3300001801: Wetland microbial communities from Twitchell Island in the Sacramento Delta, sample from surface sediment Feb2011 Site B1 Bulk Metatranscriptome (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300001801
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0017769 | Gp0056248 | Ga0003256
• Sample Name: Wetland microbial communities from Twitchell Island in the Sacramento Delta, sample from surface sediment Feb2011 Site B1 Bulk Metatranscriptome (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 1028623
• Sequencing Scaffolds: 12
• Novel Protein Genes: 14
• Associated Families: 14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	10
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → Solibacteraceae → Candidatus Sulfopaludibacter → unclassified Candidatus Sulfopaludibacter → Candidatus Sulfopaludibacter sp. SbA4	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Microbial Community Impact On Carbon Sequestration In Managed Wetland Carbon Farming
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Freshwater → Wetlands → Sediment → Wetland → Microbial Community Impact On Carbon Sequestration In Managed Wetland Carbon Farming

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): aquatic biome → delta → sediment
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Sediment (saline)

Location Information

• Location: Twitchell Island, Sacramento and San Joaquin Delta, California, USA
• Coordinates
  • Lat. (^o): 38.1072
  • Long. (^o): -121.6485
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001346	Metagenome / Metatranscriptome	718	Y
F004925	Metagenome / Metatranscriptome	418	Y
F007695	Metagenome / Metatranscriptome	346	Y
F016476	Metagenome / Metatranscriptome	247	Y
F025295	Metagenome / Metatranscriptome	202	Y
F026580	Metagenome / Metatranscriptome	197	Y
F027406	Metagenome / Metatranscriptome	194	Y
F041780	Metagenome / Metatranscriptome	159	Y
F045132	Metagenome / Metatranscriptome	153	Y
F051759	Metagenome / Metatranscriptome	143	Y
F054015	Metagenome / Metatranscriptome	140	Y
F055278	Metagenome / Metatranscriptome	139	Y
F078768	Metagenome / Metatranscriptome	116	Y
F105212	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI20217J20340_10064	Not Available	625
JGI20217J20340_10070	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	771
JGI20217J20340_10145	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → Solibacteraceae → Candidatus Sulfopaludibacter → unclassified Candidatus Sulfopaludibacter → Candidatus Sulfopaludibacter sp. SbA4	509
JGI20217J20340_10233	Not Available	500
JGI20217J20340_10248	Not Available	673
JGI20217J20340_10256	Not Available	827
JGI20217J20340_10286	Not Available	1057
JGI20217J20340_10357	Not Available	769
JGI20217J20340_10375	Not Available	558
JGI20217J20340_10422	Not Available	585
JGI20217J20340_10434	Not Available	877
JGI20217J20340_10741	Not Available	511

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI20217J20340_10064	JGI20217J20340_100641	F105212	HKGSPKNGGSGQWFLIELEAKSNGSQDLRHRRVGVQDHKEQSDVIRTAKKC*
JGI20217J20340_10070	JGI20217J20340_100701	F026580	MRNRSESSQVARAGFELGRIAVTQRVSGCYCASARAGGSGGLRKEVSQMKDAERRDKVSVRTGKDTRPGQDP*
JGI20217J20340_10070	JGI20217J20340_100702	F001346	VKTFREVGDVKNDTADLWTKGNLRVKRRDPWHRANALSKAAADPALSGEDADKKTQTCLDLVRKPVAQPPAQAS*
JGI20217J20340_10145	JGI20217J20340_101452	F051759	MGFAQAGVVAGEGKAVTSDQPQAGEKKGCDAPGSIDPVAGENGCRGAERRSVQRSRLRCSVPGMPVVGKAANRV
JGI20217J20340_10233	JGI20217J20340_102331	F027406	VVPSDPISSLAHCRHARH*TSQLEAPDASPLGSPTAGFANGRIGALKRAATLFQLGPVARNGLSLACNGPRFHEVHSRVKGPGLPLRSLACRFPRPFGPDLRYRTRFAPVPAASSIHARCAAHGSRA*LRLPLPLPFGILRSLRIKAFRGICRPPTRLPIRPISDH
JGI20217J20340_10248	JGI20217J20340_102481	F025295	IMVTGPGEAAELLRRREVLIPEKLKFITRKSNLQKLI*
JGI20217J20340_10256	JGI20217J20340_102561	F045132	MHSSNHYPLGNCDSPKPETDLDYLTRLGAVSNRTSSPSSFFAFTDSARTLPEELVNPASIAKYISTRLQRGLVNQPDPAFPRSPGRILETSVGELLLTDLRLSS
JGI20217J20340_10256	JGI20217J20340_102562	F007695	MAALKKAPLNCEQDALRVKRRDPWLEVNAPPKAVAVLELSGQDAETSYRRVLVWFAGRWRNHQSKRAEKPHSKSSGGDALDGPATRPETPLAVENSVGKLAALEAPNASMGKRAWRTPIPHFGP
JGI20217J20340_10286	JGI20217J20340_102861	F055278	VKECSSRPSEFSGLPLGPRSLPP*AVLLWNRVLVQSIRPLKYHRYCFGDPALPLVLTSAVRFSFSGLDRRLFRLPIAPSRRASPSFRVLPSNSYPVATTTGSSHGLLLPTALEGYEVHFSRASPTRYVPPSGFGYPLGGLLPRVPCRFCFTPAALLGFTLRRFPLPKGFRGVSAERNPHTVNLRVTPAPKCQTGHGGLGFWVHTFRKCLVIDGCLSRRPLAPPLGFTPPGPSRESLDQDFSWPPLTRFADPTITRRIHRRPRVSISSRLASTSLTPECTSVEATLLGFLHRPHPDHSNSAPPGLLSSPCTGSHITADSPVLFGR*
JGI20217J20340_10357	JGI20217J20340_103571	F004925	VSRIIPGDWGKAVPGWWARPLESQVERPGGGGRIHQFLWRRSRVVSNAKKELGGQER*
JGI20217J20340_10375	JGI20217J20340_103751	F078768	ARRVVAVNRLTLRVSRIIPGDWGKVGPGWLAQPL*
JGI20217J20340_10422	JGI20217J20340_104221	F041780	VPSDPQLQFAPRPACTARTRHLEWLGLNSLSSPRSPFSEGASTLRAQLARQSNRNRNLKTAFLLPCGDFPYPELRDRLERSQPASSISMPRSMQVRSVLNSLPDTFGIRQGHGHKTRFLSATLQSRPILRPPLPFGDSPPPDHCAQSDSDRKVCLGRMPDFPSLPERLNE*
JGI20217J20340_10434	JGI20217J20340_104341	F016476	GDVKEMLARPSEFSVSLLDPSRCRLKSSSSGIGYSFRV*RPRKYRPYCFCDPALPLALASAVRFSVLRAAADDCLGYRPRPLVELHLPLESYPATPTRPPRRPSPLMGFCSLQHIRNPRSTCRGPSQPAKFRLQGLATLLTAYSLESRAGFVSHRRRSWDSPFGGFLSRQASAVFRPGRTHVPLAQRYFRRRSVRPARRASVSGSTPARVALRPCGVLARQPPAPPLGFAPLGLTCEDLAPDFSRTPLTCFTSPGDCSPGQPAPQSLIRSPPCLTRPIPKYRPAGATLVGFL
JGI20217J20340_10741	JGI20217J20340_107411	F054015	VTLAVARKRDLPNERRPTAGQSEHTHREGHQISAGLVTTFRHVGDVEMNTAGL*