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_TG2030, 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_AMIJ0100010322821594219,167RefSeq:NZ_AMIJ01000103
NZ_AMIJ0100008317817503186,917RefSeq:NZ_AMIJ01000083
NZ_AMIJ0100007816816161185,543RefSeq:NZ_AMIJ01000078
NZ_AMIJ0100003918217624175,548RefSeq:NZ_AMIJ01000039
NZ_AMIJ0100005515514843173,316RefSeq:NZ_AMIJ01000055
NZ_AMIJ0100014115414932173,130RefSeq:NZ_AMIJ01000141
NZ_AMIJ0100002517517140171,752RefSeq:NZ_AMIJ01000025
NZ_AMIJ0100009814414211148,685RefSeq:NZ_AMIJ01000098
NZ_AMIJ0100009510710421115,624RefSeq:NZ_AMIJ01000095
NZ_AMIJ0100009111310922109,110RefSeq:NZ_AMIJ01000091
NZ_AMIJ0100008589861294,854RefSeq:NZ_AMIJ01000085
NZ_AMIJ0100006587824188,608RefSeq:NZ_AMIJ01000065
NZ_AMIJ0100010276750187,911RefSeq:NZ_AMIJ01000102
NZ_AMIJ0100010581791186,868RefSeq:NZ_AMIJ01000105
NZ_AMIJ0100006175740174,459RefSeq:NZ_AMIJ01000061
NZ_AMIJ0100002068660272,901RefSeq:NZ_AMIJ01000020
NZ_AMIJ0100015166660071,008RefSeq:NZ_AMIJ01000151
NZ_AMIJ0100014851482167,390RefSeq:NZ_AMIJ01000148
NZ_AMIJ0100001562620062,868RefSeq:NZ_AMIJ01000015
NZ_AMIJ0100008654531062,688RefSeq:NZ_AMIJ01000086
NZ_AMIJ0100005854530153,185RefSeq:NZ_AMIJ01000058
NZ_AMIJ0100000846440247,549RefSeq:NZ_AMIJ01000008
NZ_AMIJ0100011141400143,898RefSeq:NZ_AMIJ01000111
NZ_AMIJ0100009038341343,566RefSeq:NZ_AMIJ01000090
NZ_AMIJ0100008839380142,451RefSeq:NZ_AMIJ01000088
NZ_AMIJ0100010741410042,250RefSeq:NZ_AMIJ01000107
NZ_AMIJ0100011234340041,548RefSeq:NZ_AMIJ01000112
NZ_AMIJ0100014337360138,453RefSeq:NZ_AMIJ01000143
NZ_AMIJ0100009937370036,336RefSeq:NZ_AMIJ01000099
NZ_AMIJ0100005932320036,082RefSeq:NZ_AMIJ01000059
NZ_AMIJ0100014032310134,381RefSeq:NZ_AMIJ01000140
NZ_AMIJ0100012933301233,613RefSeq:NZ_AMIJ01000129
NZ_AMIJ0100004529280131,637RefSeq:NZ_AMIJ01000045
NZ_AMIJ0100012732300231,562RefSeq:NZ_AMIJ01000127
NZ_AMIJ0100007132310130,139RefSeq:NZ_AMIJ01000071
NZ_AMIJ0100010129271127,960RefSeq:NZ_AMIJ01000101
NZ_AMIJ0100002822220027,638RefSeq:NZ_AMIJ01000028
NZ_AMIJ0100006328243127,076RefSeq:NZ_AMIJ01000063
NZ_AMIJ0100011720200026,674RefSeq:NZ_AMIJ01000117
NZ_AMIJ0100010025250026,605RefSeq:NZ_AMIJ01000100
NZ_AMIJ0100012320190125,254RefSeq:NZ_AMIJ01000123
NZ_AMIJ0100011626233023,668RefSeq:NZ_AMIJ01000116
NZ_AMIJ0100014720190123,009RefSeq:NZ_AMIJ01000147
NZ_AMIJ0100014420190122,284RefSeq:NZ_AMIJ01000144
NZ_AMIJ0100009721191122,275RefSeq:NZ_AMIJ01000097
NZ_AMIJ0100007423230021,630RefSeq:NZ_AMIJ01000074
NZ_AMIJ0100009617160121,289RefSeq:NZ_AMIJ01000096
NZ_AMIJ0100014917160121,284RefSeq:NZ_AMIJ01000149
NZ_AMIJ0100011420180219,945RefSeq:NZ_AMIJ01000114
NZ_AMIJ0100013326240219,730RefSeq:NZ_AMIJ01000133
NZ_AMIJ0100004824230119,704RefSeq:NZ_AMIJ01000048
NZ_AMIJ0100006918170119,609RefSeq:NZ_AMIJ01000069
NZ_AMIJ0100013420180219,558RefSeq:NZ_AMIJ01000134
NZ_AMIJ0100000917170018,597RefSeq:NZ_AMIJ01000009
NZ_AMIJ0100001118180017,344RefSeq:NZ_AMIJ01000011
NZ_AMIJ0100013114140015,193RefSeq:NZ_AMIJ01000131
NZ_AMIJ010000771615018,264RefSeq:NZ_AMIJ01000077
NZ_AMIJ010000841312017,484RefSeq:NZ_AMIJ01000084
NZ_AMIJ01000037129035,132RefSeq:NZ_AMIJ01000037
92 Undisplayed Contigs/Replicons208202654262,190
Total:3,6183,439581213,764,393
Ortholog data available?Yes
Database Contents
Genes3,618
Pathways266
Enzymatic Reactions1,294
Transport Reactions98
Polypeptides3,495
Protein Complexes51
Enzymes751
Transporters348
Compounds1,045
Transcription Units2,562
tRNAs50
GO Terms1,356
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_TG2030
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471240
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221279
Environmentsputum
HostHomo sapiens
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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