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 AB5711, 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_AHAJ0100004347046505497,971RefSeq:NZ_AHAJ01000043
NZ_AHAJ01000040497475913497,385RefSeq:NZ_AHAJ01000040
NZ_AHAJ0100003824924036259,414RefSeq:NZ_AHAJ01000038
NZ_AHAJ01000036222205116257,754RefSeq:NZ_AHAJ01000036
NZ_AHAJ0100004222622114217,296RefSeq:NZ_AHAJ01000042
NZ_AHAJ0100002520018587204,227RefSeq:NZ_AHAJ01000025
NZ_AHAJ01000041188177110195,433RefSeq:NZ_AHAJ01000041
NZ_AHAJ0100001116615655173,805RefSeq:NZ_AHAJ01000011
NZ_AHAJ0100001816716052157,467RefSeq:NZ_AHAJ01000018
NZ_AHAJ0100002114413905155,015RefSeq:NZ_AHAJ01000021
NZ_AHAJ0100003113212255141,204RefSeq:NZ_AHAJ01000031
NZ_AHAJ010000071019173104,737RefSeq:NZ_AHAJ01000007
NZ_AHAJ010000131029903104,195RefSeq:NZ_AHAJ01000013
NZ_AHAJ01000029103925699,439RefSeq:NZ_AHAJ01000029
NZ_AHAJ0100004487841285,076RefSeq:NZ_AHAJ01000044
NZ_AHAJ0100001775696078,950RefSeq:NZ_AHAJ01000017
NZ_AHAJ0100002669626173,489RefSeq:NZ_AHAJ01000026
NZ_AHAJ0100001559571169,844RefSeq:NZ_AHAJ01000015
NZ_AHAJ0100000663585066,540RefSeq:NZ_AHAJ01000006
NZ_AHAJ0100003980733462,510RefSeq:NZ_AHAJ01000039
NZ_AHAJ0100000859498260,588RefSeq:NZ_AHAJ01000008
NZ_AHAJ0100003547450251,455RefSeq:NZ_AHAJ01000035
NZ_AHAJ0100003435350040,110RefSeq:NZ_AHAJ01000034
NZ_AHAJ01000019402910139,102RefSeq:NZ_AHAJ01000019
NZ_AHAJ0100004552490336,897RefSeq:NZ_AHAJ01000045
NZ_AHAJ0100003335331134,557RefSeq:NZ_AHAJ01000033
NZ_AHAJ0100002731292033,903RefSeq:NZ_AHAJ01000027
NZ_AHAJ0100001223185029,234RefSeq:NZ_AHAJ01000012
NZ_AHAJ0100003729290026,925RefSeq:NZ_AHAJ01000037
NZ_AHAJ0100000922190323,008RefSeq:NZ_AHAJ01000009
NZ_AHAJ0100002028270119,035RefSeq:NZ_AHAJ01000020
NZ_AHAJ0100001017170017,457RefSeq:NZ_AHAJ01000010
NZ_AHAJ0100001415150015,835RefSeq:NZ_AHAJ01000014
NZ_AHAJ0100001621191114,806RefSeq:NZ_AHAJ01000016
NZ_AHAJ0100002815140113,128RefSeq:NZ_AHAJ01000028
NZ_AHAJ0100002213110210,483RefSeq:NZ_AHAJ01000022
NZ_AHAJ010000231915049,048RefSeq:NZ_AHAJ01000023
NZ_AHAJ010000241414006,950RefSeq:NZ_AHAJ01000024
7 Undisplayed Contigs/Replicons1495616,129
Total:3,9353,7061141154,000,401
Ortholog data available?Yes
Database Contents
Genes3,930
Pathways258
Enzymatic Reactions1,285
Transport Reactions109
Polypeptides3,716
Protein Complexes52
Enzymes787
Transporters358
Compounds1,045
Transcription Units2,691
tRNAs79
GO Terms2,200
Database Version29.0
Synonyms Acinetobacter baumannii MRSN1310
Acinetobacter baumannii str. AB5711
Acinetobacter baumannii strain AB5711
Acinetobacter baumannii AB5711
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB5711
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436013
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1116236
Environmentblood
Geographic LocationUSA
Collection Date2009
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-22
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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