Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 29-Oct-2024 from the annotated genome of Achromobacter marplatensis ANA, as obtained from RefSeq (annotation date: 16-JAN-2024). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [Karp11, Karp16] using MetaCyc version 28.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_ALJE0100000551550096537,020RefSeq:NZ_ALJE01000005
NZ_ALJE0100000647346706507,447RefSeq:NZ_ALJE01000006
NZ_ALJE0100000841941540471,029RefSeq:NZ_ALJE01000008
NZ_ALJE0100001136636312428,481RefSeq:NZ_ALJE01000011
NZ_ALJE0100000238037325412,915RefSeq:NZ_ALJE01000002
NZ_ALJE01000016329319100356,526RefSeq:NZ_ALJE01000016
NZ_ALJE0100002032432040348,307RefSeq:NZ_ALJE01000020
NZ_ALJE0100001525525311257,856RefSeq:NZ_ALJE01000015
NZ_ALJE0100002921020442243,576RefSeq:NZ_ALJE01000029
NZ_ALJE0100001717417400187,170RefSeq:NZ_ALJE01000017
NZ_ALJE0100003615215020158,976RefSeq:NZ_ALJE01000036
NZ_ALJE0100003213213101153,458RefSeq:NZ_ALJE01000032
NZ_ALJE0100004214814323151,703RefSeq:NZ_ALJE01000042
NZ_ALJE0100002212011703145,960RefSeq:NZ_ALJE01000022
NZ_ALJE0100000411611420145,356RefSeq:NZ_ALJE01000004
NZ_ALJE0100004012412121132,287RefSeq:NZ_ALJE01000040
NZ_ALJE0100003410310300130,951RefSeq:NZ_ALJE01000034
NZ_ALJE0100002710810800124,176RefSeq:NZ_ALJE01000027
NZ_ALJE0100003310510410119,733RefSeq:NZ_ALJE01000033
NZ_ALJE0100005210410310107,926RefSeq:NZ_ALJE01000052
NZ_ALJE0100001310510122104,776RefSeq:NZ_ALJE01000013
NZ_ALJE01000043858500101,582RefSeq:NZ_ALJE01000043
NZ_ALJE010000241091060398,474RefSeq:NZ_ALJE01000024
NZ_ALJE010000191031020197,898RefSeq:NZ_ALJE01000019
NZ_ALJE0100000988861197,858RefSeq:NZ_ALJE01000009
NZ_ALJE0100006171710087,983RefSeq:NZ_ALJE01000061
NZ_ALJE0100005868671085,545RefSeq:NZ_ALJE01000058
NZ_ALJE0100002387852082,293RefSeq:NZ_ALJE01000023
NZ_ALJE0100000766651071,281RefSeq:NZ_ALJE01000007
NZ_ALJE0100005563620169,992RefSeq:NZ_ALJE01000055
NZ_ALJE0100005769680168,787RefSeq:NZ_ALJE01000057
NZ_ALJE0100005150491058,209RefSeq:NZ_ALJE01000051
NZ_ALJE0100002652520053,143RefSeq:NZ_ALJE01000026
NZ_ALJE0100003528270144,736RefSeq:NZ_ALJE01000035
NZ_ALJE0100001050490142,317RefSeq:NZ_ALJE01000010
NZ_ALJE0100001436360041,210RefSeq:NZ_ALJE01000014
NZ_ALJE0100003923230034,001RefSeq:NZ_ALJE01000039
NZ_ALJE0100004933320133,147RefSeq:NZ_ALJE01000049
NZ_ALJE0100004430290132,140RefSeq:NZ_ALJE01000044
NZ_ALJE0100005331283026,384RefSeq:NZ_ALJE01000053
NZ_ALJE0100000123230024,368RefSeq:NZ_ALJE01000001
NZ_ALJE0100003719161223,494RefSeq:NZ_ALJE01000037
NZ_ALJE0100005922193022,853RefSeq:NZ_ALJE01000059
NZ_ALJE0100003834330122,742RefSeq:NZ_ALJE01000038
NZ_ALJE0100001225240120,923RefSeq:NZ_ALJE01000012
NZ_ALJE0100006218180020,289RefSeq:NZ_ALJE01000062
NZ_ALJE0100005419180119,556RefSeq:NZ_ALJE01000054
NZ_ALJE0100002816160018,986RefSeq:NZ_ALJE01000028
NZ_ALJE0100005614130117,864RefSeq:NZ_ALJE01000056
NZ_ALJE0100004816160017,175RefSeq:NZ_ALJE01000048
NZ_ALJE0100002523212014,416RefSeq:NZ_ALJE01000025
132 Undisplayed Contigs/Replicons1441351438216,926
Total:6,3206,15776876,892,201
Ortholog data available?No
Database Contents
Genes6,313
Pathways360
Enzymatic Reactions1,970
Transport Reactions115
Polypeptides6,317
Protein Complexes241
Enzymes1,163
Transporters851
Compounds1,614
Transcription Units4,294
tRNAs59
Protein Features8,297
GO Terms8,571
Database Version29.0
Sequence SourceGCF_000286415.1
Synonyms Achromobacter group 10
Achromobacter sp. CCUG 47382
Achromobacter spiritinus
Achromobacter sp. LMG 26696
Achromobacter sp. R-46660
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter marplatensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01083790
NCBI BioProjectPRJNA224116
NCBI-Taxonomy470868
Environmentsoil
Geographic LocationUSA
Collection Date1974
Annotation ProviderNCBI RefSeq
Annotation Date2024-01-16
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.6
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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