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 IS-235, 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_AMEI01000012454435145463,299RefSeq:NZ_AMEI01000012
NZ_AMEI0100006931531311325,746RefSeq:NZ_AMEI01000069
NZ_AMEI0100004924723548266,522RefSeq:NZ_AMEI01000049
NZ_AMEI0100003223522933250,138RefSeq:NZ_AMEI01000032
NZ_AMEI01000027195178116197,842RefSeq:NZ_AMEI01000027
NZ_AMEI01000058184171211178,675RefSeq:NZ_AMEI01000058
NZ_AMEI0100007517216903177,474RefSeq:NZ_AMEI01000075
NZ_AMEI0100005916616312169,343RefSeq:NZ_AMEI01000059
NZ_AMEI0100005513813611151,506RefSeq:NZ_AMEI01000055
NZ_AMEI0100006112612501134,153RefSeq:NZ_AMEI01000061
NZ_AMEI0100002811010442120,037RefSeq:NZ_AMEI01000028
NZ_AMEI0100003810810701113,354RefSeq:NZ_AMEI01000038
NZ_AMEI01000065959203111,833RefSeq:NZ_AMEI01000065
NZ_AMEI0100005110410103108,829RefSeq:NZ_AMEI01000051
NZ_AMEI01000054989305104,320RefSeq:NZ_AMEI01000054
NZ_AMEI010000171009514100,823RefSeq:NZ_AMEI01000017
NZ_AMEI0100001682802086,185RefSeq:NZ_AMEI01000016
NZ_AMEI0100004860591071,328RefSeq:NZ_AMEI01000048
NZ_AMEI0100004153474267,947RefSeq:NZ_AMEI01000041
NZ_AMEI0100006770646067,653RefSeq:NZ_AMEI01000067
NZ_AMEI0100003172691266,521RefSeq:NZ_AMEI01000031
NZ_AMEI0100002550482064,515RefSeq:NZ_AMEI01000025
NZ_AMEI0100000465574463,067RefSeq:NZ_AMEI01000004
NZ_AMEI0100002955522156,345RefSeq:NZ_AMEI01000029
NZ_AMEI0100007459554052,947RefSeq:NZ_AMEI01000074
NZ_AMEI0100003671710052,347RefSeq:NZ_AMEI01000036
NZ_AMEI0100007350472151,845RefSeq:NZ_AMEI01000073
NZ_AMEI0100000150463139,440RefSeq:NZ_AMEI01000001
NZ_AMEI0100000637352039,197RefSeq:NZ_AMEI01000006
NZ_AMEI0100006840400036,743RefSeq:NZ_AMEI01000068
NZ_AMEI0100001930272127,687RefSeq:NZ_AMEI01000019
NZ_AMEI0100006626242027,350RefSeq:NZ_AMEI01000066
NZ_AMEI0100007121190220,589RefSeq:NZ_AMEI01000071
NZ_AMEI0100003721190219,470RefSeq:NZ_AMEI01000037
NZ_AMEI0100000928280017,143RefSeq:NZ_AMEI01000009
NZ_AMEI0100000815120316,808RefSeq:NZ_AMEI01000008
NZ_AMEI0100004430271216,774RefSeq:NZ_AMEI01000044
NZ_AMEI0100005615150012,214RefSeq:NZ_AMEI01000056
NZ_AMEI0100007022210110,379RefSeq:NZ_AMEI01000070
NZ_AMEI010000622020009,329RefSeq:NZ_AMEI01000062
NZ_AMEI010000401816028,131RefSeq:NZ_AMEI01000040
35 Undisplayed Contigs/Replicons878722784,539
Total:4,0233,831821104,060,387
Ortholog data available?Yes
Database Contents
Genes4,013
Pathways269
Enzymatic Reactions1,300
Transport Reactions108
Polypeptides3,846
Protein Complexes52
Enzymes795
Transporters356
Compounds1,052
Transcription Units2,758
tRNAs63
GO Terms2,467
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii IS-235
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761221
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903905
Environmentblood
Geographic LocationIraq
Collection Date2008-08-24
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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