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_2008-15-52, 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_AMHM0100006424823954270,672RefSeq:NZ_AMHM01000064
NZ_AMHM0100008921320562212,152RefSeq:NZ_AMHM01000089
NZ_AMHM0100003517817413195,080RefSeq:NZ_AMHM01000035
NZ_AMHM0100007717717016182,619RefSeq:NZ_AMHM01000077
NZ_AMHM0100010416315904170,688RefSeq:NZ_AMHM01000104
NZ_AMHM0100003815615123164,017RefSeq:NZ_AMHM01000038
NZ_AMHM0100002313913243149,800RefSeq:NZ_AMHM01000023
NZ_AMHM0100005113813053143,440RefSeq:NZ_AMHM01000051
NZ_AMHM0100005614413626142,905RefSeq:NZ_AMHM01000056
NZ_AMHM0100004114413923136,081RefSeq:NZ_AMHM01000041
NZ_AMHM0100009811910982121,985RefSeq:NZ_AMHM01000098
NZ_AMHM01000018989611119,999RefSeq:NZ_AMHM01000018
NZ_AMHM010000781009703118,190RefSeq:NZ_AMHM01000078
NZ_AMHM0100000910910504116,140RefSeq:NZ_AMHM01000009
NZ_AMHM0100008510410211110,235RefSeq:NZ_AMHM01000085
NZ_AMHM0100003283810288,877RefSeq:NZ_AMHM01000032
NZ_AMHM0100007484830180,816RefSeq:NZ_AMHM01000074
NZ_AMHM0100001776740277,329RefSeq:NZ_AMHM01000017
NZ_AMHM0100003175750077,235RefSeq:NZ_AMHM01000031
NZ_AMHM0100006067650270,389RefSeq:NZ_AMHM01000060
NZ_AMHM0100003053510262,782RefSeq:NZ_AMHM01000030
NZ_AMHM0100004853520160,243RefSeq:NZ_AMHM01000048
NZ_AMHM0100003455511357,977RefSeq:NZ_AMHM01000034
NZ_AMHM0100005554484257,278RefSeq:NZ_AMHM01000055
NZ_AMHM0100004259544156,661RefSeq:NZ_AMHM01000042
NZ_AMHM0100004052511055,877RefSeq:NZ_AMHM01000040
NZ_AMHM0100001638353053,221RefSeq:NZ_AMHM01000016
NZ_AMHM0100005250490151,773RefSeq:NZ_AMHM01000052
NZ_AMHM0100004549460350,375RefSeq:NZ_AMHM01000045
NZ_AMHM0100006955522147,360RefSeq:NZ_AMHM01000069
NZ_AMHM0100006239350439,711RefSeq:NZ_AMHM01000062
NZ_AMHM0100002038322439,213RefSeq:NZ_AMHM01000020
NZ_AMHM0100007927260135,003RefSeq:NZ_AMHM01000079
NZ_AMHM0100004935340132,697RefSeq:NZ_AMHM01000049
NZ_AMHM0100005928280026,407RefSeq:NZ_AMHM01000059
NZ_AMHM0100003720190124,513RefSeq:NZ_AMHM01000037
NZ_AMHM0100007022210124,243RefSeq:NZ_AMHM01000070
NZ_AMHM0100009625231123,747RefSeq:NZ_AMHM01000096
NZ_AMHM0100004621190223,505RefSeq:NZ_AMHM01000046
NZ_AMHM0100007222220023,205RefSeq:NZ_AMHM01000072
NZ_AMHM0100001226260020,448RefSeq:NZ_AMHM01000012
NZ_AMHM0100006616150117,806RefSeq:NZ_AMHM01000066
NZ_AMHM0100004415150017,574RefSeq:NZ_AMHM01000044
NZ_AMHM0100004316150116,310RefSeq:NZ_AMHM01000043
NZ_AMHM0100006317160114,609RefSeq:NZ_AMHM01000063
NZ_AMHM0100005713120114,088RefSeq:NZ_AMHM01000057
NZ_AMHM0100002613110213,368RefSeq:NZ_AMHM01000026
NZ_AMHM0100004719180113,236RefSeq:NZ_AMHM01000047
NZ_AMHM0100003321200111,036RefSeq:NZ_AMHM01000033
55 Undisplayed Contigs/Replicons137130740156,467
Total:3,7433,548631323,889,382
Ortholog data available?Yes
Database Contents
Genes3,743
Pathways271
Enzymatic Reactions1,309
Transport Reactions100
Polypeptides3,575
Protein Complexes54
Enzymes775
Transporters355
Compounds1,067
Transcription Units2,634
tRNAs56
GO Terms1,294
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_2008-15-52
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471259
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221257
Environmentwound
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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