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 Actinobacillus ureae ATCC 25976, 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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_GL8310801,6021,404321661,666,151RefSeq:NZ_GL831080
NZ_GL8310816595862251650,708RefSeq:NZ_GL831081
25 Undisplayed Contigs/Replicons353061037,612
Total:2,3072,020602272,354,471
Ortholog data available?No
Database Contents
Genes2,306
Pathways244
Enzymatic Reactions1,286
Transport Reactions90
Polypeptides2,070
Protein Complexes72
Enzymes656
Transporters207
Compounds929
Transcription Units1,577
tRNAs52
Protein Features2,694
GO Terms261
Database Version29.0
Sequence SourceGCF_000188255.1
Synonyms Actinobacillus ureae CCUG 2139
Actinobacillus ureae CIP 62.8
Actinobacillus ureae NCTC 10219
Actinobacillus ureae strain ATCC 25976
Actinobacillus ureae strain Henriksen 3520/59
Actinobacillus ureae str. ATCC 25976
Actinobacillus ureae ATCC 25976
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Pasteurellales
Pasteurellaceae
Actinobacillus
Actinobacillus ureae
Actinobacillus ureae ATCC 25976
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00253301
NCBI BioProjectPRJNA224116
NCBI-Taxonomy887324
Environmentairways, nasal
HostHomo sapiens
Human Microbiome Body Siteairways
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-11
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.