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 sp. HA HA, 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_AJXD0100001719418509196,008RefSeq:NZ_AJXD01000017
NZ_AJXD0100009817916766190,187RefSeq:NZ_AJXD01000098
NZ_AJXD0100004914012929151,169RefSeq:NZ_AJXD01000049
NZ_AJXD01000096146126713145,845RefSeq:NZ_AJXD01000096
NZ_AJXD0100009513412077139,875RefSeq:NZ_AJXD01000095
NZ_AJXD0100009711110407125,639RefSeq:NZ_AJXD01000097
NZ_AJXD0100003911510618124,762RefSeq:NZ_AJXD01000039
NZ_AJXD0100000613112344110,617RefSeq:NZ_AJXD01000006
NZ_AJXD01000045887918101,384RefSeq:NZ_AJXD01000045
NZ_AJXD0100001282750789,990RefSeq:NZ_AJXD01000012
NZ_AJXD01000074786511284,169RefSeq:NZ_AJXD01000074
NZ_AJXD0100000370630778,341RefSeq:NZ_AJXD01000003
NZ_AJXD0100001576671868,401RefSeq:NZ_AJXD01000015
NZ_AJXD0100000262600267,883RefSeq:NZ_AJXD01000002
NZ_AJXD0100000156512362,040RefSeq:NZ_AJXD01000001
NZ_AJXD0100000856465561,669RefSeq:NZ_AJXD01000008
NZ_AJXD0100002267592658,629RefSeq:NZ_AJXD01000022
NZ_AJXD0100009455520356,277RefSeq:NZ_AJXD01000094
NZ_AJXD0100001649450456,100RefSeq:NZ_AJXD01000016
NZ_AJXD0100000950470354,633RefSeq:NZ_AJXD01000009
NZ_AJXD0100001150460454,320RefSeq:NZ_AJXD01000011
NZ_AJXD0100003154484252,999RefSeq:NZ_AJXD01000031
NZ_AJXD0100002578741351,345RefSeq:NZ_AJXD01000025
NZ_AJXD0100001347432249,220RefSeq:NZ_AJXD01000013
NZ_AJXD0100000456464648,581RefSeq:NZ_AJXD01000004
NZ_AJXD0100000544430146,353RefSeq:NZ_AJXD01000005
NZ_AJXD0100008535295134,301RefSeq:NZ_AJXD01000085
NZ_AJXD0100002430290133,783RefSeq:NZ_AJXD01000024
NZ_AJXD0100003434301333,641RefSeq:NZ_AJXD01000034
NZ_AJXD0100006728225131,424RefSeq:NZ_AJXD01000067
NZ_AJXD0100002737297131,094RefSeq:NZ_AJXD01000027
NZ_AJXD0100002929250430,407RefSeq:NZ_AJXD01000029
NZ_AJXD0100001828224228,542RefSeq:NZ_AJXD01000018
NZ_AJXD0100008325230227,699RefSeq:NZ_AJXD01000083
NZ_AJXD0100001930251427,100RefSeq:NZ_AJXD01000019
NZ_AJXD0100003322210126,094RefSeq:NZ_AJXD01000033
NZ_AJXD0100003020180225,682RefSeq:NZ_AJXD01000030
NZ_AJXD0100004824231024,541RefSeq:NZ_AJXD01000048
NZ_AJXD0100004020180222,231RefSeq:NZ_AJXD01000040
NZ_AJXD0100004721191121,997RefSeq:NZ_AJXD01000047
NZ_AJXD0100000719180119,986RefSeq:NZ_AJXD01000007
NZ_AJXD0100002319180119,615RefSeq:NZ_AJXD01000023
NZ_AJXD0100001415140118,508RefSeq:NZ_AJXD01000014
NZ_AJXD010000321282214,025RefSeq:NZ_AJXD01000032
NZ_AJXD0100001015122113,921RefSeq:NZ_AJXD01000010
NZ_AJXD0100002613120113,637RefSeq:NZ_AJXD01000026
NZ_AJXD0100002014130113,517RefSeq:NZ_AJXD01000020
NZ_AJXD0100006313110212,903RefSeq:NZ_AJXD01000063
NZ_AJXD0100005312101111,598RefSeq:NZ_AJXD01000053
NZ_AJXD0100003515112210,777RefSeq:NZ_AJXD01000035
52 Undisplayed Contigs/Replicons190187545251,626
Total:3,0352,716872323,125,085
Ortholog data available?Yes
Database Contents
Genes3,028
Pathways199
Enzymatic Reactions1,263
Transport Reactions66
Polypeptides2,740
Protein Complexes34
Enzymes632
Transporters244
Compounds1,048
Transcription Units2,161
tRNAs64
GO Terms12,348
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter sp. HA
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471709
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1173062
Environmentgut
HostHelicoverpa armigera
Annotation ProviderNCBI
Annotation Date2017-04-6
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
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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