Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Acidocella facilis ATCC 35904, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_JHYG0100000147045956477,655RefSeq:NZ_JHYG01000001
NZ_JHYG0100000244443644444,101RefSeq:NZ_JHYG01000002
NZ_JHYG0100000329429121322,054RefSeq:NZ_JHYG01000003
NZ_JHYG0100000429128731301,248RefSeq:NZ_JHYG01000004
NZ_JHYG0100000528627583286,929RefSeq:NZ_JHYG01000005
NZ_JHYG0100000623723601267,969RefSeq:NZ_JHYG01000006
NZ_JHYG01000007244231103240,499RefSeq:NZ_JHYG01000007
NZ_JHYG0100000816716322166,813RefSeq:NZ_JHYG01000008
NZ_JHYG01000009898801102,282RefSeq:NZ_JHYG01000009
NZ_JHYG0100001086842090,997RefSeq:NZ_JHYG01000010
NZ_JHYG0100001173675179,040RefSeq:NZ_JHYG01000011
NZ_JHYG0100001268670173,555RefSeq:NZ_JHYG01000012
NZ_JHYG0100001356551061,879RefSeq:NZ_JHYG01000013
NZ_JHYG0100001449480150,696RefSeq:NZ_JHYG01000014
NZ_JHYG0100001530290142,931RefSeq:NZ_JHYG01000015
NZ_JHYG0100001644400442,554RefSeq:NZ_JHYG01000016
NZ_JHYG0100001746451041,743RefSeq:NZ_JHYG01000017
NZ_JHYG0100001832292135,594RefSeq:NZ_JHYG01000018
NZ_JHYG0100001925240129,583RefSeq:NZ_JHYG01000019
NZ_JHYG0100002026230323,614RefSeq:NZ_JHYG01000020
NZ_JHYG0100002116160020,887RefSeq:NZ_JHYG01000021
NZ_JHYG0100002221180320,767RefSeq:NZ_JHYG01000022
NZ_JHYG0100002323201220,193RefSeq:NZ_JHYG01000023
NZ_JHYG0100002422211019,298RefSeq:NZ_JHYG01000024
NZ_JHYG0100002614110312,655RefSeq:NZ_JHYG01000026
NZ_JHYG0100002714140011,567RefSeq:NZ_JHYG01000027
NZ_JHYG0100002814110311,217RefSeq:NZ_JHYG01000028
21 Undisplayed Contigs/Replicons8175711105,611
Total:3,2743,16354573,403,931
Ortholog data available?Yes
Database Contents
Genes3,273
Pathways292
Enzymatic Reactions1,352
Transport Reactions56
Polypeptides3,195
Protein Complexes52
Enzymes762
Transporters311
Compounds996
Transcription Units1,893
tRNAs45
Protein Features4,075
Database Version29.0
Sequence SourceGCF_000687875.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acidocella
Acidocella facilis
Acidocella facilis ATCC 35904
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02743889
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1408419
EnvironmentMine
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-9
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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