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 Acinetobacter sp. WCHAc060041 WCHAc060041, 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_PYIX0200000127826963299,895RefSeq:NZ_PYIX02000001
NZ_PYIX0200000229028442295,115RefSeq:NZ_PYIX02000002
NZ_PYIX02000003195179142200,819RefSeq:NZ_PYIX02000003
NZ_PYIX0200000417016613182,419RefSeq:NZ_PYIX02000004
NZ_PYIX02000005168157101170,095RefSeq:NZ_PYIX02000005
NZ_PYIX0200000615715412165,885RefSeq:NZ_PYIX02000006
NZ_PYIX020000071099892120,954RefSeq:NZ_PYIX02000007
NZ_PYIX0200000813312940116,180RefSeq:NZ_PYIX02000008
NZ_PYIX0200000911010802112,449RefSeq:NZ_PYIX02000009
NZ_PYIX0200001010910810110,776RefSeq:NZ_PYIX02000010
NZ_PYIX02000011908604100,246RefSeq:NZ_PYIX02000011
NZ_PYIX0200001278780094,605RefSeq:NZ_PYIX02000012
NZ_PYIX0200001395894291,906RefSeq:NZ_PYIX02000013
NZ_PYIX0200001470690191,545RefSeq:NZ_PYIX02000014
NZ_PYIX0200001588870190,187RefSeq:NZ_PYIX02000015
NZ_PYIX0200001671700185,841RefSeq:NZ_PYIX02000016
NZ_PYIX0200001774670784,630RefSeq:NZ_PYIX02000017
NZ_PYIX0200001879724383,910RefSeq:NZ_PYIX02000018
NZ_PYIX0200001974740080,909RefSeq:NZ_PYIX02000019
NZ_PYIX0200002076740280,225RefSeq:NZ_PYIX02000020
NZ_PYIX0200002169680176,940RefSeq:NZ_PYIX02000021
NZ_PYIX0200002264620272,507RefSeq:NZ_PYIX02000022
NZ_PYIX0200002366570972,220RefSeq:NZ_PYIX02000023
NZ_PYIX0200002474730172,190RefSeq:NZ_PYIX02000024
NZ_PYIX0200002573730070,842RefSeq:NZ_PYIX02000025
NZ_PYIX0200002655520359,992RefSeq:NZ_PYIX02000026
NZ_PYIX0200002757542157,196RefSeq:NZ_PYIX02000027
NZ_PYIX0200002850490155,173RefSeq:NZ_PYIX02000028
NZ_PYIX0200002944421153,705RefSeq:NZ_PYIX02000029
NZ_PYIX0200003060571253,356RefSeq:NZ_PYIX02000030
NZ_PYIX0200003147460150,711RefSeq:NZ_PYIX02000031
NZ_PYIX0200003237350250,668RefSeq:NZ_PYIX02000032
NZ_PYIX0200003350490149,987RefSeq:NZ_PYIX02000033
NZ_PYIX0200003447452049,977RefSeq:NZ_PYIX02000034
NZ_PYIX0200003545440147,129RefSeq:NZ_PYIX02000035
NZ_PYIX0200003644430144,664RefSeq:NZ_PYIX02000036
NZ_PYIX0200003732302043,525RefSeq:NZ_PYIX02000037
NZ_PYIX0200003831310042,492RefSeq:NZ_PYIX02000038
NZ_PYIX0200003941410041,777RefSeq:NZ_PYIX02000039
NZ_PYIX0200004032310139,749RefSeq:NZ_PYIX02000040
NZ_PYIX0200004139390035,508RefSeq:NZ_PYIX02000041
NZ_PYIX0200004224240033,350RefSeq:NZ_PYIX02000042
NZ_PYIX0200004326260032,849RefSeq:NZ_PYIX02000043
NZ_PYIX0200004428210731,008RefSeq:NZ_PYIX02000044
NZ_PYIX0200004527250229,297RefSeq:NZ_PYIX02000045
NZ_PYIX0200004633310226,671RefSeq:NZ_PYIX02000046
NZ_PYIX0200004723230025,795RefSeq:NZ_PYIX02000047
NZ_PYIX0200004824230123,958RefSeq:NZ_PYIX02000048
NZ_PYIX0200004932310123,479RefSeq:NZ_PYIX02000049
NZ_PYIX0200005024230123,002RefSeq:NZ_PYIX02000050
NZ_PYIX0200005122210122,782RefSeq:NZ_PYIX02000051
NZ_PYIX0200005221173122,766RefSeq:NZ_PYIX02000052
NZ_PYIX0200005327250220,966RefSeq:NZ_PYIX02000053
NZ_PYIX0200005425240120,901RefSeq:NZ_PYIX02000054
NZ_PYIX0200005530230718,212RefSeq:NZ_PYIX02000055
NZ_PYIX0200005614140018,095RefSeq:NZ_PYIX02000056
NZ_PYIX0200005725221216,267RefSeq:NZ_PYIX02000057
NZ_PYIX0200005814120215,699RefSeq:NZ_PYIX02000058
NZ_PYIX0200005914100413,618RefSeq:NZ_PYIX02000059
NZ_PYIX0200006015150011,833RefSeq:NZ_PYIX02000060
NZ_PYIX0200006114130111,314RefSeq:NZ_PYIX02000061
NZ_PYIX020000661210029,512RefSeq:NZ_PYIX02000066
NZ_PYIX020000691212008,645RefSeq:NZ_PYIX02000069
NZ_PYIX020000701212008,301RefSeq:NZ_PYIX02000070
169 Undisplayed Contigs/Replicons3593491092399,391
Total:4,5204,245801954,666,610
Ortholog data available?Yes
Database Contents
Genes4,520
Pathways291
Enzymatic Reactions1,359
Transport Reactions81
Polypeptides4,352
Protein Complexes50
Enzymes842
Transporters359
Compounds1,035
Transcription Units3,266
tRNAs73
Protein Features4,672
GO Terms16,868
Database Version29.0
Sequence SourceGCF_003024515.2
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
unclassified Acinetobacter
Acinetobacter sp. WCHAc060041
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN08772518
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2136183
EnvironmentSewage
Geographic LocationChina
Collection Date2018
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-20
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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