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 OIFC338, 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_AMFX01000021351334107370,834RefSeq:NZ_AMFX01000021
NZ_AMFX0100007532231417315,852RefSeq:NZ_AMFX01000075
NZ_AMFX0100006129328715302,539RefSeq:NZ_AMFX01000061
NZ_AMFX0100007228026686295,594RefSeq:NZ_AMFX01000072
NZ_AMFX0100003219518717210,526RefSeq:NZ_AMFX01000032
NZ_AMFX0100010016716214192,866RefSeq:NZ_AMFX01000100
NZ_AMFX01000038186172122191,380RefSeq:NZ_AMFX01000038
NZ_AMFX0100007918217408188,952RefSeq:NZ_AMFX01000079
NZ_AMFX0100008614814611137,927RefSeq:NZ_AMFX01000086
NZ_AMFX0100005512111047131,133RefSeq:NZ_AMFX01000055
NZ_AMFX0100010313212354129,189RefSeq:NZ_AMFX01000103
NZ_AMFX0100001412211228119,402RefSeq:NZ_AMFX01000014
NZ_AMFX0100001810910135114,326RefSeq:NZ_AMFX01000018
NZ_AMFX0100001212011550110,737RefSeq:NZ_AMFX01000012
NZ_AMFX0100008881717378,110RefSeq:NZ_AMFX01000088
NZ_AMFX0100006250444269,956RefSeq:NZ_AMFX01000062
NZ_AMFX0100003757560169,045RefSeq:NZ_AMFX01000037
NZ_AMFX0100002884830162,711RefSeq:NZ_AMFX01000028
NZ_AMFX0100005957488161,796RefSeq:NZ_AMFX01000059
NZ_AMFX0100000161554259,189RefSeq:NZ_AMFX01000001
NZ_AMFX0100007660551459,104RefSeq:NZ_AMFX01000076
NZ_AMFX0100000443410251,022RefSeq:NZ_AMFX01000004
NZ_AMFX0100010447450250,411RefSeq:NZ_AMFX01000104
NZ_AMFX0100005741383047,060RefSeq:NZ_AMFX01000057
NZ_AMFX0100002546405146,446RefSeq:NZ_AMFX01000025
NZ_AMFX0100001644390545,579RefSeq:NZ_AMFX01000016
NZ_AMFX0100004139380142,083RefSeq:NZ_AMFX01000041
NZ_AMFX0100000235295137,719RefSeq:NZ_AMFX01000002
NZ_AMFX0100004634300434,543RefSeq:NZ_AMFX01000046
NZ_AMFX0100008734286032,460RefSeq:NZ_AMFX01000087
NZ_AMFX0100009929250430,962RefSeq:NZ_AMFX01000099
NZ_AMFX0100005433290428,015RefSeq:NZ_AMFX01000054
NZ_AMFX0100000721173123,673RefSeq:NZ_AMFX01000007
NZ_AMFX0100007722200223,561RefSeq:NZ_AMFX01000077
NZ_AMFX0100005023200323,300RefSeq:NZ_AMFX01000050
NZ_AMFX0100010119180121,624RefSeq:NZ_AMFX01000101
NZ_AMFX0100008217160121,452RefSeq:NZ_AMFX01000082
NZ_AMFX0100008137370021,406RefSeq:NZ_AMFX01000081
NZ_AMFX0100009518170120,840RefSeq:NZ_AMFX01000095
NZ_AMFX0100001521191118,254RefSeq:NZ_AMFX01000015
NZ_AMFX0100001318160217,885RefSeq:NZ_AMFX01000013
NZ_AMFX0100000918180016,803RefSeq:NZ_AMFX01000009
NZ_AMFX0100009815140116,656RefSeq:NZ_AMFX01000098
NZ_AMFX0100007313110216,197RefSeq:NZ_AMFX01000073
NZ_AMFX0100004915121216,056RefSeq:NZ_AMFX01000049
NZ_AMFX0100003525230212,121RefSeq:NZ_AMFX01000035
NZ_AMFX010000901212006,401RefSeq:NZ_AMFX01000090
61 Undisplayed Contigs/Replicons125125059161,984
Total:4,0813,7921021874,155,681
Ortholog data available?Yes
Database Contents
Genes4,078
Pathways258
Enzymatic Reactions1,287
Transport Reactions34
Polypeptides3,828
Protein Complexes41
Enzymes788
Transporters382
Compounds1,031
Transcription Units2,850
tRNAs75
GO Terms2,294
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii OIFC338
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761245
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903934
Geographic LocationUSA
Collection Date2003
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-24
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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