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 13-Mar-2021 from the annotated genome of Achromobacter denitrificans NBRC 15125, 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 24.5 [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_BCTQ0100000149448374516,154RefSeq:NZ_BCTQ01000001
NZ_BCTQ0100000226826431316,014RefSeq:NZ_BCTQ01000002
NZ_BCTQ0100000320820503263,260RefSeq:NZ_BCTQ01000003
NZ_BCTQ0100000419018712211,975RefSeq:NZ_BCTQ01000004
NZ_BCTQ0100000520119722204,535RefSeq:NZ_BCTQ01000005
NZ_BCTQ0100000619819341198,623RefSeq:NZ_BCTQ01000006
NZ_BCTQ0100000719519230196,252RefSeq:NZ_BCTQ01000007
NZ_BCTQ0100000819719412187,445RefSeq:NZ_BCTQ01000008
NZ_BCTQ0100000916816800186,329RefSeq:NZ_BCTQ01000009
NZ_BCTQ0100001017016721180,344RefSeq:NZ_BCTQ01000010
NZ_BCTQ0100001115214903168,080RefSeq:NZ_BCTQ01000011
NZ_BCTQ0100001213213020153,618RefSeq:NZ_BCTQ01000012
NZ_BCTQ0100001314614321152,843RefSeq:NZ_BCTQ01000013
NZ_BCTQ0100001413313102152,391RefSeq:NZ_BCTQ01000014
NZ_BCTQ0100001513513500147,895RefSeq:NZ_BCTQ01000015
NZ_BCTQ0100001613813602142,232RefSeq:NZ_BCTQ01000016
NZ_BCTQ0100001712712601131,589RefSeq:NZ_BCTQ01000017
NZ_BCTQ0100001811811710124,894RefSeq:NZ_BCTQ01000018
NZ_BCTQ0100001911411211122,700RefSeq:NZ_BCTQ01000019
NZ_BCTQ0100002012712511119,702RefSeq:NZ_BCTQ01000020
NZ_BCTQ0100002110410112117,962RefSeq:NZ_BCTQ01000021
NZ_BCTQ0100002211411022115,119RefSeq:NZ_BCTQ01000022
NZ_BCTQ0100002311211101113,401RefSeq:NZ_BCTQ01000023
NZ_BCTQ0100002495922199,810RefSeq:NZ_BCTQ01000024
NZ_BCTQ0100002587870096,563RefSeq:NZ_BCTQ01000025
NZ_BCTQ0100002693902195,044RefSeq:NZ_BCTQ01000026
NZ_BCTQ0100002787850290,388RefSeq:NZ_BCTQ01000027
NZ_BCTQ0100002890890189,188RefSeq:NZ_BCTQ01000028
NZ_BCTQ0100002978753084,018RefSeq:NZ_BCTQ01000029
NZ_BCTQ0100003075740179,199RefSeq:NZ_BCTQ01000030
NZ_BCTQ0100003177734077,993RefSeq:NZ_BCTQ01000031
NZ_BCTQ0100003264594172,636RefSeq:NZ_BCTQ01000032
NZ_BCTQ0100003375676271,537RefSeq:NZ_BCTQ01000033
NZ_BCTQ0100003462620070,781RefSeq:NZ_BCTQ01000034
NZ_BCTQ0100003569680170,648RefSeq:NZ_BCTQ01000035
NZ_BCTQ0100003666632165,769RefSeq:NZ_BCTQ01000036
NZ_BCTQ0100003752520065,176RefSeq:NZ_BCTQ01000037
NZ_BCTQ0100003849490063,086RefSeq:NZ_BCTQ01000038
NZ_BCTQ0100003960590160,194RefSeq:NZ_BCTQ01000039
NZ_BCTQ0100004058571058,924RefSeq:NZ_BCTQ01000040
NZ_BCTQ0100004151500158,295RefSeq:NZ_BCTQ01000041
NZ_BCTQ0100004256560052,819RefSeq:NZ_BCTQ01000042
NZ_BCTQ0100004348480048,823RefSeq:NZ_BCTQ01000043
