Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Achromobacter xylosoxidans HMSC057D05, 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_KV8205408748553161,010,526RefSeq:NZ_KV820540
NZ_KV82051552451176605,436RefSeq:NZ_KV820515
NZ_KV820547509496013581,514RefSeq:NZ_KV820547
NZ_KV82048036335517411,310RefSeq:NZ_KV820480
NZ_KV820539313300310323,615RefSeq:NZ_KV820539
NZ_KV82052830229705314,966RefSeq:NZ_KV820528
NZ_KV82055224823738264,419RefSeq:NZ_KV820552
NZ_KV82052420419815240,296RefSeq:NZ_KV820524
NZ_KV82049316616231164,547RefSeq:NZ_KV820493
NZ_KV82054416115632163,041RefSeq:NZ_KV820544
NZ_KV82049514614600156,472RefSeq:NZ_KV820495
NZ_KV82048514214101153,866RefSeq:NZ_KV820485
NZ_KV82046715114920151,515RefSeq:NZ_KV820467
NZ_KV82053611511032127,297RefSeq:NZ_KV820536
NZ_KV82050211011000122,148RefSeq:NZ_KV820502
NZ_KV82054311411112119,272RefSeq:NZ_KV820543
NZ_KV82053811110911110,684RefSeq:NZ_KV820538
NZ_KV820512969510102,429RefSeq:NZ_KV820512
NZ_KV820518868330101,420RefSeq:NZ_KV820518
NZ_KV820501939111101,316RefSeq:NZ_KV820501
NZ_KV82054885811387,342RefSeq:NZ_KV820548
NZ_KV82050471701080,533RefSeq:NZ_KV820504
NZ_KV82051762611072,048RefSeq:NZ_KV820517
NZ_KV82047963620167,454RefSeq:NZ_KV820479
NZ_KV82049055540161,374RefSeq:NZ_KV820490
NZ_KV82050961590259,620RefSeq:NZ_KV820509
NZ_KV82046152520050,186RefSeq:NZ_KV820461
NZ_KV82048953520148,554RefSeq:NZ_KV820489
NZ_KV82052651446146,046RefSeq:NZ_KV820526
NZ_KV82052041400141,760RefSeq:NZ_KV820520
NZ_KV82046653530041,037RefSeq:NZ_KV820466
NZ_KV82047438380040,378RefSeq:NZ_KV820474
NZ_KV82047135323040,247RefSeq:NZ_KV820471
NZ_KV82049937370039,688RefSeq:NZ_KV820499
NZ_KV82047832320038,620RefSeq:NZ_KV820478
NZ_KV82054540371234,154RefSeq:NZ_KV820545
NZ_KV82047629280132,950RefSeq:NZ_KV820476
NZ_KV82048722220024,835RefSeq:NZ_KV820487
NZ_KV82050318171023,311RefSeq:NZ_KV820503
NZ_KV82047721210022,172RefSeq:NZ_KV820477
NZ_KV82046821192021,301RefSeq:NZ_KV820468
NZ_KV82050012120020,133RefSeq:NZ_KV820500
NZ_KV82055017170018,023RefSeq:NZ_KV820550
NZ_KV82047218170117,603RefSeq:NZ_KV820472
NZ_KV82048412120016,461RefSeq:NZ_KV820484
NZ_KV820541117139,575RefSeq:NZ_KV820541
46 Undisplayed Contigs/Replicons6560523100,196
Total:5,9265,748581206,481,690
Ortholog data available?No
Database Contents
Genes5,926
Pathways306
Enzymatic Reactions1,592
Transport Reactions95
Polypeptides5,934
Protein Complexes216
Enzymes1,012
Transporters769
Compounds1,152
Transcription Units3,960
tRNAs50
Protein Features7,536
GO Terms2,211
Database Version29.0
Sequence SourceGCF_001815425.1
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)
BIOSAMPLESAMN04480442
NCBI BioProjectPRJNA224116
NCBI-Taxonomy85698
Environmentsputum
HostHomo sapiens
Human Microbiome Body Siteoral
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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