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 Abiotrophia sp. HMSC24B09 HMSC24B09, 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_KV82219550349652554,391RefSeq:NZ_KV822195
NZ_KV82221027827602282,282RefSeq:NZ_KV822210
NZ_KV82220321520528215,753RefSeq:NZ_KV822203
NZ_KV82218713213101145,338RefSeq:NZ_KV822187
NZ_KV82221312111911137,156RefSeq:NZ_KV822213
NZ_KV82221410110010122,204RefSeq:NZ_KV822214
NZ_KV82221111310940111,809RefSeq:NZ_KV822211
NZ_KV822192897612196,640RefSeq:NZ_KV822192
NZ_KV82220294930196,302RefSeq:NZ_KV822202
NZ_KV82220659561267,226RefSeq:NZ_KV822206
NZ_KV82220151492057,728RefSeq:NZ_KV822201
NZ_KV82219745420349,870RefSeq:NZ_KV822197
NZ_KV82221531310037,425RefSeq:NZ_KV822215
NZ_KV8222081601601,527RefSeq:NZ_KV822208
17 Undisplayed Contigs/Replicons20173445,133
Total:1,8721,80047252,020,784
Ortholog data available?No
Database Contents
Genes1,872
Pathways145
Enzymatic Reactions809
Transport Reactions64
Polypeptides1,837
Protein Complexes79
Enzymes412
Transporters159
Compounds609
Transcription Units1,067
tRNAs40
Protein Features2,368
GO Terms145
Database Version29.0
Sequence SourceGCF_001815865.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Lactobacillales
Aerococcaceae
Abiotrophia
unclassified Abiotrophia
Abiotrophia sp. HMSC24B09
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03436211
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1581061
EnvironmentRespiratory
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-07-27
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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, BIOCYC17.