Summary The Simons Collaboration on Principles of Microbial Ecosystems (PriME) brings together 9 research teams across the US and Switzerland to elucidate the principles underpinning the self-organization, structure and function of microbial communities. As part of this effort, the collaboration is developing model microbial communities, composed of heterotrophic bacteria known to co-assemble on nutrient patches in the ocean. This sequenced genome is a member of those communities.

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp16, Karp11] component of Pathway Tools software version 23.0 and MetaCyc [Caspi18] version 22.6 on 19-Dec-2018 11:25:48.

Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
6C06_E-6C06_S1_L_contig_2753724290835,434
6C06_E-6C06_S1_L_contig_1650636140726,279
6C06_E-6C06_S1_L_contig_6493483100540,039
6C06_E-6C06_S1_L_contig_921021000216,580
6C06_E-6C06_S1_L_contig_817417310202,483
6C06_E-6C06_S1_L_contig_715115010183,541
6C06_E-6C06_S1_L_contig_515415040175,106
6C06_E-6C06_S1_L_contig_4150139110169,117
6C06_E-6C06_S1_L_contig_1014714700150,750
6C06_E-6C06_S1_L_contig_1277770090,857
6C06_E-6C06_S1_L_contig_1372711078,861
6C06_E-6C06_S1_L_contig_1158571058,538
6C06_E-6C06_S1_L_contig_1454540058,222
6C06_E-6C06_S1_L_contig_1547461050,039
6C06_E-6C06_S1_L_contig_1640391046,182
6C06_E-6C06_S1_L_contig_331310043,318
6C06_E-6C06_S1_L_contig_1937325036,624
16 Undisplayed Contigs/Replicons73721063,716
Total:3,3713,2918003,725,686
Ortholog data available?Yes
Database Contents
Genes3,371
Pathways308
Enzymatic Reactions1,765
Transport Reactions172
Polypeptides3,293
Protein Complexes49
Enzymes888
Transporters336
Compounds1,384
Transcription Units2,167
tRNAs70
Protein Features4,331
Database Version29.6
Sequence SourcePriME Project
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Alteromonadales
Psychromonadaceae
Psychromonas
Psychromonas sp.
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI-Taxonomy1884585

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

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