Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Actinoalloteichus hoggarensis DSM 45943, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0225215,4315,28460876,606,717RefSeq:NZ_CP022521
Ortholog data available?Yes
Database Contents
Genes5,431
Pathways259
Enzymatic Reactions1,359
Transport Reactions48
Polypeptides5,284
Protein Complexes146
Enzymes809
Transporters349
Compounds1,038
Transcription Units4,056
tRNAs48
Protein Features6,101
GO Terms373
Database Version29.0
Sequence SourceGCF_002234535.1
Synonyms Actinoalloteichus sp. AH97
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Actinoalloteichus
Actinoalloteichus hoggarensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN07353059
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1470176
Environmentsoil
Geographic LocationAlgeria
Latitude/Longitude22.78333 N 5.51667 E
Collection Date2000
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-19
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

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

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