3300011976: Human subgingival plaque microbial communities from Los Angeles, CA, USA - S13-02-D

Overview

Basic Information

• IMG/M Taxon OID: 3300011976
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0113963 | Gp0134628 | Ga0119798
• Sample Name: Human subgingival plaque microbial communities from Los Angeles, CA, USA - S13-02-D
• Sequencing Status: Permanent Draft
• Sequencing Center: University of California, Los Angeles
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 176269073
• Sequencing Scaffolds: 8
• Novel Protein Genes: 11
• Associated Families: 8

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales → Porphyromonadaceae → Porphyromonas → unclassified Porphyromonas → Porphyromonas sp. oral taxon 278	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	1
Not Available	1
All Organisms → Viruses → Predicted Viral	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales → Porphyromonadaceae → Porphyromonas → unclassified Porphyromonas → Porphyromonas sp. oral taxon 275	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Saccharibacteria	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Human Oral Microbial Communities From Los Angeles, Ca, Usa
• Type: Host-Associated
• Taxonomy: Host-Associated → Human → Digestive System → Oral Cavity → Subgingival Plaque → Human Subgingival Plaque → Human Oral Microbial Communities From Los Angeles, Ca, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): Host-associated → Animal → Animal secretion

Location Information

• Location: USA: Los Angeles
• Coordinates
  • Lat. (^o): 34.0722
  • Long. (^o): -118.4441
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F022002	Metagenome	216	Y
F051211	Metagenome	144	N
F051213	Metagenome	144	N
F066860	Metagenome	126	N
F070224	Metagenome	123	N
F077403	Metagenome	117	N
F084362	Metagenome	112	N
F095630	Metagenome	105	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0119798_1000215	All Organisms → cellular organisms → Bacteria	66629
Ga0119798_1000264	All Organisms → cellular organisms → Bacteria	56391
Ga0119798_1001453	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales → Porphyromonadaceae → Porphyromonas → unclassified Porphyromonas → Porphyromonas sp. oral taxon 278	15147
Ga0119798_1001699	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	13379
Ga0119798_1004001	Not Available	6165
Ga0119798_1005234	All Organisms → Viruses → Predicted Viral	4735
Ga0119798_1006937	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales → Porphyromonadaceae → Porphyromonas → unclassified Porphyromonas → Porphyromonas sp. oral taxon 275	3609
Ga0119798_1031836	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Saccharibacteria	849

