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 OIFC087, 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_AMFS0100003436735377391,463RefSeq:NZ_AMFS01000034
NZ_AMFS0100008623422284243,307RefSeq:NZ_AMFS01000086
NZ_AMFS0100004420819945224,579RefSeq:NZ_AMFS01000044
NZ_AMFS0100009321621114213,891RefSeq:NZ_AMFS01000093
NZ_AMFS0100001920219606211,968RefSeq:NZ_AMFS01000019
NZ_AMFS0100008716815486181,186RefSeq:NZ_AMFS01000087
NZ_AMFS0100003615714872155,133RefSeq:NZ_AMFS01000036
NZ_AMFS0100000213713403142,251RefSeq:NZ_AMFS01000002
NZ_AMFS0100000113112713130,598RefSeq:NZ_AMFS01000001
NZ_AMFS0100003811010613112,056RefSeq:NZ_AMFS01000038
NZ_AMFS01000051100971299,179RefSeq:NZ_AMFS01000051
NZ_AMFS0100003082780491,156RefSeq:NZ_AMFS01000030
NZ_AMFS0100008990825390,965RefSeq:NZ_AMFS01000089
NZ_AMFS0100002097923289,686RefSeq:NZ_AMFS01000020
NZ_AMFS01000092102946288,075RefSeq:NZ_AMFS01000092
NZ_AMFS0100001391822783,637RefSeq:NZ_AMFS01000013
NZ_AMFS0100005676740282,241RefSeq:NZ_AMFS01000056
NZ_AMFS0100006068650377,190RefSeq:NZ_AMFS01000060
NZ_AMFS0100008468630576,707RefSeq:NZ_AMFS01000084
NZ_AMFS0100005768634167,236RefSeq:NZ_AMFS01000057
NZ_AMFS0100003365529465,042RefSeq:NZ_AMFS01000033
NZ_AMFS0100007359560362,996RefSeq:NZ_AMFS01000073
NZ_AMFS0100005258530562,714RefSeq:NZ_AMFS01000052
NZ_AMFS0100007665547461,242RefSeq:NZ_AMFS01000076
NZ_AMFS0100006461590259,502RefSeq:NZ_AMFS01000064
NZ_AMFS0100002765577157,184RefSeq:NZ_AMFS01000027
NZ_AMFS01000054634701651,168RefSeq:NZ_AMFS01000054
NZ_AMFS0100006646440248,779RefSeq:NZ_AMFS01000066
NZ_AMFS0100004239380143,590RefSeq:NZ_AMFS01000042
NZ_AMFS0100005336293440,090RefSeq:NZ_AMFS01000053
NZ_AMFS0100003238360238,420RefSeq:NZ_AMFS01000032
NZ_AMFS0100007741380338,206RefSeq:NZ_AMFS01000077
NZ_AMFS0100000534310337,148RefSeq:NZ_AMFS01000005
NZ_AMFS0100000833320135,915RefSeq:NZ_AMFS01000008
NZ_AMFS0100000738325133,421RefSeq:NZ_AMFS01000007
NZ_AMFS0100000428260232,818RefSeq:NZ_AMFS01000004
NZ_AMFS0100006524171630,956RefSeq:NZ_AMFS01000065
NZ_AMFS0100002840380225,404RefSeq:NZ_AMFS01000028
NZ_AMFS0100004625220325,147RefSeq:NZ_AMFS01000046
NZ_AMFS0100005025232023,014RefSeq:NZ_AMFS01000050
NZ_AMFS0100001719180121,397RefSeq:NZ_AMFS01000017
NZ_AMFS0100009619190019,747RefSeq:NZ_AMFS01000096
NZ_AMFS0100009519151319,723RefSeq:NZ_AMFS01000095
NZ_AMFS0100008816130318,770RefSeq:NZ_AMFS01000088
NZ_AMFS0100004115120318,633RefSeq:NZ_AMFS01000041
NZ_AMFS0100008515130216,131RefSeq:NZ_AMFS01000085
NZ_AMFS0100007915130213,572RefSeq:NZ_AMFS01000079
NZ_AMFS0100009113120113,280RefSeq:NZ_AMFS01000091
NZ_AMFS0100006818160212,296RefSeq:NZ_AMFS01000068
NZ_AMFS010000801290311,979RefSeq:NZ_AMFS01000080
NZ_AMFS0100004013100311,953RefSeq:NZ_AMFS01000040
NZ_AMFS010000551210026,851RefSeq:NZ_AMFS01000055
NZ_AMFS010000261312016,798RefSeq:NZ_AMFS01000026
43 Undisplayed Contigs/Replicons595814988,292
Total:3,9623,654942144,004,682
Ortholog data available?Yes
Database Contents
Genes3,955
Pathways265
Enzymatic Reactions1,313
Transport Reactions113
Polypeptides3,677
Protein Complexes54
Enzymes802
Transporters359
Compounds1,080
Transcription Units2,774
tRNAs73
GO Terms1,450
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii OIFC087
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761219
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903929
Environmentperineum
Geographic LocationUSA
Collection Date2003-08-12
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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