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. Ac_877 AC 877, 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_LWRV0100003514714322141,290RefSeq:NZ_LWRV01000035
NZ_LWRV0100008012411554136,874RefSeq:NZ_LWRV01000080
NZ_LWRV0100000211310814111,943RefSeq:NZ_LWRV01000002
NZ_LWRV01000091878106102,343RefSeq:NZ_LWRV01000091
NZ_LWRV0100004789845095,811RefSeq:NZ_LWRV01000047
NZ_LWRV0100008296940295,718RefSeq:NZ_LWRV01000082
NZ_LWRV0100011381718291,344RefSeq:NZ_LWRV01000113
NZ_LWRV0100003280770388,818RefSeq:NZ_LWRV01000032
NZ_LWRV0100007776720483,833RefSeq:NZ_LWRV01000077
NZ_LWRV0100005877663880,416RefSeq:NZ_LWRV01000058
NZ_LWRV0100003872680479,769RefSeq:NZ_LWRV01000038
NZ_LWRV0100004075704177,619RefSeq:NZ_LWRV01000040
NZ_LWRV0100008974730173,994RefSeq:NZ_LWRV01000089
NZ_LWRV0100004957510667,797RefSeq:NZ_LWRV01000049
NZ_LWRV0100005758551264,830RefSeq:NZ_LWRV01000057
NZ_LWRV0100003457533161,636RefSeq:NZ_LWRV01000034
NZ_LWRV0100010857550257,175RefSeq:NZ_LWRV01000108
NZ_LWRV0100004251480352,109RefSeq:NZ_LWRV01000042
NZ_LWRV0100009438380050,228RefSeq:NZ_LWRV01000094
NZ_LWRV0100003046440249,863RefSeq:NZ_LWRV01000030
NZ_LWRV0100007145420347,672RefSeq:NZ_LWRV01000071
NZ_LWRV0100003348434145,487RefSeq:NZ_LWRV01000033
NZ_LWRV0100007663611143,222RefSeq:NZ_LWRV01000076
NZ_LWRV0100006934313038,596RefSeq:NZ_LWRV01000069
NZ_LWRV0100006838371036,853RefSeq:NZ_LWRV01000068
NZ_LWRV0100008329280136,781RefSeq:NZ_LWRV01000083
NZ_LWRV0100005332301136,087RefSeq:NZ_LWRV01000053
NZ_LWRV0100003134340036,015RefSeq:NZ_LWRV01000031
NZ_LWRV0100009537350235,927RefSeq:NZ_LWRV01000095
NZ_LWRV0100006432301131,747RefSeq:NZ_LWRV01000064
NZ_LWRV0100003929270229,125RefSeq:NZ_LWRV01000039
NZ_LWRV0100002931290228,392RefSeq:NZ_LWRV01000029
NZ_LWRV0100005028242227,824RefSeq:NZ_LWRV01000050
NZ_LWRV0100008724220226,702RefSeq:NZ_LWRV01000087
NZ_LWRV0100006230282026,047RefSeq:NZ_LWRV01000062
NZ_LWRV0100009218180025,946RefSeq:NZ_LWRV01000092
NZ_LWRV0100010233257125,378RefSeq:NZ_LWRV01000102
NZ_LWRV0100010419161224,701RefSeq:NZ_LWRV01000104
NZ_LWRV0100004120180224,632RefSeq:NZ_LWRV01000041
NZ_LWRV0100007023220124,568RefSeq:NZ_LWRV01000070
NZ_LWRV0100005918160224,235RefSeq:NZ_LWRV01000059
NZ_LWRV0100007937370023,455RefSeq:NZ_LWRV01000079
NZ_LWRV0100003728210722,650RefSeq:NZ_LWRV01000037
NZ_LWRV0100011026224022,222RefSeq:NZ_LWRV01000110
NZ_LWRV0100006520173021,990RefSeq:NZ_LWRV01000065
NZ_LWRV0100005522190321,754RefSeq:NZ_LWRV01000055
NZ_LWRV0100008120190120,828RefSeq:NZ_LWRV01000081
NZ_LWRV0100007518140420,770RefSeq:NZ_LWRV01000075
NZ_LWRV0100006617170020,595RefSeq:NZ_LWRV01000066
NZ_LWRV0100010714140020,441RefSeq:NZ_LWRV01000107
NZ_LWRV0100009720190118,949RefSeq:NZ_LWRV01000097
NZ_LWRV0100011916141118,406RefSeq:NZ_LWRV01000119
NZ_LWRV0100008817140318,376RefSeq:NZ_LWRV01000088
NZ_LWRV0100009621170418,318RefSeq:NZ_LWRV01000096
NZ_LWRV0100009019180117,974RefSeq:NZ_LWRV01000090
NZ_LWRV0100010620200017,751RefSeq:NZ_LWRV01000106
NZ_LWRV0100010013121016,465RefSeq:NZ_LWRV01000100
NZ_LWRV0100010911100114,777RefSeq:NZ_LWRV01000109
NZ_LWRV010000611280414,381RefSeq:NZ_LWRV01000061
NZ_LWRV0100005412110111,932RefSeq:NZ_LWRV01000054
NZ_LWRV0100004313130011,093RefSeq:NZ_LWRV01000043
NZ_LWRV010000981513209,849RefSeq:NZ_LWRV01000098
61 Undisplayed Contigs/Replicons143138522174,958
Total:2,7762,569711362,897,281
Ortholog data available?Yes
Database Contents
Genes2,776
Pathways211
Enzymatic Reactions1,110
Transport Reactions73
Polypeptides2,608
Protein Complexes38
Enzymes640
Transporters264
Compounds814
Transcription Units1,991
tRNAs64
Protein Features3,189
GO Terms7
Database Version29.0
Sequence SourceGCF_009372215.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
unclassified Acinetobacter
Acinetobacter sp. Ac_877
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04884745
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1839785
Environmentpork meat
Geographic LocationPortugal
Collection Date2014-09-30
Annotation ProviderNCBI RefSeq
Annotation Date2020-11-9
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.13
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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