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 Naval-18 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
Replicon/ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AFDA02000003 contig1,3201,3091101,308,645RefSeq:NZ_AFDA02000003
NZ_AFDA02000002 contig1,0611,0184301,079,655RefSeq:NZ_AFDA02000002
NZ_AFDA02000004 contig865831340862,794RefSeq:NZ_AFDA02000004
NZ_AFDA02000005 contig54153650541,232RefSeq:NZ_AFDA02000005
NZ_AFDA02000001 contig42842710429,999RefSeq:NZ_AFDA02000001
NZ_AFDA02000009 plasmid14314300130,660RefSeq:NZ_AFDA02000009
NZ_AFDA02000007 plasmid1081080074,420RefSeq:NZ_AFDA02000007
NZ_AFDA02000008 plasmid88008,422RefSeq:NZ_AFDA02000008
NZ_AFDA02000011 plasmid88007,032RefSeq:NZ_AFDA02000011
NZ_AFDA02000006 plasmid55006,078RefSeq:NZ_AFDA02000006
NZ_AFDA02000010 plasmid88005,676RefSeq:NZ_AFDA02000010
Total:4,4954,4019404,454,613
Ortholog data available?Yes
Database Contents
Genes4,495
Pathways318
Enzymatic Reactions1,341
Transport Reactions110
Polypeptides4,407
Protein Complexes24
Enzymes944
Transporters409
Compounds1,061
Transcription Units3,031
tRNAs72
Protein Features4,895
GO Terms37
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii Naval-18
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0008518
NCBI-Taxonomy903897
Geographic LocationUSA
Collection Date2006-06-8

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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