Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Tim Holland1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic program [Karp02, Dale10, Karp11, Caspi12] using Pathway Tools software version 18.5 and MetaCyc version 18.5 on 10-Aug-2014 18:43:19 from the annotated genome of Acinetobacter baumannii AC12 as obtained from RefSeq downloaded on 21-May-2014.

This BioCyc Tier 3 PGDB was computationally generated. It has not undergone any manual curation nor manual review, and thus may contain errors. Development of this PGDB was supported by grant GM080746 from the NIH.

Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_ALAM01000006 contig24524500245,498RefSeq:NZ_ALAM01000006
NZ_ALAM01000020 contig17617420194,343RefSeq:NZ_ALAM01000020
NZ_ALAM01000015 contig18918900194,109RefSeq:NZ_ALAM01000015
NZ_ALAM01000013 contig15415400167,763RefSeq:NZ_ALAM01000013
NZ_ALAM01000009 contig14914720166,353RefSeq:NZ_ALAM01000009
NZ_ALAM01000003 contig15315120162,225RefSeq:NZ_ALAM01000003
NZ_ALAM01000028 contig15515500161,388RefSeq:NZ_ALAM01000028
NZ_ALAM01000022 contig13313120140,683RefSeq:NZ_ALAM01000022
NZ_ALAM01000002 contig12212200130,899RefSeq:NZ_ALAM01000002
NZ_ALAM01000010 contig10510500118,361RefSeq:NZ_ALAM01000010
NZ_ALAM01000005 contig10510320115,225RefSeq:NZ_ALAM01000005
NZ_ALAM01000039 contig10110100114,347RefSeq:NZ_ALAM01000039
NZ_ALAM01000011 contig10410310109,999RefSeq:NZ_ALAM01000011
NZ_ALAM01000026 contig949220100,076RefSeq:NZ_ALAM01000026
NZ_ALAM01000012 contig88871099,797RefSeq:NZ_ALAM01000012
NZ_ALAM01000029 contig84831097,053RefSeq:NZ_ALAM01000029
NZ_ALAM01000036 contig80791083,397RefSeq:NZ_ALAM01000036
NZ_ALAM01000023 contig73712072,735RefSeq:NZ_ALAM01000023
NZ_ALAM01000007 contig71710072,721RefSeq:NZ_ALAM01000007
NZ_ALAM01000040 contig61610070,239RefSeq:NZ_ALAM01000040
NZ_ALAM01000042 contig54540069,102RefSeq:NZ_ALAM01000042
NZ_ALAM01000027 contig68644067,687RefSeq:NZ_ALAM01000027
NZ_ALAM01000049 contig67670067,093RefSeq:NZ_ALAM01000049
NZ_ALAM01000018 contig54522055,662RefSeq:NZ_ALAM01000018
NZ_ALAM01000031 contig63621051,253RefSeq:NZ_ALAM01000031
NZ_ALAM01000016 contig48480050,036RefSeq:NZ_ALAM01000016
NZ_ALAM01000017 contig40382047,050RefSeq:NZ_ALAM01000017
NZ_ALAM01000030 contig44440043,513RefSeq:NZ_ALAM01000030
NZ_ALAM01000025 contig38380042,643RefSeq:NZ_ALAM01000025
NZ_ALAM01000057 contig38380038,671RefSeq:NZ_ALAM01000057
NZ_ALAM01000001 contig38380038,348RefSeq:NZ_ALAM01000001
NZ_ALAM01000037 contig29290037,751RefSeq:NZ_ALAM01000037
NZ_ALAM01000047 contig30273037,694RefSeq:NZ_ALAM01000047
NZ_ALAM01000034 contig32320036,326RefSeq:NZ_ALAM01000034
NZ_ALAM01000054 contig32302034,148RefSeq:NZ_ALAM01000054
NZ_ALAM01000064 contig55550031,609RefSeq:NZ_ALAM01000064
NZ_ALAM01000014 contig24240028,511RefSeq:NZ_ALAM01000014
NZ_ALAM01000055 contig25241027,842RefSeq:NZ_ALAM01000055
NZ_ALAM01000024 contig24240027,323RefSeq:NZ_ALAM01000024
NZ_ALAM01000059 contig21210027,037RefSeq:NZ_ALAM01000059
NZ_ALAM01000032 contig28280026,607RefSeq:NZ_ALAM01000032
NZ_ALAM01000062 contig39390025,987RefSeq:NZ_ALAM01000062
NZ_ALAM01000044 contig18180024,675RefSeq:NZ_ALAM01000044
NZ_ALAM01000019 contig24231023,768RefSeq:NZ_ALAM01000019
NZ_ALAM01000004 contig19190021,952RefSeq:NZ_ALAM01000004
NZ_ALAM01000066 contig19190020,755RefSeq:NZ_ALAM01000066
NZ_ALAM01000052 contig20200020,344RefSeq:NZ_ALAM01000052
NZ_ALAM01000043 contig14131020,138RefSeq:NZ_ALAM01000043
NZ_ALAM01000056 contig16151019,814RefSeq:NZ_ALAM01000056
NZ_ALAM01000045 contig23194019,573RefSeq:NZ_ALAM01000045
NZ_ALAM01000008 contig15150014,720RefSeq:NZ_ALAM01000008
NZ_ALAM01000060 contig13130013,627RefSeq:NZ_ALAM01000060
NZ_ALAM01000065 contig12120011,583RefSeq:NZ_ALAM01000065
NZ_ALAM01000063 contig1111007,681RefSeq:NZ_ALAM01000063
32 Undisplayed Contigs/Replicons797450100,578
Total:3,6163,5714503,848,312
Ortholog data available?Yes
Database Contents
Genes3,616
Pathways322
Enzymatic Reactions1,496
Transport Reactions138
Polypeptides3,644
Protein Complexes28
Enzymes1,150
Transporters418
Compounds1,139
Transcription Units2,522
tRNAs42
Protein Features4,284
GO Terms37
Database Version29.0
Synonyms Acinetobacter baumannii str. AC12
Acinetobacter baumannii strain AC12
Acinetobacter baumannii AC12
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AC12
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0022006
NCBI-Taxonomy1198108
Environmentblood
Geographic LocationMalaysia
Collection Date2011
HostHomo sapiens
Human Microbiome Body Siteblood

References

Caspi12: Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD (2012). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases." Nucleic Acids Res 40(D1);D742-D753. PMID: 22102576

Dale10: Dale JM, Popescu L, Karp PD (2010). "Machine learning methods for metabolic pathway prediction." BMC Bioinformatics 11;15. PMID: 20064214

Karp02: Karp PD, Paley S, Romero P (2002). "The Pathway Tools software." Bioinformatics 18 Suppl 1;S225-32. PMID: 12169551

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

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