Database Authors
Carol A Fulcher1, Anamika Kothari1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp10, Dale10, Caspi14] component of Pathway Tools software version 20.5 and MetaCyc version 20.1 on 22-Aug-2016 15:40:02.

The primary data source for this dataset was the whole genome shotgun sequencing project for Desulfovibrio piger ATCC 29098 derived from NCBI Reference Sequence: NZ_ABXU00000000.

The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_DS996359766747181949,521RefSeq:NZ_DS996359
NZ_DS996355441426123492,021RefSeq:NZ_DS996355
NZ_DS996351293282110383,000RefSeq:NZ_DS996351
NZ_DS996354235221122239,503RefSeq:NZ_DS996354
NZ_DS99636018317940226,240RefSeq:NZ_DS996360
NZ_DS99636112612411157,119RefSeq:NZ_DS996361
NZ_DS99635612712421144,000RefSeq:NZ_DS996356
NZ_DS996353989440121,186RefSeq:NZ_DS996353
NZ_DS99635756551079,727RefSeq:NZ_DS996357
NZ_DS99635833320132,781RefSeq:NZ_DS996358
37 Undisplayed Contigs/Replicons19186242,118
Total:2,3842,30271112,867,216
Ortholog data available?Yes
Database Contents
Genes2,379
Pathways149
Enzymatic Reactions877
Transport Reactions61
Polypeptides2,324
Protein Complexes23
Enzymes563
Transporters199
Compounds769
Transcription Units1,632
tRNAs65
Growth Media19
Protein Features2,829
GO Terms14,692
Database Version29.0
Synonyms Desulfovibrio piger ATCC 29098
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Thermodesulfobacteriota
Desulfovibrionia
Desulfovibrionales
Desulfovibrionaceae
Desulfovibrio
Desulfovibrio piger
Desulfovibrio piger ATCC 29098
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA224116
NCBI-Taxonomy411464
Environmentbiological product [ENVO:02000043]
Relationship to Oxygenobligate-anaerobe
Temperature Rangemesophile
HostHomo sapiens
Copyright SRI International 2016. All Rights Reserved.

References

Caspi14: Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (2014). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases." Nucleic Acids Res. 42(1):D459-D471. PMID: 24225315

Dale10: Dale JM, Popescu L, Karp PD (2010). "Machine learning methods for metabolic pathway prediction." BMC Bioinformatics 11;15. PMID: 20064214

Karp10: Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R (2010). "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology." Brief Bioinform 11(1);40-79. PMID: 19955237

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