Database Authors
Pallavi Subhraveti1, Peter Midford, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2019 from the annotated genome of Acinetobacter baumannii AB_908-12, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.0 [Caspi18]. 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 Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AMHV0100009021221101218,529RefSeq:NZ_AMHV01000090
NZ_AMHV0100002219518654205,617RefSeq:NZ_AMHV01000022
NZ_AMHV0100001515815701174,558RefSeq:NZ_AMHV01000015
NZ_AMHV0100004212311913149,107RefSeq:NZ_AMHV01000042
NZ_AMHV0100004314113272138,368RefSeq:NZ_AMHV01000043
NZ_AMHV0100008714414040136,050RefSeq:NZ_AMHV01000087
NZ_AMHV0100005011811602126,273RefSeq:NZ_AMHV01000050
NZ_AMHV0100007412011451121,770RefSeq:NZ_AMHV01000074
NZ_AMHV0100003310510302113,556RefSeq:NZ_AMHV01000033
NZ_AMHV0100005111010802113,251RefSeq:NZ_AMHV01000051
NZ_AMHV01000036999414112,040RefSeq:NZ_AMHV01000036
NZ_AMHV010000911059843104,206RefSeq:NZ_AMHV01000091
NZ_AMHV010000731101070395,629RefSeq:NZ_AMHV01000073
NZ_AMHV0100008395931195,002RefSeq:NZ_AMHV01000083
NZ_AMHV0100006594902294,611RefSeq:NZ_AMHV01000065
NZ_AMHV0100006282780491,029RefSeq:NZ_AMHV01000062
NZ_AMHV0100007087852089,596RefSeq:NZ_AMHV01000070
NZ_AMHV0100001793881487,904RefSeq:NZ_AMHV01000017
NZ_AMHV0100009380790184,486RefSeq:NZ_AMHV01000093
NZ_AMHV0100000772674183,541RefSeq:NZ_AMHV01000007
NZ_AMHV0100004675730283,276RefSeq:NZ_AMHV01000046
NZ_AMHV0100002671690278,464RefSeq:NZ_AMHV01000026
NZ_AMHV0100004173720176,594RefSeq:NZ_AMHV01000041
NZ_AMHV0100005465613175,289RefSeq:NZ_AMHV01000054
NZ_AMHV0100005969660371,461RefSeq:NZ_AMHV01000059
NZ_AMHV0100010770670370,831RefSeq:NZ_AMHV01000107
NZ_AMHV0100005653491367,752RefSeq:NZ_AMHV01000056
NZ_AMHV0100003051500163,439RefSeq:NZ_AMHV01000030
NZ_AMHV0100000349480155,186RefSeq:NZ_AMHV01000003
NZ_AMHV0100003556551054,301RefSeq:NZ_AMHV01000035
NZ_AMHV0100007149480150,338RefSeq:NZ_AMHV01000071
NZ_AMHV0100005558551243,764RefSeq:NZ_AMHV01000055
NZ_AMHV0100011547470042,607RefSeq:NZ_AMHV01000115
NZ_AMHV0100007240370342,355RefSeq:NZ_AMHV01000072
NZ_AMHV0100007642420041,529RefSeq:NZ_AMHV01000076
NZ_AMHV0100006038370140,533RefSeq:NZ_AMHV01000060
NZ_AMHV0100006130263137,845RefSeq:NZ_AMHV01000061
NZ_AMHV0100007530290134,349RefSeq:NZ_AMHV01000075
NZ_AMHV0100002827260129,835RefSeq:NZ_AMHV01000028
NZ_AMHV0100005327250227,365RefSeq:NZ_AMHV01000053
NZ_AMHV0100006928280026,659RefSeq:NZ_AMHV01000069
NZ_AMHV0100009830280226,417RefSeq:NZ_AMHV01000098
NZ_AMHV0100005830290126,017RefSeq:NZ_AMHV01000058
NZ_AMHV0100004425231124,314RefSeq:NZ_AMHV01000044
NZ_AMHV0100003217160123,717RefSeq:NZ_AMHV01000032
NZ_AMHV0100004525214021,885RefSeq:NZ_AMHV01000045
NZ_AMHV0100008225213121,264RefSeq:NZ_AMHV01000082
NZ_AMHV0100005718180020,241RefSeq:NZ_AMHV01000057
NZ_AMHV0100001018153020,236RefSeq:NZ_AMHV01000010
NZ_AMHV0100006732320019,570RefSeq:NZ_AMHV01000067
NZ_AMHV0100011430300018,671RefSeq:NZ_AMHV01000114
NZ_AMHV0100004016151018,385RefSeq:NZ_AMHV01000040
NZ_AMHV0100011112120014,052RefSeq:NZ_AMHV01000111
NZ_AMHV0100006611101013,820RefSeq:NZ_AMHV01000066
NZ_AMHV0100010011110012,760RefSeq:NZ_AMHV01000100
60 Undisplayed Contigs/Replicons140136634162,377
Total:3,8673,692651103,992,621
Ortholog data available?Yes
Database Contents
Genes3,865
Pathways265
Enzymatic Reactions1,361
Transport Reactions112
Polypeptides3,732
Protein Complexes53
Enzymes813
Transporters364
Compounds1,060
Transcription Units2,712
tRNAs57
GO Terms2,276
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_908-12
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471252
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221266
Environmenthospital surface
Annotation ProviderNCBI
Annotation Date2017-11-23
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.3
Annotation CommentBest-placed reference protein set; GeneMarkS+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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