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0119798_1000215	Ga0119798_100021552	F051211	MKAKKAIRIFEKIRDLPYGTSGSDEVWSCYQKCVLLKQELQHIGITSQLLIGVFDWQDLPIPEHILNLRRQRHERHVILRVFINGSTYNIDPSIDIGLASTLPIAHWDGTSSTATMASLKHLHVYRPHSLHERILSRLRSKLFRGNPKEFYTAIDKWLADTRAHQSS*
Ga0119798_1000264	Ga0119798_100026411	F095630	MRYSSLYKISKDNGLLAHVYEHLLAQYILKYLQDKGFFILSDIILTAKTYGDTCYMDVELYNPAVHNAYNEALQAFDKHTIPEKAVRRAVSECGIEMNRAVLELKQDELMSNLSRMQSSDWRQQSEMTYHKSYDKSSVNMLFCVPYLKYGKKSKKLFPEYVLEYSIDEEYINSPIDQALAAIIMQAVALNFLVAVRENYTVYDRGDQWSEASLSVGYRIFLGLVKEDKRIASQLKSEFAAYIQYLLKSPFCSNLQKALLRCSRNLEQVLLGRSTLNNILGGCVIGGRGWLEMADDARIKQMIAAIQLDVYDI*
Ga0119798_1001453	Ga0119798_10014536	F051213	MNLYKILGALILALSCVFTSCDWVDNEPTIEGDRYKTFDSSAQRKSFRVVNASGKRYNHKVDWDIVGIKQLWVKTFLTKKVDTLSNGDLKISYDWVSFTVKERKSVIEVEVQKNETGQARSVFFATSNSRYQAHLPNMIITQWAK*
Ga0119798_1001699	Ga0119798_100169910	F022002	MTNIYSFLSPSSVGREVVLAFGILLLALLLSLPSHAQDGRSKVPINRTISGFTLGVTTPAEARAIIQRQGGKIILEVGVHAGSKDASYIVSGLNYARRPTQTVAMFFYKGHLHSIDFIFDGWDVLEQIESELEDKYGKMIESEGMFKKKVIVDAFTSLEVVRTFEYEGHVRINHAYIAYTDEELERARSAEKESEN*
Ga0119798_1001699	Ga0119798_10016998	F022002	MKNIYSPSFRSMSRRLALTLGLLLALLLSLPSHAQDGRSKVPINRTISGFTLGVTTPAEARAIIQRQGGKIEGTQAGSDEQAYAITGLKYARCSTLMAGLYFYKGHLRRISFTFDDLDVLEQIESDLEDKYETMAEGKETSKMKSKVIFDAFTALEVVRNFEYEGHSMFKNAYIAYTDLELERARSAEKESEI*
Ga0119798_1001699	Ga0119798_10016999	F022002	MSSRLALTLGLLLALLLSLPSYAQDGQSKEPINRTISGFTLGVTTPAEARAIIQRQGGEIEETQAWSDEVVYAITGLKYARRPTLSVRLYFYKGHLRSISFTFGDLKIFEQIESGLENKYGTMAEGKATSKMRVKGIADAFTSLEVVVHSFEDDGHVGFAYAYISYTDLELDRAYSAENENEI*
Ga0119798_1004001	Ga0119798_10040016	F084362	MNCTFTVRWSDDKNKPHAKTYATEADAKRAKKWLLEHGVRSIDIAVKINNKPAGSLQDSEKRPEVAAEQKGFWWEK*
Ga0119798_1005234	Ga0119798_10052343	F077403	MNTIMLLLRRLVLIILLLPSMCTVYAEDRISVHFEVRWHREHNPMDTLRRELDVPYLHVVYQNHTDTAYYLVRQDQSNWIFPRLRYYTVIEDGSRPEKYNLTYYVPRWATYPLKGAGRSVRERRHYTHHVLLRDQAWEVELEPSIVDGQPKPRIAYGEGMDNWSECAYYLQGYLYYLMTPQLDHDWYQVTYLSEHMEYSVGMEMVETEGTLKPFVHRLAFVPAHSRREYVYSLLAFAVIHGRWQFLLPDWEASGRLRDECIPLNVYQLRGKGSTASAPSGYPLPEHYEGYQLYRGWVRGDSISIKM*
Ga0119798_1006937	Ga0119798_10069371	F070224	MKRLLFLLLTLFHCTAWSQVYNAPDSLYVASGAVYIPPVSGEPIYLLASPLKSGHTPGSKIRTRDWVKVDYSDENNIITIGFGDSLVIENRFIYQADCYPKAKEYKLYHKGTGVEITKEDFDSIKFTRMPTALREIKKYKLPRTRRSSGEVDRWQHPHLFVVEHNKKADRYYKYRIALVIYMDYDHPEACIIH*
Ga0119798_1006937	Ga0119798_10069372	F070224	MKRLLFLLLTLLHCTAWSQGYNAPDSIYVASGAVYIPPISGEPIYLLASPLKSGHTPGSKIRTRDWVKVDFSDQNNLHIMGFGDSLILENRFVYKADRYPNAKEYELYYKGTGEEITKEDFDSIKFSRMPTALREIKKHKLPRTRRFSGEVDRWQHPHLFVIEHNKKAGRYYKYRIALVIYMDYNHPEAKIIH*
Ga0119798_1031836	Ga0119798_10318362	F066860	MTTKKQKLQKQQAIDTWIVIALWASAIWFSLARGFITGIGGWVLALLGPWALIVSCICLAIISRQVKKRHASKDYLTTIVRVSFIVMSISLFICGLAMPDFSDIETFSTLSVYTNNAISFETSKAIAIISGFVVVLSLFVAVTFGIAEDREETTEDIAI*