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 AB_TG27335, 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_AMIQ0100002924423266257,208RefSeq:NZ_AMIQ01000029
NZ_AMIQ0100007724924315255,862RefSeq:NZ_AMIQ01000077
NZ_AMIQ0100007219218723217,275RefSeq:NZ_AMIQ01000072
NZ_AMIQ0100007020520302211,225RefSeq:NZ_AMIQ01000070
NZ_AMIQ0100006618717683191,400RefSeq:NZ_AMIQ01000066
NZ_AMIQ0100001417116182177,990RefSeq:NZ_AMIQ01000014
NZ_AMIQ0100008515915324164,052RefSeq:NZ_AMIQ01000085
NZ_AMIQ0100007315614925160,500RefSeq:NZ_AMIQ01000073
NZ_AMIQ0100008614113173147,114RefSeq:NZ_AMIQ01000086
NZ_AMIQ0100013614013712145,288RefSeq:NZ_AMIQ01000136
NZ_AMIQ0100012713212804143,627RefSeq:NZ_AMIQ01000127
NZ_AMIQ0100000912912342136,522RefSeq:NZ_AMIQ01000009
NZ_AMIQ0100007512312003133,579RefSeq:NZ_AMIQ01000075
NZ_AMIQ0100013710810512114,204RefSeq:NZ_AMIQ01000137
NZ_AMIQ0100001512111911111,035RefSeq:NZ_AMIQ01000015
NZ_AMIQ010000781009901107,989RefSeq:NZ_AMIQ01000078
NZ_AMIQ0100004610310102107,184RefSeq:NZ_AMIQ01000046
NZ_AMIQ010000641051003297,353RefSeq:NZ_AMIQ01000064
NZ_AMIQ0100009961564182,739RefSeq:NZ_AMIQ01000099
NZ_AMIQ0100004371683082,401RefSeq:NZ_AMIQ01000043
NZ_AMIQ0100005472690372,814RefSeq:NZ_AMIQ01000054
NZ_AMIQ0100006065594269,518RefSeq:NZ_AMIQ01000060
NZ_AMIQ0100012864604063,062RefSeq:NZ_AMIQ01000128
NZ_AMIQ0100008746430354,548RefSeq:NZ_AMIQ01000087
NZ_AMIQ0100005849480153,717RefSeq:NZ_AMIQ01000058
NZ_AMIQ0100002156531252,335RefSeq:NZ_AMIQ01000021
NZ_AMIQ0100003248470150,125RefSeq:NZ_AMIQ01000032
NZ_AMIQ0100002851490247,202RefSeq:NZ_AMIQ01000028
NZ_AMIQ0100011137360144,337RefSeq:NZ_AMIQ01000111
NZ_AMIQ0100008039390042,738RefSeq:NZ_AMIQ01000080
NZ_AMIQ0100008339370241,306RefSeq:NZ_AMIQ01000083
NZ_AMIQ0100006929280131,477RefSeq:NZ_AMIQ01000069
NZ_AMIQ0100012028270129,772RefSeq:NZ_AMIQ01000120
NZ_AMIQ0100003828280026,695RefSeq:NZ_AMIQ01000038
NZ_AMIQ0100007124220224,856RefSeq:NZ_AMIQ01000071
NZ_AMIQ0100006525231123,783RefSeq:NZ_AMIQ01000065
NZ_AMIQ0100007421150617,569RefSeq:NZ_AMIQ01000074
NZ_AMIQ0100003628280017,092RefSeq:NZ_AMIQ01000036
NZ_AMIQ0100008228270116,501RefSeq:NZ_AMIQ01000082
NZ_AMIQ0100008426250115,580RefSeq:NZ_AMIQ01000084
NZ_AMIQ0100004012100214,301RefSeq:NZ_AMIQ01000040
NZ_AMIQ0100013521210014,215RefSeq:NZ_AMIQ01000135
NZ_AMIQ0100010212110114,111RefSeq:NZ_AMIQ01000102
NZ_AMIQ0100009621200111,074RefSeq:NZ_AMIQ01000096
NZ_AMIQ0100004112100210,658RefSeq:NZ_AMIQ01000041
NZ_AMIQ010001241515009,715RefSeq:NZ_AMIQ01000124
NZ_AMIQ010000491410049,517RefSeq:NZ_AMIQ01000049
90 Undisplayed Contigs/Replicons111107659138,236
Total:3,9793,758691524,061,401
Ortholog data available?Yes
Database Contents
Genes3,977
Pathways261
Enzymatic Reactions1,298
Transport Reactions112
Polypeptides3,793
Protein Complexes53
Enzymes805
Transporters365
Compounds1,054
Transcription Units2,780
tRNAs61
GO Terms2,404
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_TG27335
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471234
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221286
Annotation ProviderNCBI
Annotation Date2017-11-23
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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