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 xylosoxidans GAD3, 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_PHGT010000011,3531,344271,547,200RefSeq:NZ_PHGT01000001
NZ_PHGT010000029058851641,002,103RefSeq:NZ_PHGT01000002
NZ_PHGT0100000364063334734,314RefSeq:NZ_PHGT01000003
NZ_PHGT0100000644543681473,173RefSeq:NZ_PHGT01000006
NZ_PHGT0100000744743836449,832RefSeq:NZ_PHGT01000007
NZ_PHGT0100000835135001364,418RefSeq:NZ_PHGT01000008
NZ_PHGT0100000933232660349,303RefSeq:NZ_PHGT01000009
NZ_PHGT0100000431130821327,389RefSeq:NZ_PHGT01000004
NZ_PHGT0100001028227192285,769RefSeq:NZ_PHGT01000010
NZ_PHGT0100001118418202182,277RefSeq:NZ_PHGT01000011
NZ_PHGT0100001215415220154,501RefSeq:NZ_PHGT01000012
NZ_PHGT0100000513713520148,003RefSeq:NZ_PHGT01000005
NZ_PHGT0100001311611132137,199RefSeq:NZ_PHGT01000013
NZ_PHGT0100001410710331114,921RefSeq:NZ_PHGT01000014
NZ_PHGT0100001587834095,067RefSeq:NZ_PHGT01000015
NZ_PHGT0100001638360234,410RefSeq:NZ_PHGT01000016
NZ_PHGT0100001719171123,467RefSeq:NZ_PHGT01000017
NZ_PHGT0100001822220023,129RefSeq:NZ_PHGT01000018
11 Undisplayed Contigs/Replicons991129,008
Total:5,9415,84165356,475,483
Ortholog data available?No
Database Contents
Genes5,939
Pathways307
Enzymatic Reactions1,605
Transport Reactions95
Polypeptides5,863
Protein Complexes209
Enzymes1,019
Transporters760
Compounds1,150
Transcription Units3,776
tRNAs54
Protein Features7,740
GO Terms2,233
Database Version29.0
Sequence SourceGCF_003031105.1
Synonyms Achromobacter sp. 2789STDY5608606
Achromobacter sp. 2789STDY5608609
Achromobacter sp. 2789STDY5608611
Achromobacter sp. 2789STDY5608612
Achromobacter sp. 2789STDY5608616
Achromobacter sp. 2789STDY5608618
Achromobacter sp. 2789STDY5608619
Achromobacter sp. 2789STDY5608620
Achromobacter sp. 2789STDY5608622
Achromobacter sp. 2789STDY5608623
Achromobacter sp. 2789STDY5608624
Achromobacter sp. 2789STDY5608629
Achromobacter sp. 2789STDY5608630
Achromobacter sp. 2789STDY5608632
Achromobacter sp. 2789STDY5663426
Achromobacter sp. 2789STDY5663429
Achromobacter sp. 2789STDY5663443
Achromobacter sp. 2789STDY5663447
Achromobacter sp. AHJR1
Achromobacter sp. CCUG 2349
Achromobacter sp. CCUG 48135
Achromobacter sp. CCUG 48386
Achromobacter sp. ES-6
Achromobacter sp. GAD3
Achromobacter sp. HMSC056C09
Achromobacter sp. HMSC057D05
Achromobacter sp. HMSC070F04
Achromobacter sp. HMSC15D03
Achromobacter sp. HMSC18C08
Achromobacter xilosoxidans
Achromobacter xylosoxidans KF701
Achromobacter xylosoxidans subsp. xylosoxidans
Achromobacter xylosoxydans
Alcaligenes denitrificans subsp. xylosoxydans
Alcaligenes xylosoxidans subsp. xylosoxidans
Alcaligenes xylosoxidans
Alcaligenes xylosoxydans
Flavobacterium sp. 650
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter xylosoxidans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06251565
NCBI BioProjectPRJNA224116
NCBI-Taxonomy85698
Environmentlandfill leachate treatment systems
Geographic LocationChina
Annotation ProviderNCBI RefSeq
Annotation Date2022-01-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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