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 ATCC 19606 = CIP 70.34 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
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.1, whole genome shotgun sequence.1,1791,173601,263,432RefSeq:NZ_GG704572
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.2, whole genome shotgun sequence.450440100450,878RefSeq:NZ_GG704573
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.3, whole genome shotgun sequence.41740890443,868RefSeq:NZ_GG704574
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.4, whole genome shotgun sequence.391381100427,000RefSeq:NZ_GG704575
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.5, whole genome shotgun sequence.277265120276,678RefSeq:NZ_GG704576
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.6, whole genome shotgun sequence.23823080257,274RefSeq:NZ_GG704577
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.7, whole genome shotgun sequence.24224020254,501RefSeq:NZ_GG704578
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.8, whole genome shotgun sequence.20520320205,658RefSeq:NZ_GG704579
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.9, whole genome shotgun sequence.17217200193,541RefSeq:NZ_GG704580
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.10, whole genome shotgun sequence.1041022091,011RefSeq:NZ_GG704581
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.11, whole genome shotgun sequence.49490050,636RefSeq:NZ_GG704582
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.12, whole genome shotgun sequence.29290026,358RefSeq:NZ_GG704583
Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.13, whole genome shotgun sequence.1313006,625RefSeq:NZ_GG704584
9 Undisplayed Contigs/Replicons21192024,056
Total:3,7873,7246303,971,516
Ortholog data available?Yes
Database Contents
Genes3,787
Pathways317
Enzymatic Reactions1,427
Transport Reactions95
Polypeptides3,767
Protein Complexes28
Enzymes999
Transporters367
Compounds1,085
Transcription Units2,615
tRNAs63
Protein Features4,401
GO Terms1,014
Database Version29.0
Synonyms Acinetobacter baumannii JCM 6841
Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Acinetobacter baumannii 19606
Acinetobacter baumannii ATCC 19606
Acinetobacter baumannii CIP 70.34
Acinetobacter baumannii ATCC 19606 = CIP 70.34
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0032321
NCBI-Taxonomy575584
EnvironmentUrogenital tract
HostHomo sapiens
Health/Disease StateNosocomial infections
Human Microbiome Body Siteurogenital-tract

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(Database issue);D742-53. 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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