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 HMSC070F04, 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_KV80324965464716764,510RefSeq:NZ_KV803249
NZ_KV80327035634808396,523RefSeq:NZ_KV803270
NZ_KV80324230830341354,747RefSeq:NZ_KV803242
NZ_KV80327328027721308,024RefSeq:NZ_KV803273
NZ_KV80323126926144307,906RefSeq:NZ_KV803231
NZ_KV80322927827035279,427RefSeq:NZ_KV803229
NZ_KV80326424223426268,988RefSeq:NZ_KV803264
NZ_KV80327624123812261,519RefSeq:NZ_KV803276
NZ_KV80329926626501261,447RefSeq:NZ_KV803299
NZ_KV80329121921513255,847RefSeq:NZ_KV803291
NZ_KV80321223523032249,432RefSeq:NZ_KV803212
NZ_KV80322821520942226,218RefSeq:NZ_KV803228
NZ_KV80329423422761218,794RefSeq:NZ_KV803294
NZ_KV80326317116812205,503RefSeq:NZ_KV803263
NZ_KV80324619218606205,112RefSeq:NZ_KV803246
NZ_KV80322518918531194,952RefSeq:NZ_KV803225
NZ_KV80330615414905172,975RefSeq:NZ_KV803306
NZ_KV80328317717340169,678RefSeq:NZ_KV803283
NZ_KV80329816816332163,285RefSeq:NZ_KV803298
NZ_KV80323515114920153,805RefSeq:NZ_KV803235
NZ_KV80325014413617135,755RefSeq:NZ_KV803250
NZ_KV80325810810620121,850RefSeq:NZ_KV803258
NZ_KV80323210410310113,078RefSeq:NZ_KV803232
NZ_KV803284989611102,338RefSeq:NZ_KV803284
NZ_KV80329370650572,341RefSeq:NZ_KV803293
NZ_KV80324762600266,309RefSeq:NZ_KV803247
NZ_KV80321564640063,034RefSeq:NZ_KV803215
NZ_KV80327246460062,319RefSeq:NZ_KV803272
NZ_KV80329253520159,544RefSeq:NZ_KV803292
NZ_KV80324540370348,010RefSeq:NZ_KV803245
NZ_KV80323350434347,398RefSeq:NZ_KV803233
NZ_KV80328740381142,976RefSeq:NZ_KV803287
NZ_KV80327841400141,546RefSeq:NZ_KV803278
NZ_KV80322138380040,387RefSeq:NZ_KV803221
NZ_KV80327932320039,147RefSeq:NZ_KV803279
NZ_KV80321317160126,827RefSeq:NZ_KV803213
NZ_KV80325421190225,029RefSeq:NZ_KV803254
NZ_KV80322722220024,847RefSeq:NZ_KV803227
NZ_KV80321719171124,383RefSeq:NZ_KV803217
NZ_KV80322018180017,686RefSeq:NZ_KV803220
NZ_KV80323715150016,074RefSeq:NZ_KV803237
NZ_KV80323816160014,869RefSeq:NZ_KV803238
NZ_KV8033031070310,243RefSeq:NZ_KV803303
55 Undisplayed Contigs/Replicons6961819106,735
Total:6,2156,044631086,741,417
Ortholog data available?No
Database Contents
Genes6,215
Pathways310
Enzymatic Reactions1,625
Transport Reactions94
Polypeptides6,173
Protein Complexes10
Enzymes1,088
Transporters1,101
Compounds1,170
Transcription Units4,060
tRNAs55
Protein Features7,819
GO Terms2,355
Database Version29.0
Sequence SourceGCF_001810925.1
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)
BIOSAMPLESAMN04477589
NCBI BioProjectPRJNA224116
NCBI-Taxonomy85698
Environmentwound mouth
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2022-01-13
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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