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 UMB001, 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_AEPK01000007241227311252,959RefSeq:NZ_AEPK01000007
NZ_AEPK0100000121120029235,768RefSeq:NZ_AEPK01000001
NZ_AEPK0100000416415257173,196RefSeq:NZ_AEPK01000004
NZ_AEPK0100000514513519153,552RefSeq:NZ_AEPK01000005
NZ_AEPK0100001513712647148,241RefSeq:NZ_AEPK01000015
NZ_AEPK0100001313312607143,280RefSeq:NZ_AEPK01000013
NZ_AEPK010000301059708115,852RefSeq:NZ_AEPK01000030
NZ_AEPK0100001111410707112,316RefSeq:NZ_AEPK01000011
NZ_AEPK01000010999405104,452RefSeq:NZ_AEPK01000010
NZ_AEPK010000091009262101,185RefSeq:NZ_AEPK01000009
NZ_AEPK0100001787841285,056RefSeq:NZ_AEPK01000017
NZ_AEPK0100001281762383,537RefSeq:NZ_AEPK01000012
NZ_AEPK0100003379716279,841RefSeq:NZ_AEPK01000033
NZ_AEPK0100001668640478,712RefSeq:NZ_AEPK01000016
NZ_AEPK0100000378711676,917RefSeq:NZ_AEPK01000003
NZ_AEPK0100003291880376,777RefSeq:NZ_AEPK01000032
NZ_AEPK0100002270660473,837RefSeq:NZ_AEPK01000022
NZ_AEPK0100001873642770,782RefSeq:NZ_AEPK01000018
NZ_AEPK0100002065611369,552RefSeq:NZ_AEPK01000020
NZ_AEPK0100000862580468,608RefSeq:NZ_AEPK01000008
NZ_AEPK0100002376730367,919RefSeq:NZ_AEPK01000023
NZ_AEPK0100002764591464,923RefSeq:NZ_AEPK01000027
NZ_AEPK0100001967640364,831RefSeq:NZ_AEPK01000019
NZ_AEPK0100002163572462,982RefSeq:NZ_AEPK01000021
NZ_AEPK0100000256500662,736RefSeq:NZ_AEPK01000002
NZ_AEPK0100003149452254,319RefSeq:NZ_AEPK01000031
NZ_AEPK0100002852444453,364RefSeq:NZ_AEPK01000028
NZ_AEPK0100002666613253,130RefSeq:NZ_AEPK01000026
NZ_AEPK0100002550462251,906RefSeq:NZ_AEPK01000025
NZ_AEPK0100003750470350,969RefSeq:NZ_AEPK01000037
NZ_AEPK0100003555490650,215RefSeq:NZ_AEPK01000035
NZ_AEPK0100001446363749,038RefSeq:NZ_AEPK01000014
NZ_AEPK0100002949462148,329RefSeq:NZ_AEPK01000029
NZ_AEPK0100003465590647,095RefSeq:NZ_AEPK01000034
NZ_AEPK0100002446390746,480RefSeq:NZ_AEPK01000024
NZ_AEPK0100000632300243,141RefSeq:NZ_AEPK01000006
NZ_AEPK0100004142400241,263RefSeq:NZ_AEPK01000041
NZ_AEPK0100003935283439,334RefSeq:NZ_AEPK01000039
NZ_AEPK0100003842380436,578RefSeq:NZ_AEPK01000038
NZ_AEPK0100004341370434,714RefSeq:NZ_AEPK01000043
NZ_AEPK0100004034284234,676RefSeq:NZ_AEPK01000040
NZ_AEPK0100004232290333,635RefSeq:NZ_AEPK01000042
NZ_AEPK0100003638353032,952RefSeq:NZ_AEPK01000036
NZ_AEPK0100004437320530,416RefSeq:NZ_AEPK01000044
NZ_AEPK0100004627220529,263RefSeq:NZ_AEPK01000046
NZ_AEPK0100005734320226,573RefSeq:NZ_AEPK01000057
NZ_AEPK0100004530262225,848RefSeq:NZ_AEPK01000045
NZ_AEPK0100004925220325,066RefSeq:NZ_AEPK01000049
NZ_AEPK0100004723180524,135RefSeq:NZ_AEPK01000047
NZ_AEPK0100005021190222,785RefSeq:NZ_AEPK01000050
NZ_AEPK0100005119170222,683RefSeq:NZ_AEPK01000051
NZ_AEPK0100005216150122,329RefSeq:NZ_AEPK01000052
NZ_AEPK0100005525210421,385RefSeq:NZ_AEPK01000055
NZ_AEPK0100004819160320,087RefSeq:NZ_AEPK01000048
NZ_AEPK0100005322192119,088RefSeq:NZ_AEPK01000053
NZ_AEPK0100005421161418,527RefSeq:NZ_AEPK01000054
NZ_AEPK0100005611110016,960RefSeq:NZ_AEPK01000056
NZ_AEPK0100006425240115,600RefSeq:NZ_AEPK01000064
NZ_AEPK0100005812100215,449RefSeq:NZ_AEPK01000058
NZ_AEPK0100005915130214,705RefSeq:NZ_AEPK01000059
NZ_AEPK010000601191114,402RefSeq:NZ_AEPK01000060
NZ_AEPK0100006115100513,105RefSeq:NZ_AEPK01000061
NZ_AEPK010000681190212,881RefSeq:NZ_AEPK01000068
NZ_AEPK0100006522170511,137RefSeq:NZ_AEPK01000065
NZ_AEPK010000621292110,834RefSeq:NZ_AEPK01000062
NZ_AEPK010000631481510,525RefSeq:NZ_AEPK01000063
NZ_AEPK010000731614028,244RefSeq:NZ_AEPK01000073
51 Undisplayed Contigs/Replicons94871474132,504
Total:4,0113,595863304,013,480
Ortholog data available?Yes
Database Contents
Genes3,996
Pathways259
Enzymatic Reactions1,276
Transport Reactions111
Polypeptides3,632
Protein Complexes52
Enzymes776
Transporters351
Compounds1,037
Transcription Units2,811
tRNAs59
GO Terms2,108
Database Version29.0
Synonyms Acinetobacter baumannii str. UMB001
Acinetobacter baumannii strain UMB001
Acinetobacter baumannii UMB001
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii UMB001
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02435970
NCBI BioProjectPRJNA224116
NCBI-Taxonomy933263
Environmentblood
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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