Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 12-July-2021 from the annotated genome of Achromobacter deleyi LMG 3458, 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 25.0) [Karp16, Karp11] using MetaCyc version 25.0 [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_CADIJO01000000150850080583,542RefSeq:NZ_CADIJO010000001
NZ_CADIJO01000000248447617541,222RefSeq:NZ_CADIJO010000002
NZ_CADIJO01000000342041442442,863RefSeq:NZ_CADIJO010000003
NZ_CADIJO01000000437236741394,241RefSeq:NZ_CADIJO010000004
NZ_CADIJO01000000532531537320,867RefSeq:NZ_CADIJO010000005
NZ_CADIJO01000000628928432297,100RefSeq:NZ_CADIJO010000006
NZ_CADIJO01000000727526654276,663RefSeq:NZ_CADIJO010000007
NZ_CADIJO01000000822722502247,410RefSeq:NZ_CADIJO010000008
NZ_CADIJO01000000919519500244,613RefSeq:NZ_CADIJO010000009
NZ_CADIJO01000001022021721234,996RefSeq:NZ_CADIJO010000010
NZ_CADIJO01000001121120281220,412RefSeq:NZ_CADIJO010000011
NZ_CADIJO01000001219218912212,416RefSeq:NZ_CADIJO010000012
NZ_CADIJO01000001315715502183,103RefSeq:NZ_CADIJO010000013
NZ_CADIJO01000001416216200173,227RefSeq:NZ_CADIJO010000014
NZ_CADIJO01000001514814503161,681RefSeq:NZ_CADIJO010000015
NZ_CADIJO01000001616515735152,007RefSeq:NZ_CADIJO010000016
NZ_CADIJO01000001711310904125,000RefSeq:NZ_CADIJO010000017
NZ_CADIJO01000001812011901117,325RefSeq:NZ_CADIJO010000018
NZ_CADIJO01000001910510311107,250RefSeq:NZ_CADIJO010000019
NZ_CADIJO01000002010310210101,755RefSeq:NZ_CADIJO010000020
NZ_CADIJO010000021101962399,607RefSeq:NZ_CADIJO010000021
NZ_CADIJO01000002275750092,228RefSeq:NZ_CADIJO010000022
NZ_CADIJO01000002372700291,472RefSeq:NZ_CADIJO010000023
NZ_CADIJO01000002488870191,318RefSeq:NZ_CADIJO010000024
NZ_CADIJO01000002578724286,506RefSeq:NZ_CADIJO010000025
NZ_CADIJO01000002666660081,614RefSeq:NZ_CADIJO010000026
NZ_CADIJO01000002773720172,187RefSeq:NZ_CADIJO010000027
NZ_CADIJO01000002861601065,928RefSeq:NZ_CADIJO010000028
NZ_CADIJO01000002960570362,719RefSeq:NZ_CADIJO010000029
NZ_CADIJO01000003055521262,393RefSeq:NZ_CADIJO010000030
NZ_CADIJO01000003154530161,942RefSeq:NZ_CADIJO010000031
NZ_CADIJO01000003252501159,357RefSeq:NZ_CADIJO010000032
NZ_CADIJO01000003343430056,829RefSeq:NZ_CADIJO010000033
NZ_CADIJO01000003457560154,944RefSeq:NZ_CADIJO010000034
NZ_CADIJO01000003545430252,717RefSeq:NZ_CADIJO010000035
NZ_CADIJO01000003648480052,528RefSeq:NZ_CADIJO010000036
NZ_CADIJO01000003744421149,760RefSeq:NZ_CADIJO010000037
NZ_CADIJO01000003842420047,629RefSeq:NZ_CADIJO010000038
NZ_CADIJO01000003933330041,158RefSeq:NZ_CADIJO010000039
NZ_CADIJO01000004032320041,089RefSeq:NZ_CADIJO010000040
NZ_CADIJO01000004129280140,151RefSeq:NZ_CADIJO010000041
NZ_CADIJO01000004232310136,969RefSeq:NZ_CADIJO010000042
NZ_CADIJO01000004337334034,071RefSeq:NZ_CADIJO010000043
NZ_CADIJO01000004417160131,785RefSeq:NZ_CADIJO010000044
NZ_CADIJO01000004526260031,094RefSeq:NZ_CADIJO010000045
NZ_CADIJO01000004627250226,745RefSeq:NZ_CADIJO010000046
NZ_CADIJO01000004720190122,492RefSeq:NZ_CADIJO010000047
NZ_CADIJO01000004820190122,034RefSeq:NZ_CADIJO010000048
NZ_CADIJO01000004914140020,327RefSeq:NZ_CADIJO010000049
NZ_CADIJO01000005013120117,130RefSeq:NZ_CADIJO010000050
NZ_CADIJO01000005114130114,767RefSeq:NZ_CADIJO010000051
20 Undisplayed Contigs/Replicons35315850,325
Total:6,2636,11863826,809,508
Ortholog data available?No
Database Contents
Genes6,261
Pathways295
Enzymatic Reactions1,502
Transport Reactions110
Polypeptides6,177
Protein Complexes100
Enzymes1,023
Transporters1,064
Compounds1,113
Transcription Units4,031
tRNAs53
Protein Features7,991
GO Terms107
Database Version29.0
Sequence SourceGCF_902859705.1
Synonyms Achromobacter sp. LMG 3458
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter deleyi
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA6647249
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1353891
EnvironmentMouse
Annotation ProviderNCBI RefSeq
Annotation Date2020-06-18
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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