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_TG2018, 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_AMIE0100014131830486333,031RefSeq:NZ_AMIE01000141
NZ_AMIE0100003413412662148,937RefSeq:NZ_AMIE01000034
NZ_AMIE0100000514313814145,225RefSeq:NZ_AMIE01000005
NZ_AMIE0100001713913504143,600RefSeq:NZ_AMIE01000017
NZ_AMIE0100009612612411136,135RefSeq:NZ_AMIE01000096
NZ_AMIE0100008513312904135,484RefSeq:NZ_AMIE01000085
NZ_AMIE0100012512311904129,317RefSeq:NZ_AMIE01000125
NZ_AMIE0100011912111731121,714RefSeq:NZ_AMIE01000119
NZ_AMIE0100005410510302109,278RefSeq:NZ_AMIE01000054
NZ_AMIE0100008810710313107,046RefSeq:NZ_AMIE01000088
NZ_AMIE01000080979340100,289RefSeq:NZ_AMIE01000080
NZ_AMIE0100006885830289,923RefSeq:NZ_AMIE01000068
NZ_AMIE0100008779771189,850RefSeq:NZ_AMIE01000087
NZ_AMIE0100009785840187,609RefSeq:NZ_AMIE01000097
NZ_AMIE0100008492920084,938RefSeq:NZ_AMIE01000084
NZ_AMIE0100005091844384,900RefSeq:NZ_AMIE01000050
NZ_AMIE0100013779750482,772RefSeq:NZ_AMIE01000137
NZ_AMIE0100006986860079,872RefSeq:NZ_AMIE01000069
NZ_AMIE0100010777732270,905RefSeq:NZ_AMIE01000107
NZ_AMIE0100011559572066,032RefSeq:NZ_AMIE01000115
NZ_AMIE0100001560560465,535RefSeq:NZ_AMIE01000015
NZ_AMIE0100000864640065,097RefSeq:NZ_AMIE01000008
NZ_AMIE0100013956530364,845RefSeq:NZ_AMIE01000139
NZ_AMIE0100006450481159,152RefSeq:NZ_AMIE01000064
NZ_AMIE0100011058570155,599RefSeq:NZ_AMIE01000110
NZ_AMIE0100010056522254,346RefSeq:NZ_AMIE01000100
NZ_AMIE0100003052444451,133RefSeq:NZ_AMIE01000030
NZ_AMIE0100012945430247,904RefSeq:NZ_AMIE01000129
NZ_AMIE0100003940380247,207RefSeq:NZ_AMIE01000039
NZ_AMIE0100005940390147,013RefSeq:NZ_AMIE01000059
NZ_AMIE0100005340380243,128RefSeq:NZ_AMIE01000053
NZ_AMIE0100009443400342,703RefSeq:NZ_AMIE01000094
NZ_AMIE0100010541390242,311RefSeq:NZ_AMIE01000105
NZ_AMIE0100010842373242,232RefSeq:NZ_AMIE01000108
NZ_AMIE0100008135350041,802RefSeq:NZ_AMIE01000081
NZ_AMIE0100009941371341,057RefSeq:NZ_AMIE01000099
NZ_AMIE0100006538371040,912RefSeq:NZ_AMIE01000065
NZ_AMIE0100007131271340,349RefSeq:NZ_AMIE01000071
NZ_AMIE0100010338380036,392RefSeq:NZ_AMIE01000103
NZ_AMIE0100012430273036,279RefSeq:NZ_AMIE01000124
NZ_AMIE0100001128270135,761RefSeq:NZ_AMIE01000011
NZ_AMIE0100001227250234,125RefSeq:NZ_AMIE01000012
NZ_AMIE0100011225240130,886RefSeq:NZ_AMIE01000112
NZ_AMIE0100012131300130,222RefSeq:NZ_AMIE01000121
NZ_AMIE0100010420200026,971RefSeq:NZ_AMIE01000104
NZ_AMIE0100011328243126,759RefSeq:NZ_AMIE01000113
NZ_AMIE0100002224240026,208RefSeq:NZ_AMIE01000022
NZ_AMIE0100007542420024,317RefSeq:NZ_AMIE01000075
NZ_AMIE0100004725231122,788RefSeq:NZ_AMIE01000047
NZ_AMIE0100008235330222,095RefSeq:NZ_AMIE01000082
NZ_AMIE0100010123220121,703RefSeq:NZ_AMIE01000101
NZ_AMIE0100003624230121,702RefSeq:NZ_AMIE01000036
NZ_AMIE0100013033300320,153RefSeq:NZ_AMIE01000130
NZ_AMIE0100006015150019,163RefSeq:NZ_AMIE01000060
NZ_AMIE0100005715112216,636RefSeq:NZ_AMIE01000057
NZ_AMIE0100002613111114,079RefSeq:NZ_AMIE01000026
NZ_AMIE0100000116141113,612RefSeq:NZ_AMIE01000001
NZ_AMIE0100014421210013,261RefSeq:NZ_AMIE01000144
NZ_AMIE0100000212120012,356RefSeq:NZ_AMIE01000002
NZ_AMIE0100009517170010,349RefSeq:NZ_AMIE01000095
NZ_AMIE010000741310039,088RefSeq:NZ_AMIE01000074
86 Undisplayed Contigs/Replicons181175850211,109
Total:3,8993,684651503,975,196
Ortholog data available?Yes
Database Contents
Genes3,897
Pathways269
Enzymatic Reactions1,307
Transport Reactions101
Polypeptides3,707
Protein Complexes54
Enzymes776
Transporters352
Compounds1,065
Transcription Units2,713
tRNAs57
GO Terms1,305
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_TG2018
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471238
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221274
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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