3300026058: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNW_TuleA_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026058
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116089 | Ga0208421
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNW_TuleA_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 64856408
• Sequencing Scaffolds: 41
• Novel Protein Genes: 44
• Associated Families: 43

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	3
All Organisms → cellular organisms → Bacteria	7
Not Available	7
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	15
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Rhodothermaeota → Rhodothermia → Rhodothermales → unclassified Rhodothermales → Rhodothermales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Archaea	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → unclassified Acidimicrobiia → Acidimicrobiia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Rhizorhabdus → Rhizorhabdus wittichii	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Anaeromyxobacteraceae → Anaeromyxobacter	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	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 → Terrestrial → Soil → 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): terrestrial biome → wetland area → soil
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: Antioch, San Francisco Bay, California
• Coordinates
  • Lat. (^o): 38.05246563
  • Long. (^o): -121.76914021
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000925	Metagenome / Metatranscriptome	832	Y
F002252	Metagenome / Metatranscriptome	578	Y
F003187	Metagenome / Metatranscriptome	502	Y
F003255	Metagenome / Metatranscriptome	497	Y
F003627	Metagenome / Metatranscriptome	476	Y
F003912	Metagenome / Metatranscriptome	462	Y
F006079	Metagenome / Metatranscriptome	382	Y
F006851	Metagenome	363	Y
F010354	Metagenome / Metatranscriptome	305	Y
F017250	Metagenome / Metatranscriptome	242	Y
F019205	Metagenome / Metatranscriptome	231	Y
F020203	Metagenome / Metatranscriptome	225	Y
F021102	Metagenome / Metatranscriptome	220	Y
F021418	Metagenome / Metatranscriptome	219	Y
F021619	Metagenome / Metatranscriptome	218	Y
F025512	Metagenome / Metatranscriptome	201	Y
F027211	Metagenome / Metatranscriptome	195	Y
F027905	Metagenome / Metatranscriptome	193	Y
F028853	Metagenome / Metatranscriptome	190	Y
F031150	Metagenome / Metatranscriptome	183	N
F035704	Metagenome	171	N
F037757	Metagenome / Metatranscriptome	167	Y
F038132	Metagenome	166	Y
F040782	Metagenome / Metatranscriptome	161	Y
F041850	Metagenome / Metatranscriptome	159	Y
F041902	Metagenome	159	Y
F045206	Metagenome / Metatranscriptome	153	Y
F054295	Metagenome	140	Y
F055518	Metagenome / Metatranscriptome	138	Y
F057190	Metagenome	136	Y
F058251	Metagenome	135	Y
F063008	Metagenome	130	Y
F067213	Metagenome / Metatranscriptome	126	Y
F070289	Metagenome / Metatranscriptome	123	N
F072476	Metagenome	121	Y
F072481	Metagenome / Metatranscriptome	121	Y
F073898	Metagenome	120	Y
