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_TG2031, 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_AMIK0100001220119722222,320RefSeq:NZ_AMIK01000012
NZ_AMIK0100001022822062207,020RefSeq:NZ_AMIK01000010
NZ_AMIK0100003618417761197,384RefSeq:NZ_AMIK01000036
NZ_AMIK0100000116816422189,168RefSeq:NZ_AMIK01000001
NZ_AMIK0100000516015604170,189RefSeq:NZ_AMIK01000005
NZ_AMIK0100001414614033170,047RefSeq:NZ_AMIK01000014
NZ_AMIK0100000816616312167,535RefSeq:NZ_AMIK01000008
NZ_AMIK0100002116715629161,636RefSeq:NZ_AMIK01000021
NZ_AMIK0100002216215714161,162RefSeq:NZ_AMIK01000022
NZ_AMIK0100006013012703141,904RefSeq:NZ_AMIK01000060
NZ_AMIK0100004112912351140,361RefSeq:NZ_AMIK01000041
NZ_AMIK0100007313413202138,899RefSeq:NZ_AMIK01000073
NZ_AMIK0100003811111010130,252RefSeq:NZ_AMIK01000038
NZ_AMIK0100002413413112128,182RefSeq:NZ_AMIK01000024
NZ_AMIK0100005311710962120,044RefSeq:NZ_AMIK01000053
NZ_AMIK0100007081790293,300RefSeq:NZ_AMIK01000070
NZ_AMIK0100002686824087,856RefSeq:NZ_AMIK01000026
NZ_AMIK0100004483802187,188RefSeq:NZ_AMIK01000044
NZ_AMIK0100006981810075,041RefSeq:NZ_AMIK01000069
NZ_AMIK0100005469680173,497RefSeq:NZ_AMIK01000054
NZ_AMIK0100002566660070,693RefSeq:NZ_AMIK01000025
NZ_AMIK0100001671700168,851RefSeq:NZ_AMIK01000016
NZ_AMIK0100007563611167,817RefSeq:NZ_AMIK01000075
NZ_AMIK0100005248471055,876RefSeq:NZ_AMIK01000052
NZ_AMIK0100002361601052,814RefSeq:NZ_AMIK01000023
NZ_AMIK0100004549450445,691RefSeq:NZ_AMIK01000045
NZ_AMIK0100002740390142,077RefSeq:NZ_AMIK01000027
NZ_AMIK0100001933330040,074RefSeq:NZ_AMIK01000019
NZ_AMIK0100004340364039,875RefSeq:NZ_AMIK01000043
NZ_AMIK0100003437370036,341RefSeq:NZ_AMIK01000034
NZ_AMIK0100003230290134,059RefSeq:NZ_AMIK01000032
NZ_AMIK0100006828253033,394RefSeq:NZ_AMIK01000068
NZ_AMIK0100002929280131,904RefSeq:NZ_AMIK01000029
NZ_AMIK0100003120200028,072RefSeq:NZ_AMIK01000031
NZ_AMIK0100003028280026,455RefSeq:NZ_AMIK01000030
NZ_AMIK0100004026230325,906RefSeq:NZ_AMIK01000040
NZ_AMIK0100001731271325,839RefSeq:NZ_AMIK01000017
NZ_AMIK0100004920190123,419RefSeq:NZ_AMIK01000049
NZ_AMIK0100005118180021,975RefSeq:NZ_AMIK01000051
NZ_AMIK0100006117170020,877RefSeq:NZ_AMIK01000061
NZ_AMIK0100002823220119,704RefSeq:NZ_AMIK01000028
NZ_AMIK0100003920190116,775RefSeq:NZ_AMIK01000039
NZ_AMIK0100004817170014,310RefSeq:NZ_AMIK01000048
32 Undisplayed Contigs/Replicons665791577,005
Total:3,6333,49562763,782,788
Ortholog data available?Yes
Database Contents
Genes3,633
Pathways267
Enzymatic Reactions1,297
Transport Reactions99
Polypeptides3,516
Protein Complexes51
Enzymes756
Transporters350
Compounds1,047
Transcription Units2,543
tRNAs54
GO Terms1,365
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_TG2031
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471264
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221280
Environmentsputum
HostHomo sapiens
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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