NZ_BCTQ0100004436360044,296RefSeq:NZ_BCTQ01000044
NZ_BCTQ0100004537350241,453RefSeq:NZ_BCTQ01000045
NZ_BCTQ0100004635340140,641RefSeq:NZ_BCTQ01000046
NZ_BCTQ0100004734320240,376RefSeq:NZ_BCTQ01000047
NZ_BCTQ0100004839380139,779RefSeq:NZ_BCTQ01000048
NZ_BCTQ0100004930290138,100RefSeq:NZ_BCTQ01000049
NZ_BCTQ0100005038370138,085RefSeq:NZ_BCTQ01000050
NZ_BCTQ0100005132310137,669RefSeq:NZ_BCTQ01000051
NZ_BCTQ0100005233330036,591RefSeq:NZ_BCTQ01000052
NZ_BCTQ0100005323230035,434RefSeq:NZ_BCTQ01000053
NZ_BCTQ0100005430290135,286RefSeq:NZ_BCTQ01000054
NZ_BCTQ0100005527270034,365RefSeq:NZ_BCTQ01000055
NZ_BCTQ0100005629263032,974RefSeq:NZ_BCTQ01000056
NZ_BCTQ0100005733311132,517RefSeq:NZ_BCTQ01000057
NZ_BCTQ0100005823230030,835RefSeq:NZ_BCTQ01000058
NZ_BCTQ0100005932290328,173RefSeq:NZ_BCTQ01000059
NZ_BCTQ0100006028270127,661RefSeq:NZ_BCTQ01000060
NZ_BCTQ0100006120200027,337RefSeq:NZ_BCTQ01000061
NZ_BCTQ0100006225250026,177RefSeq:NZ_BCTQ01000062
NZ_BCTQ0100006329290025,271RefSeq:NZ_BCTQ01000063
NZ_BCTQ0100006421210024,497RefSeq:NZ_BCTQ01000064
NZ_BCTQ0100006522210123,656RefSeq:NZ_BCTQ01000065
NZ_BCTQ0100006612110122,709RefSeq:NZ_BCTQ01000066
NZ_BCTQ0100006718180021,163RefSeq:NZ_BCTQ01000067
NZ_BCTQ0100006826250120,028RefSeq:NZ_BCTQ01000068
NZ_BCTQ0100006914130117,007RefSeq:NZ_BCTQ01000069
NZ_BCTQ0100007019180116,083RefSeq:NZ_BCTQ01000070
NZ_BCTQ0100007114140015,959RefSeq:NZ_BCTQ01000071
NZ_BCTQ0100007217170015,606RefSeq:NZ_BCTQ01000072
NZ_BCTQ0100007315130214,566RefSeq:NZ_BCTQ01000073
NZ_BCTQ0100007413130014,502RefSeq:NZ_BCTQ01000074
NZ_BCTQ0100007512100214,135RefSeq:NZ_BCTQ01000075
NZ_BCTQ0100007611110012,959RefSeq:NZ_BCTQ01000076
NZ_BCTQ010000791210029,709RefSeq:NZ_BCTQ01000079
21 Undisplayed Contigs/Replicons43416970,406
Total:6,2286,08167806,700,253
Ortholog data available?Yes
Database Contents
Genes6,224
Pathways305
Enzymatic Reactions1,533
Transport Reactions105
Polypeptides6,143
Protein Complexes113
Enzymes1,110
Transporters1,109
Compounds1,139
Transcription Units3,919
tRNAs54
Protein Features8,090
GO Terms43
Database Version29.0
Sequence SourceGCF_001571365.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter denitrificans
Achromobacter denitrificans NBRC 15125
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00046748
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1255278
Annotation ProviderNCBI RefSeq
Annotation Date2020-06-29
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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