F074523	Metagenome / Metatranscriptome	119	Y
F075472	Metagenome / Metatranscriptome	119	Y
F079375	Metagenome / Metatranscriptome	116	Y
F090229	Metagenome	108	Y
F097998	Metagenome / Metatranscriptome	104	Y
F101965	Metagenome	102	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208421_1000120	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	3892
Ga0208421_1000801	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	2154
Ga0208421_1001069	All Organisms → cellular organisms → Bacteria	1946
Ga0208421_1003496	Not Available	1260
Ga0208421_1003939	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium	1204
Ga0208421_1004093	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1185
Ga0208421_1004289	All Organisms → cellular organisms → Bacteria	1161
Ga0208421_1005189	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1073
Ga0208421_1006617	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Rhodothermaeota → Rhodothermia → Rhodothermales → unclassified Rhodothermales → Rhodothermales bacterium	969
Ga0208421_1008562	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	871
Ga0208421_1009536	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	834
Ga0208421_1009647	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	829
Ga0208421_1010062	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	815
Ga0208421_1010215	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	810
Ga0208421_1011679	Not Available	765
Ga0208421_1011855	All Organisms → cellular organisms → Archaea	760
Ga0208421_1012365	All Organisms → cellular organisms → Bacteria	746
Ga0208421_1012712	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	736
Ga0208421_1013298	All Organisms → cellular organisms → Archaea	723
Ga0208421_1013705	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	714
Ga0208421_1014483	All Organisms → cellular organisms → Bacteria	697
Ga0208421_1014486	Not Available	697
Ga0208421_1014632	All Organisms → cellular organisms → Bacteria	694
Ga0208421_1014747	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	692
Ga0208421_1015624	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	675
Ga0208421_1017968	All Organisms → cellular organisms → Bacteria	637
Ga0208421_1018676	Not Available	626
Ga0208421_1019564	Not Available	613
Ga0208421_1021489	Not Available	589
Ga0208421_1022124	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → unclassified Acidimicrobiia → Acidimicrobiia bacterium	582
Ga0208421_1022848	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	573
Ga0208421_1023537	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	565
Ga0208421_1023577	All Organisms → cellular organisms → Bacteria	565
Ga0208421_1024626	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	554
Ga0208421_1024812	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Rhizorhabdus → Rhizorhabdus wittichii	552
Ga0208421_1024947	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	551
Ga0208421_1026659	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Anaeromyxobacteraceae → Anaeromyxobacter	535
