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 13-Mar-2021 from the annotated genome of Actinoalloteichus hymeniacidonis HPA177(T) (=DSM 45092(T)), 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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_CP0148595,4425,268601146,306,386RefSeq:NZ_CP014859
Ortholog data available?Yes
Database Contents
Genes5,442
Pathways263
Enzymatic Reactions1,284
Transport Reactions70
Polypeptides5,268
Protein Complexes42
Enzymes820
Transporters514
Compounds988
Transcription Units4,029
tRNAs48
Protein Features6,336
GO Terms1
Database Version29.0
Sequence SourceGCF_001747425.1
Synonyms Actinomycetales bacterium HPA177
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Actinoalloteichus
Actinoalloteichus hymeniacidonis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03295676
NCBI BioProjectPRJNA224116
NCBI-Taxonomy340345
Environmentintertidal marine sponge from the beach of Dalian
Geographic LocationChina
Latitude/Longitude38.8667 N 121.6833 E
Collection Date2006
HostHymeniacidon perlevis
Annotation ProviderNCBI RefSeq
Annotation Date2020-06-5
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

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