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 12-July-2021 from the annotated genome of Actinokineospora fastidiosa JCM 3276, 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 25.0 [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_BMRB010000012,0211,9852792,105,053RefSeq:NZ_BMRB01000001
NZ_BMRB010000021,7441,7142281,923,813RefSeq:NZ_BMRB01000002
NZ_BMRB01000003657633168678,196RefSeq:NZ_BMRB01000003
NZ_BMRB01000004471460110537,881RefSeq:NZ_BMRB01000004
NZ_BMRB0100000533632844372,937RefSeq:NZ_BMRB01000005
NZ_BMRB0100000630530032318,777RefSeq:NZ_BMRB01000006
NZ_BMRB01000007194181013252,024RefSeq:NZ_BMRB01000007
NZ_BMRB0100000818918234208,041RefSeq:NZ_BMRB01000008
NZ_BMRB0100000915114722194,991RefSeq:NZ_BMRB01000009
NZ_BMRB01000010918902133,678RefSeq:NZ_BMRB01000010
NZ_BMRB010000111029921100,236RefSeq:NZ_BMRB01000011
NZ_BMRB0100001261610078,179RefSeq:NZ_BMRB01000012
NZ_BMRB0100001363630063,594RefSeq:NZ_BMRB01000013
NZ_BMRB0100001424240033,551RefSeq:NZ_BMRB01000014
NZ_BMRB0100001519190016,715RefSeq:NZ_BMRB01000015
NZ_BMRB0100001619190014,703RefSeq:NZ_BMRB01000016
13 Undisplayed Contigs/Replicons555010,481
Total:6,4576,30965837,042,850
Ortholog data available?No
Database Contents
Genes6,451
Pathways263
Enzymatic Reactions1,328
Transport Reactions53
Polypeptides6,316
Protein Complexes52
Enzymes939
Transporters418
Compounds1,026
Transcription Units4,137
tRNAs53
Protein Features7,450
GO Terms3
Database Version29.0
Sequence SourceGCF_014648415.1
Synonyms Amycolatopsis fastidiosa
Pseudonocardia fastidiosa
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Actinokineospora
Actinokineospora fastidiosa
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00245342
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1816
Annotation ProviderNCBI RefSeq
Annotation Date2020-11-23
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.13
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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