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 ABNIH1, 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_AFSZ01000016241223513251,784RefSeq:NZ_AFSZ01000016
NZ_AFSZ0100006716415158173,201RefSeq:NZ_AFSZ01000067
NZ_AFSZ0100005614813567159,605RefSeq:NZ_AFSZ01000056
NZ_AFSZ0100006815014406158,829RefSeq:NZ_AFSZ01000068
NZ_AFSZ0100001913112209144,315RefSeq:NZ_AFSZ01000019
NZ_AFSZ01000027120109011126,242RefSeq:NZ_AFSZ01000027
NZ_AFSZ010000441059717125,675RefSeq:NZ_AFSZ01000044
NZ_AFSZ0100004512011316124,237RefSeq:NZ_AFSZ01000045
NZ_AFSZ0100000511010172115,705RefSeq:NZ_AFSZ01000005
NZ_AFSZ0100003411010406108,848RefSeq:NZ_AFSZ01000034
NZ_AFSZ0100010312512302106,965RefSeq:NZ_AFSZ01000103
NZ_AFSZ010000741029705102,550RefSeq:NZ_AFSZ01000074
NZ_AFSZ0100007584770788,296RefSeq:NZ_AFSZ01000075
NZ_AFSZ0100008489831587,473RefSeq:NZ_AFSZ01000084
NZ_AFSZ0100004662524681,821RefSeq:NZ_AFSZ01000046
NZ_AFSZ0100010179716279,828RefSeq:NZ_AFSZ01000101
NZ_AFSZ0100006167630478,177RefSeq:NZ_AFSZ01000061
NZ_AFSZ0100010073710277,237RefSeq:NZ_AFSZ01000100
NZ_AFSZ0100002679712676,185RefSeq:NZ_AFSZ01000026
NZ_AFSZ0100003868610771,999RefSeq:NZ_AFSZ01000038
NZ_AFSZ0100001473690470,086RefSeq:NZ_AFSZ01000014
NZ_AFSZ0100003374720267,485RefSeq:NZ_AFSZ01000033
NZ_AFSZ0100000659550463,239RefSeq:NZ_AFSZ01000006
NZ_AFSZ0100006463594062,497RefSeq:NZ_AFSZ01000064
NZ_AFSZ0100007254500460,671RefSeq:NZ_AFSZ01000072
NZ_AFSZ0100003947442153,663RefSeq:NZ_AFSZ01000039
NZ_AFSZ0100009966603353,129RefSeq:NZ_AFSZ01000099
NZ_AFSZ0100002953490450,640RefSeq:NZ_AFSZ01000029
NZ_AFSZ0100000749460350,330RefSeq:NZ_AFSZ01000007
NZ_AFSZ0100007347420547,868RefSeq:NZ_AFSZ01000073
NZ_AFSZ0100008246430346,652RefSeq:NZ_AFSZ01000082
NZ_AFSZ0100005749414446,505RefSeq:NZ_AFSZ01000057
NZ_AFSZ0100003143391345,671RefSeq:NZ_AFSZ01000031
NZ_AFSZ0100002442400245,602RefSeq:NZ_AFSZ01000024
NZ_AFSZ0100008751501045,350RefSeq:NZ_AFSZ01000087
NZ_AFSZ0100002041353343,789RefSeq:NZ_AFSZ01000020
NZ_AFSZ0100008140360443,344RefSeq:NZ_AFSZ01000081
NZ_AFSZ0100000433320138,407RefSeq:NZ_AFSZ01000004
NZ_AFSZ0100004040380235,706RefSeq:NZ_AFSZ01000040
NZ_AFSZ0100000332261531,100RefSeq:NZ_AFSZ01000003
NZ_AFSZ0100007928260230,550RefSeq:NZ_AFSZ01000079
NZ_AFSZ0100002824220228,835RefSeq:NZ_AFSZ01000028
NZ_AFSZ0100001524230128,454RefSeq:NZ_AFSZ01000015
NZ_AFSZ0100004233310227,918RefSeq:NZ_AFSZ01000042
NZ_AFSZ0100006324220226,156RefSeq:NZ_AFSZ01000063
NZ_AFSZ0100005126260024,734RefSeq:NZ_AFSZ01000051
NZ_AFSZ0100009825221223,646RefSeq:NZ_AFSZ01000098
NZ_AFSZ0100002519190023,002RefSeq:NZ_AFSZ01000025
NZ_AFSZ0100004317160121,918RefSeq:NZ_AFSZ01000043
NZ_AFSZ0100003221200120,593RefSeq:NZ_AFSZ01000032
NZ_AFSZ0100006019180119,194RefSeq:NZ_AFSZ01000060
NZ_AFSZ0100007716150119,020RefSeq:NZ_AFSZ01000077
NZ_AFSZ0100010223202118,662RefSeq:NZ_AFSZ01000102
NZ_AFSZ010000781270518,628RefSeq:NZ_AFSZ01000078
NZ_AFSZ0100003017160116,615RefSeq:NZ_AFSZ01000030
NZ_AFSZ0100001716133015,618RefSeq:NZ_AFSZ01000017
NZ_AFSZ0100009716160014,654RefSeq:NZ_AFSZ01000097
NZ_AFSZ0100006614130113,879RefSeq:NZ_AFSZ01000066
NZ_AFSZ0100009114130113,362RefSeq:NZ_AFSZ01000091
NZ_AFSZ010000221111007,565RefSeq:NZ_AFSZ01000022
NZ_AFSZ010000861514017,509RefSeq:NZ_AFSZ01000086
NZ_AFSZ01000092129035,957RefSeq:NZ_AFSZ01000092
41 Undisplayed Contigs/Replicons111105623132,011
Total:3,7893,491692293,899,186
Ortholog data available?Yes
Database Contents
Genes3,789
Pathways257
Enzymatic Reactions1,217
Transport Reactions109
Polypeptides3,535
Protein Complexes53
Enzymes764
Transporters346
Compounds1,007
Transcription Units2,634
tRNAs62
GO Terms2,039
Database Version29.0
Synonyms Acinetobacter baumannii str. ABNIH1
Acinetobacter baumannii strain ABNIH1
Acinetobacter baumannii ABNIH1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii ABNIH1
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00855421
NCBI BioProjectPRJNA224116
NCBI-Taxonomy992402
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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