDASSPCEAIKVDRVFEIETKVLDEDFFGDDEVYITVEASSGLGPDAAGEDPLMGRSNTVIGDF*
Ga0055478_10301579	Ga0055478_103015791	F068850	LCLLLITSILWLLPAGAQEQLEQETISIKGNQGLPKTLYIAPWKRVGAPLESDRLDAEIKEETEPVERDIFQRELELQRQGYSVE*