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_TG27331, 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_AMIP0100005534733467364,335RefSeq:NZ_AMIP01000055
NZ_AMIP0100003322522023246,302RefSeq:NZ_AMIP01000033
NZ_AMIP0100001720520302211,229RefSeq:NZ_AMIP01000017
NZ_AMIP0100004919418284206,034RefSeq:NZ_AMIP01000049
NZ_AMIP0100008316916162177,754RefSeq:NZ_AMIP01000083
NZ_AMIP0100010817717241171,972RefSeq:NZ_AMIP01000108
NZ_AMIP0100002515715313162,416RefSeq:NZ_AMIP01000025
NZ_AMIP0100003614414004154,025RefSeq:NZ_AMIP01000036
NZ_AMIP0100004214113173147,118RefSeq:NZ_AMIP01000042
NZ_AMIP0100008514113812145,292RefSeq:NZ_AMIP01000085
NZ_AMIP0100008614013226140,920RefSeq:NZ_AMIP01000086
NZ_AMIP0100005814012983140,609RefSeq:NZ_AMIP01000058
NZ_AMIP0100004012312003133,583RefSeq:NZ_AMIP01000040
NZ_AMIP0100014810810512114,208RefSeq:NZ_AMIP01000148
NZ_AMIP0100004510510302114,129RefSeq:NZ_AMIP01000045
NZ_AMIP010000621009901107,993RefSeq:NZ_AMIP01000062
NZ_AMIP0100011011010712101,450RefSeq:NZ_AMIP01000110
NZ_AMIP0100005988850386,929RefSeq:NZ_AMIP01000059
NZ_AMIP0100009367643077,988RefSeq:NZ_AMIP01000093
NZ_AMIP0100007572701174,404RefSeq:NZ_AMIP01000075
NZ_AMIP0100009472690372,818RefSeq:NZ_AMIP01000094
NZ_AMIP0100011150454170,582RefSeq:NZ_AMIP01000111
NZ_AMIP0100014468634165,549RefSeq:NZ_AMIP01000144
NZ_AMIP0100008846430354,552RefSeq:NZ_AMIP01000088
NZ_AMIP0100010356531252,344RefSeq:NZ_AMIP01000103
NZ_AMIP0100008248470150,384RefSeq:NZ_AMIP01000082
NZ_AMIP0100013136360043,863RefSeq:NZ_AMIP01000131
NZ_AMIP0100009239390042,742RefSeq:NZ_AMIP01000092
NZ_AMIP0100013938370141,310RefSeq:NZ_AMIP01000139
NZ_AMIP0100012929280137,893RefSeq:NZ_AMIP01000129
NZ_AMIP0100006533320131,901RefSeq:NZ_AMIP01000065
NZ_AMIP0100010029290031,854RefSeq:NZ_AMIP01000100
NZ_AMIP0100006828270129,772RefSeq:NZ_AMIP01000068
NZ_AMIP0100007028280026,699RefSeq:NZ_AMIP01000070
NZ_AMIP0100009124220224,856RefSeq:NZ_AMIP01000091
NZ_AMIP0100008121150617,574RefSeq:NZ_AMIP01000081
NZ_AMIP0100009821210014,219RefSeq:NZ_AMIP01000098
NZ_AMIP0100009613120114,200RefSeq:NZ_AMIP01000096
NZ_AMIP0100007711100113,792RefSeq:NZ_AMIP01000077
NZ_AMIP0100001912100210,662RefSeq:NZ_AMIP01000019
NZ_AMIP010001191515009,719RefSeq:NZ_AMIP01000119
NZ_AMIP010001011211019,629RefSeq:NZ_AMIP01000101
NZ_AMIP010001371310039,521RefSeq:NZ_AMIP01000137
NZ_AMIP010000871211018,839RefSeq:NZ_AMIP01000087
104 Undisplayed Contigs/Replicons2071961564198,232
Total:3,9823,757751504,062,196
Ortholog data available?Yes
Database Contents
Genes3,978
Pathways261
Enzymatic Reactions1,298
Transport Reactions111
Polypeptides3,794
Protein Complexes53
Enzymes808
Transporters365
Compounds1,054
Transcription Units2,794
tRNAs65
GO Terms2,405
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_TG27331
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471233
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221285
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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