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 C54, 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_GL6360606165901115741,255RefSeq:NZ_GL636060
NZ_GL636061587559622646,463RefSeq:NZ_GL636061
NZ_GL636027364348313441,386RefSeq:NZ_GL636027
NZ_GL636058280262108289,004RefSeq:NZ_GL636058
NZ_GL63605525124146264,658RefSeq:NZ_GL636055
NZ_GL636059210197310238,943RefSeq:NZ_GL636059
NZ_GL63604419018217219,919RefSeq:NZ_GL636044
NZ_GL63602518317634213,294RefSeq:NZ_GL636025
NZ_GL63605314713935139,307RefSeq:NZ_GL636053
NZ_GL63605711210903137,710RefSeq:NZ_GL636057
NZ_GL636054958645130,946RefSeq:NZ_GL636054
NZ_GL63580011511302119,196RefSeq:NZ_GL635800
NZ_GL63605110910405117,810RefSeq:NZ_GL636051
NZ_GL636056939021100,520RefSeq:NZ_GL636056
NZ_GL63605079750495,332RefSeq:NZ_GL636050
NZ_GL63580171630887,999RefSeq:NZ_GL635801
NZ_GL63605265610484,773RefSeq:NZ_GL636052
NZ_GL63601881740783,585RefSeq:NZ_GL636018
NZ_GL63603979750481,138RefSeq:NZ_GL636039
NZ_GL63604771680376,478RefSeq:NZ_GL636047
NZ_GL63603274701375,750RefSeq:NZ_GL636032
NZ_GL63604261546170,995RefSeq:NZ_GL636042
NZ_GL63604950460465,253RefSeq:NZ_GL636049
NZ_GL63604555520363,394RefSeq:NZ_GL636045
NZ_GL63603452490356,337RefSeq:NZ_GL636034
NZ_GL63602652481355,950RefSeq:NZ_GL636026
NZ_GL63603848470155,776RefSeq:NZ_GL636038
NZ_GL63602250470355,476RefSeq:NZ_GL636022
NZ_GL63604836340253,491RefSeq:NZ_GL636048
NZ_GL63603534330151,662RefSeq:NZ_GL636035
NZ_GL63603741381251,352RefSeq:NZ_GL636037
NZ_GL63604638360248,802RefSeq:NZ_GL636046
NZ_GL63580234320246,618RefSeq:NZ_GL635802
NZ_GL63604033280541,363RefSeq:NZ_GL636040
NZ_GL63603627240337,134RefSeq:NZ_GL636036
NZ_GL63600525220336,291RefSeq:NZ_GL636005
NZ_GL63602035330236,027RefSeq:NZ_GL636020
NZ_GL63603329280135,556RefSeq:NZ_GL636033
NZ_GL63599429260334,826RefSeq:NZ_GL635994
NZ_GL63580320180233,838RefSeq:NZ_GL635803
NZ_GL63604326240232,308RefSeq:NZ_GL636043
NZ_GL63600835320329,944RefSeq:NZ_GL636008
NZ_GL63600325230228,930RefSeq:NZ_GL636003
NZ_GL63604121200128,692RefSeq:NZ_GL636041
NZ_GL63599620180228,463RefSeq:NZ_GL635996
NZ_GL63580429260328,158RefSeq:NZ_GL635804
NZ_GL63602821190227,673RefSeq:NZ_GL636028
NZ_GL63580521200127,478RefSeq:NZ_GL635805
NZ_GL63580628270126,951RefSeq:NZ_GL635806
NZ_GL63602918170126,857RefSeq:NZ_GL636029
NZ_GL63601719150426,076RefSeq:NZ_GL636017
NZ_GL63601417170025,363RefSeq:NZ_GL636014
NZ_GL63602116140224,546RefSeq:NZ_GL636021
NZ_GL63603017170023,868RefSeq:NZ_GL636030
NZ_GL63580718170123,564RefSeq:NZ_GL635807
NZ_GL63580815140122,721RefSeq:NZ_GL635808
NZ_GL63580921210022,704RefSeq:NZ_GL635809
NZ_GL63581015150022,259RefSeq:NZ_GL635810
NZ_GL63601313110219,600RefSeq:NZ_GL636013
NZ_GL63581114140019,324RefSeq:NZ_GL635811
NZ_GL63603113100318,281RefSeq:NZ_GL636031
NZ_GL63581213120117,327RefSeq:NZ_GL635812
NZ_GL63599313120117,016RefSeq:NZ_GL635993
NZ_GL63581317150216,957RefSeq:NZ_GL635813
NZ_GL63581414140016,576RefSeq:NZ_GL635814
NZ_GL63581612100214,622RefSeq:NZ_GL635816
NZ_GL63602413130014,554RefSeq:NZ_GL636024
NZ_GL63581713120114,164RefSeq:NZ_GL635817
NZ_GL6360191190213,940RefSeq:NZ_GL636019
NZ_GL63601012100213,754RefSeq:NZ_GL636010
NZ_GL63581810100013,467RefSeq:NZ_GL635818
NZ_GL6358191090113,125RefSeq:NZ_GL635819
NZ_GL6358201091013,103RefSeq:NZ_GL635820
NZ_GL63582113120113,012RefSeq:NZ_GL635821
NZ_GL636006990012,168RefSeq:NZ_GL636006
NZ_GL636009119029,887RefSeq:NZ_GL636009
NZ_GL63601585128,944RefSeq:NZ_GL636015
185 Undisplayed Contigs/Replicons212206689442,737
Total:5,5335,144673226,514,720
Ortholog data available?No
Database Contents
Genes5,533
Pathways291
Enzymatic Reactions1,574
Transport Reactions93
Polypeptides5,877
Protein Complexes10
Enzymes1,045
Transporters1,068
Compounds1,152
Transcription Units4,209
tRNAs56
Protein Features6,654
GO Terms3,798
Database Version29.0
Sequence SourceGCF_000186185.1
Synonyms Achromobacter xylosoxidans strain C54
Achromobacter xylosoxidans str. C54
Achromobacter xylosoxidans C54
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter xylosoxidans
Achromobacter xylosoxidans C54
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02463749
NCBI BioProjectPRJNA224116
NCBI-Taxonomy562971
Environmentbiological product [ENVO:02000043]
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-19
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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