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 HMSC056C09, 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_KV8143151,2421,2161251,406,977RefSeq:NZ_KV814315
NZ_KV814313564547116645,656RefSeq:NZ_KV814313
NZ_KV81430937536915443,167RefSeq:NZ_KV814309
NZ_KV81433838237750417,209RefSeq:NZ_KV814338
NZ_KV81433435834918404,527RefSeq:NZ_KV814334
NZ_KV81431722922315256,164RefSeq:NZ_KV814317
NZ_KV81429222621916243,444RefSeq:NZ_KV814292
NZ_KV81426521021000215,113RefSeq:NZ_KV814265
NZ_KV81430620119623215,113RefSeq:NZ_KV814306
NZ_KV81430021120731198,233RefSeq:NZ_KV814300
NZ_KV81432818818332197,324RefSeq:NZ_KV814328
NZ_KV81429816716232193,204RefSeq:NZ_KV814298
NZ_KV81427917016631165,574RefSeq:NZ_KV814279
NZ_KV81428114914720151,298RefSeq:NZ_KV814281
NZ_KV81428413012811131,021RefSeq:NZ_KV814284
NZ_KV81430411110911130,766RefSeq:NZ_KV814304
NZ_KV81429010910531118,626RefSeq:NZ_KV814290
NZ_KV81433510310300108,164RefSeq:NZ_KV814335
NZ_KV814282969411102,657RefSeq:NZ_KV814282
NZ_KV81427188844095,311RefSeq:NZ_KV814271
NZ_KV81428982802091,692RefSeq:NZ_KV814289
NZ_KV81430858560264,323RefSeq:NZ_KV814308
NZ_KV81427052510159,071RefSeq:NZ_KV814270
NZ_KV81428052520058,950RefSeq:NZ_KV814280
NZ_KV81432553466148,584RefSeq:NZ_KV814325
NZ_KV81429939380148,069RefSeq:NZ_KV814299
NZ_KV81432139390041,715RefSeq:NZ_KV814321
NZ_KV81432322220027,026RefSeq:NZ_KV814323
NZ_KV81427622220024,810RefSeq:NZ_KV814276
NZ_KV81430721210022,705RefSeq:NZ_KV814307
NZ_KV81427315141019,434RefSeq:NZ_KV814273
NZ_KV81433118170117,799RefSeq:NZ_KV814331
48 Undisplayed Contigs/Replicons463972569,702
Total:5,8535,69163996,433,428
Ortholog data available?No
Database Contents
Genes5,853
Pathways305
Enzymatic Reactions1,608
Transport Reactions96
Polypeptides5,849
Protein Complexes205
Enzymes1,014
Transporters772
Compounds1,156
Transcription Units3,914
tRNAs55
Protein Features7,492
GO Terms2,189
Database Version29.0
Sequence SourceGCF_001813885.1
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)
BIOSAMPLESAMN04480366
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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