Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Achromobacter kerstersii ATCC 31444, 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_CYTC010000011,0671,0471281,191,183RefSeq:NZ_CYTC01000001
NZ_CYTC01000002775757216875,985RefSeq:NZ_CYTC01000002
NZ_CYTC01000003736717613868,802RefSeq:NZ_CYTC01000003
NZ_CYTC01000004769746167843,792RefSeq:NZ_CYTC01000004
NZ_CYTC0100000543843215522,912RefSeq:NZ_CYTC01000005
NZ_CYTC0100000640239318443,895RefSeq:NZ_CYTC01000006
NZ_CYTC0100000733332634362,807RefSeq:NZ_CYTC01000007
NZ_CYTC0100000816616105218,653RefSeq:NZ_CYTC01000008
NZ_CYTC0100000917817431187,773RefSeq:NZ_CYTC01000009
NZ_CYTC0100001015415301175,335RefSeq:NZ_CYTC01000010
NZ_CYTC0100001114914630155,454RefSeq:NZ_CYTC01000011
NZ_CYTC0100001212011730143,020RefSeq:NZ_CYTC01000012
NZ_CYTC0100001311511023126,601RefSeq:NZ_CYTC01000013
NZ_CYTC01000014949202115,147RefSeq:NZ_CYTC01000014
NZ_CYTC01000015969123111,336RefSeq:NZ_CYTC01000015
NZ_CYTC010000161049941109,486RefSeq:NZ_CYTC01000016
NZ_CYTC01000017858302100,537RefSeq:NZ_CYTC01000017
NZ_CYTC0100001834330141,767RefSeq:NZ_CYTC01000018
NZ_CYTC0100001933320139,627RefSeq:NZ_CYTC01000019
NZ_CYTC0100002019171123,593RefSeq:NZ_CYTC01000020
NZ_CYTC0100002118170123,592RefSeq:NZ_CYTC01000021
NZ_CYTC0100002313120110,306RefSeq:NZ_CYTC01000023
10 Undisplayed Contigs/Replicons17153529,135
Total:5,9215,77062896,720,738
Ortholog data available?No
Database Contents
Genes5,919
Pathways301
Enzymatic Reactions1,576
Transport Reactions92
Polypeptides5,862
Protein Complexes9
Enzymes1,086
Transporters1,102
Compounds1,150
Transcription Units3,870
tRNAs51
Protein Features7,747
GO Terms842
Database Version29.0
Sequence SourceGCF_001298955.1
Synonyms Achromobacter sp. LMG 3441
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter kerstersii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA2247603
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1353890
Environmentnot available: to be reported later
Annotation ProviderNCBI RefSeq
Annotation Date2021-08-30
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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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