Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 25-Oct-2020 from the annotated genome of Acidihalobacter prosperus DSM 5130, as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_JQSG020000061,0801,05416101,111,128RefSeq:NZ_JQSG02000006
NZ_JQSG02000001798766248807,228RefSeq:NZ_JQSG02000001
NZ_JQSG02000003708692412747,040RefSeq:NZ_JQSG02000003
NZ_JQSG0200000257055875564,464RefSeq:NZ_JQSG02000002
NZ_JQSG0200000486850171,384RefSeq:NZ_JQSG02000004
NZ_JQSG0200000730270332,905RefSeq:NZ_JQSG02000007
NZ_JQSG0200000813111116,645RefSeq:NZ_JQSG02000008
NZ_JQSG0200000565018,881RefSeq:NZ_JQSG02000005
Total:3,2913,19852413,359,675
Ortholog data available?No
Database Contents
Genes3,291
Pathways229
Enzymatic Reactions1,159
Transport Reactions62
Polypeptides3,203
Protein Complexes47
Enzymes736
Transporters314
Compounds834
Transcription Units1,896
tRNAs45
Protein Features4,140
GO Terms13,374
Database Version29.0
Sequence SourceGCF_000754095.2
Synonyms Thiobacillus prosperus
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Chromatiales
Ectothiorhodospiraceae
Acidihalobacter
Acidihalobacter prosperus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02990926
NCBI BioProjectPRJNA224116
NCBI-Taxonomy160660
Environmentshallow geothermally heated seafloor
Geographic LocationItaly
Depth (m)0.0
Collection Date1989
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-9
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17A.