Ga0208421_1027322	Not Available	530
Ga0208421_1027651	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	527
Ga0208421_1028964	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon	517
Ga0208421_1030322	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	507

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208421_1000120	Ga0208421_10001202	F019205	MFDTRKTFSIKAADATDLIIDFATLGEYGLEPVNTASGRACEARLRAGARRRSTGAWTAAISRFTVPA
Ga0208421_1000269	Ga0208421_10002696	F021102	VRRESPVKRRNPSGKVVWVAGYTGRDGKHHIAKPAWNRGKGTFERKADAQQAIEEAYGVADKPDILGAYATSWTERHPRSARTNATNTHRIGRVLDIDVEGIGLKDWPMRELRRRHALVLVDHMLRVQGRATTGVVGILRSLSARSCPFAARTSTARP
Ga0208421_1000801	Ga0208421_10008012	F090229	MPLEGHYERQTTPLYKLSSREIKTATVVLLVTVVAMLGVVVATAGDSNPPTPIGCIRANVAGVVGAETISGCGAEAEAKCAHAALFESPRAHGVVAECERQGIEF
Ga0208421_1001069	Ga0208421_10010693	F027211	MVRTYWLVPVFYEASGNLDLQPFARTDQIEACRPRAMWLPSVRRRVGWGK
Ga0208421_1003496	Ga0208421_10034962	F028853	MTSLEPKGAVHWIDHYVVGTNDLPNWSYWALNATGLPIRPINGLTTNMRKKN
Ga0208421_1003939	Ga0208421_10039391	F017250	RLPSTTPTAEKPALSEAQRIERLRLLAKRLRRPDGLDRDVLKRIEHLTGDEQ
Ga0208421_1004093	Ga0208421_10040932	F006079	MARRKPGKIVEGPELTAVTAEKVFGWMGVHKENGELIGKKQDKAGRWRSARVPAYSTDPVHAYAIDERMKQLKRWERYERELSRVTKAQNLPSEWATPEQRSRAAI
Ga0208421_1004289	Ga0208421_10042891	F038132	EGQMAYQRIFTEGNDGPDSMRVDIPKDKVPRGNRRPQGDPNRYLFVDRAEWMDQAPIRKFVKEALAERKK
Ga0208421_1004644	Ga0208421_10046442	F035704	MALHIKDSEFYAIDAHSHLGRRKTPLGHGVASFLGEDLVRNLDEAGLDCAV
Ga0208421_1005189	Ga0208421_10051892	F055518	MVNYIQNKWKLSPKVAEESYRVWLNGFTSDGKIPVKGLQEIYGEAFAAKLIPTAVPVAKVMDYTFVDQVLKEKDRPLRSRKWLARHLLIL
Ga0208421_1006617	Ga0208421_10066172	F003255	MPVTLSIHHLKDFDAWLKVFKENPPPPVGRWRVFRGADDRNRVHVVGEVAASEVQTVKDFLASDRMRDVFRRVNAMSTAPVEFVWLEEQTP
Ga0208421_1008562	Ga0208421_10085621	F101965	ANPRHEPQIGFDRVQSAEDRYLFGADGRLVYEVGHVFALQMHIVDKTHTRGLFLADFFAIEENGPRCLNKLPCEMVRAGS
Ga0208421_1009536	Ga0208421_10095362	F073898	MTQASISYHQQLRSIGQTLEAQRINVFELSCRGERIIVKGQPDKETSLLGALRKWQKQRRSEGLNSSLTFTQQDIDEIDRQGRTHRSQGNRLPDFYSLPNTLRTVGSYLDLKGAQLIEIHKQPLSLTMLSRNQAGHPEYEERSIASF
Ga0208421_1009647	Ga0208421_10096472	F002252	MTFADVLAWCKRNQADVRGVYRGKDISISHNDTALPSVLPPISAIFHWDVKMRELNHYVSSSDFERIVTGKLT
Ga0208421_1010062	Ga0208421_10100622	F072476	MALRVKSRKILIPDVPPVGESTTYQGLVIAGIGVFCGSVVIAAVLFV
Ga0208421_1010215	Ga0208421_10102151	F079375	MAEIEKEYLVGTVRPTNRPEAGQELDLDTLIPAKIKFVYLTMNFTRGTEEEFSTS
Ga0208421_1011679	Ga0208421_10116792	F000925	MQSPEDRNYAAIERLERLLDEIRSDPSKPRETEAIREIGFEIAIAVREVGAMLTKDVGWEETFVAGQRARQAGSEPAAHD
Ga0208421_1011855	Ga0208421_10118551	F074523	IASDFIEAEKQVIGSFQSQIDRNSGGVWDLYNPQKIAENHAVAVNNFTSYLLNTADLVNNALLSNIRVYNTALEQTRDNLKACAKTNTNYIQAVSGNSQNRETNTTSP
Ga0208421_1012365	Ga0208421_10123652	F057190	MSANNGGKSALHVATFSGWYRFEQNGKDLKQTKRDLTYWTLTCMSVDPDNPQKIYAGSEHSGLFYTDNGGARWKRAEPNTPKMMLFSALALNDGVMVGTIPSAVYRSKNGGWEELAGVRINSAGANFPP
Ga0208421_1012712	Ga0208421_10127122	F097998	VALFFHSDDVDQLIPFKEAVQITEFALRDLVSPKGVNAPRKRLNLHRDIGEASF
Ga0208421_1013298	Ga0208421_10132982	F072481	MYYAGSKQCDDMIARKNETKPPFRPDLESEKQVLCEHCGETYKEKEIKWDKVRERWVCKNHPKCDGSVSHLDIRHVD
Ga0208421_1013705	Ga0208421_10137052	F063008	ANVEHLRQSFSQESRRLSKCLEEIDDNILACRQYLQDYERIRSSLCGLNEKLTQLGAQSIQVPDGLPATDLGEIVRERIDFLRSQGKI
Ga0208421_1014483	Ga0208421_10144831	F058251	QPVASVVIGCEQLAPLEQNVQAAMNFRPISESGKQRLQEKVAPSRSAWENFLRTHEDSVA
Ga0208421_1014486	Ga0208421_10144861	F027905	NAPADEVLRRAEADDAPFAKSDELRAWVTQGLEELPELGR
Ga0208421_1014632	Ga0208421_10146321	F031150	MAEFIIDADGHIMEDPKDIFAHIKGNFSEMNWHSTWPMFDADGWQRG
Ga0208421_1014747	Ga0208421_10147472	F040782	WPAWRGTFVEPLACVLRGASRLPRGRVLIVGNGFVGQLFGAVLARRGDDVFSVDSDPRRSGRAPDGPVDAAVLCGPGGTDTALDAVAPGGTVLAFADAGSIPLADVYRRELTVVGARSAAPPYMPEAVALLHDLDVPEPTVLPLERFADGLELYRRRDATKVVFTA
Ga0208421_1015624	Ga0208421_10156242	F041902	MADWRMIDADGHIREVESDVFEYLPDYYKSRREAVLYFPLLPHHGWHRQAGRGGMGASFLIPTLEDWRAALEQD
Ga0208421_1017968	Ga0208421_10179681	F025512	LDRTVRLLQRAFEVPGLRLELAVLLVEYHIRRNEVARRSHAKTWWARHKGVKLLPL
Ga0208421_1018676	Ga0208421_10186762	F003627	VDRESARANITAGLVAGGIAVGVFALCFVVAMLYIAS
Ga0208421_1019564	Ga0208421_10195642	F037757	MTTAAVRRSAPFWISIFAGLALWEIAGRSTSAAFMVPFSETLVRLKQLVVGADFIAQFLDSAQLFLTGFVLALVVGMP
Ga0208421_1019741	Ga0208421_10197411	F003187	VMKKFLVIVCSLALALGVASCAGKGKAPIGKGKAPVVTKG
Ga0208421_1021489	Ga0208421_10214892	F006851	MSRAARLDLRSFQQELASRLASKTAAQVESSRLGLACGERRFLIRLSDAGE
Ga0208421_1022124	Ga0208421_10221241	F045206	IIEEIPGDELDELRIVEAMVRGPGLSKAGRSPLGVAMPKTPSPNGGP
Ga0208421_1022848	Ga0208421_10228482	F067213	HHDVVVRLIKSTVEGIRYAISNEDATKRIISKYLGVTDSDLLRQSYLYVADTFVREPFVPESVMQSMVQRMVQVNMIDAKSAQTTPTSAYFDNSYVAALKQAGVLDKIWK
Ga0208421_1023537	Ga0208421_10235372	F021418	ALYDTGDLSGYHDIVIERTLRVGKELVEHGAEAIIPLGGKIYPYVVTPEELAPHLGVPVINTKAVGVSYAELMARNKIQHSIKAYPCPTGLDPETVSQRSQ
Ga0208421_1023577	Ga0208421_10235772	F054295	FLEAKWGIKETDVRESIYRDMVGLFSRNGVASDETMNNVVQLVRDTRKSKDDKTLADIVDWSFAKKAQAELKIK
Ga0208421_1024626	Ga0208421_10246261	F041850	DHSKLVVICESTGVWDILPPALKGLVQEVESYRSMNMTLTEPASSESCAAQLQRYFFIARRLIDYMEFHVIGNDSVLKRLKVA
Ga0208421_1024812	Ga0208421_10248122	F075472	MSRIARLSLVDRAEVGLSIAAQCRLLKIARSTLYWRAVPVSEDDLRLMRRI
Ga0208421_1024947	Ga0208421_10249471	F003912	ARLAPAKMRYSSMLRCIGQALSDMQLKAVEVRTHGEDLIVQAWNRGTSMAMDFEKHYTPEDLRLLEAESRAKRRVFAGPPDFLSVSQVLRMAGNHVDRMCGRLLRVSWQDQSDKIQSVTVQWESGQPGRDRSESPLTVVEELCIHIYKQRKKINLVSERQANRPFVSVVKSL
Ga0208421_1026659	Ga0208421_10266592	F021619	LQAYAGEMRDDESVLDLRLTQLLAVDASLSDARRALLRAARIPSAFSAEVRALLALVADIDRRVMLEVAQ
Ga0208421_1027322	Ga0208421_10273221	F070289	PQRLVLTGANVSPQFLQGTCGDVNGAIVNSFLATAWTFLPKSNPVRKQAALLRKILRRPVSNFDGDAAGALWAYKAAIERGGATRARIRDALETKLRGLVTPAGKIFLSRKNHQGLQLDSMWVGRIDNCKVKPLFGKAFAKKK
Ga0208421_1027651	Ga0208421_10276511	F020203	VIIDCDTHLMPRDAFEAVGGNLAALKPILKFDSQGLYTDVDFPGYRDIAGTSPLLAPGSGAMFKSLWEPQARMKDYDDRLGIEQHVVLPQFSGWWSYLLEAELACHMARSH
Ga0208421_1028964	Ga0208421_10289641	F010354	MSNDTGPKSSSKKSTKNITTAKKVKETKSVPITVQLNILKVLINERSLIPLLRILKKNKELHTRELLITMGSWGYGQSLMKKATNLGLIERKVKKEKSPGRGKPRIYNSLTNKGRDVVGLADKVVYTK
Ga0208421_1030322	Ga0208421_10303221	F038132	TEGNDGPDSMRVDIPKDKVPRGNRRPQGDPNRYLFVDRAEWMDQAPIRKFVKEVLAARKK