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 parvus DSM 16617, 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_AIEB0100000112811945119,396RefSeq:NZ_AIEB01000001
NZ_AIEB0100000211393218118,580RefSeq:NZ_AIEB01000002
NZ_AIEB0100000390793890,991RefSeq:NZ_AIEB01000003
NZ_AIEB0100000483752686,035RefSeq:NZ_AIEB01000004
NZ_AIEB01000005887401485,928RefSeq:NZ_AIEB01000005
NZ_AIEB0100000667600766,486RefSeq:NZ_AIEB01000006
NZ_AIEB0100000765574465,243RefSeq:NZ_AIEB01000007
NZ_AIEB0100000868568464,200RefSeq:NZ_AIEB01000008
NZ_AIEB0100000962560660,390RefSeq:NZ_AIEB01000009
NZ_AIEB0100001059570259,446RefSeq:NZ_AIEB01000010
NZ_AIEB0100001153432857,917RefSeq:NZ_AIEB01000011
NZ_AIEB0100001265620356,380RefSeq:NZ_AIEB01000012
NZ_AIEB0100001356484453,328RefSeq:NZ_AIEB01000013
NZ_AIEB0100001460541553,118RefSeq:NZ_AIEB01000014
NZ_AIEB0100001550422648,076RefSeq:NZ_AIEB01000015
NZ_AIEB0100001640372144,355RefSeq:NZ_AIEB01000016
NZ_AIEB0100001752463344,319RefSeq:NZ_AIEB01000017
NZ_AIEB0100001849460341,764RefSeq:NZ_AIEB01000018
NZ_AIEB0100001944401341,593RefSeq:NZ_AIEB01000019
NZ_AIEB01000020413101040,511RefSeq:NZ_AIEB01000020
NZ_AIEB0100002140360439,629RefSeq:NZ_AIEB01000021
NZ_AIEB0100002238360238,683RefSeq:NZ_AIEB01000022
NZ_AIEB0100002338340436,980RefSeq:NZ_AIEB01000023
NZ_AIEB0100002431271335,316RefSeq:NZ_AIEB01000024
NZ_AIEB0100002530250535,261RefSeq:NZ_AIEB01000025
NZ_AIEB0100002634311234,983RefSeq:NZ_AIEB01000026
NZ_AIEB0100002732311034,592RefSeq:NZ_AIEB01000027
NZ_AIEB0100002834261734,239RefSeq:NZ_AIEB01000028
NZ_AIEB0100002933310231,124RefSeq:NZ_AIEB01000029
NZ_AIEB0100003048407131,120RefSeq:NZ_AIEB01000030
NZ_AIEB0100003136320430,886RefSeq:NZ_AIEB01000031
NZ_AIEB0100003229260330,454RefSeq:NZ_AIEB01000032
NZ_AIEB0100003328270130,304RefSeq:NZ_AIEB01000033
NZ_AIEB0100003425180728,007RefSeq:NZ_AIEB01000034
NZ_AIEB0100003534281527,421RefSeq:NZ_AIEB01000035
NZ_AIEB0100003630240627,006RefSeq:NZ_AIEB01000036
NZ_AIEB0100003720170326,478RefSeq:NZ_AIEB01000037
NZ_AIEB0100003822210125,823RefSeq:NZ_AIEB01000038
NZ_AIEB0100003925180725,682RefSeq:NZ_AIEB01000039
NZ_AIEB0100004028250325,499RefSeq:NZ_AIEB01000040
NZ_AIEB0100004121190224,733RefSeq:NZ_AIEB01000041
NZ_AIEB0100004224210324,214RefSeq:NZ_AIEB01000042
NZ_AIEB0100004318150322,542RefSeq:NZ_AIEB01000043
NZ_AIEB0100004422211021,535RefSeq:NZ_AIEB01000044
NZ_AIEB0100004524190520,099RefSeq:NZ_AIEB01000045
NZ_AIEB0100004623181419,600RefSeq:NZ_AIEB01000046
NZ_AIEB0100004725211319,378RefSeq:NZ_AIEB01000047
NZ_AIEB0100004819180119,183RefSeq:NZ_AIEB01000048
NZ_AIEB0100004920180219,028RefSeq:NZ_AIEB01000049
NZ_AIEB0100005019170218,915RefSeq:NZ_AIEB01000050
NZ_AIEB0100005117160118,905RefSeq:NZ_AIEB01000051
NZ_AIEB0100005215140118,396RefSeq:NZ_AIEB01000052
NZ_AIEB0100005318122417,750RefSeq:NZ_AIEB01000053
NZ_AIEB0100005417131317,600RefSeq:NZ_AIEB01000054
NZ_AIEB0100005521164117,379RefSeq:NZ_AIEB01000055
NZ_AIEB0100005614140016,973RefSeq:NZ_AIEB01000056
NZ_AIEB0100005723210216,891RefSeq:NZ_AIEB01000057
NZ_AIEB0100005814120216,662RefSeq:NZ_AIEB01000058
NZ_AIEB0100005917160116,522RefSeq:NZ_AIEB01000059
NZ_AIEB0100006018160216,212RefSeq:NZ_AIEB01000060
NZ_AIEB0100006114120215,878RefSeq:NZ_AIEB01000061
NZ_AIEB0100006214110315,727RefSeq:NZ_AIEB01000062
NZ_AIEB0100006320190115,639RefSeq:NZ_AIEB01000063
NZ_AIEB0100006417150215,638RefSeq:NZ_AIEB01000064
NZ_AIEB0100006517150214,144RefSeq:NZ_AIEB01000065
NZ_AIEB0100006617152013,772RefSeq:NZ_AIEB01000066
NZ_AIEB0100006715121213,330RefSeq:NZ_AIEB01000067
NZ_AIEB0100006812110113,225RefSeq:NZ_AIEB01000068
NZ_AIEB0100006913100313,171RefSeq:NZ_AIEB01000069
NZ_AIEB010000731170412,050RefSeq:NZ_AIEB01000073
NZ_AIEB0100007513111111,676RefSeq:NZ_AIEB01000075
NZ_AIEB0100007615100511,636RefSeq:NZ_AIEB01000076
NZ_AIEB0100007713100311,613RefSeq:NZ_AIEB01000077
NZ_AIEB010000791390410,716RefSeq:NZ_AIEB01000079
NZ_AIEB010000811290310,304RefSeq:NZ_AIEB01000081
NZ_AIEB010000821380510,271RefSeq:NZ_AIEB01000082
NZ_AIEB010000841390410,218RefSeq:NZ_AIEB01000084
NZ_AIEB010000891212008,079RefSeq:NZ_AIEB01000089
NZ_AIEB010000911312017,885RefSeq:NZ_AIEB01000091
146 Undisplayed Contigs/Replicons23621823145333,010
Total:3,0102,500874232,878,042
Ortholog data available?Yes
Database Contents
Genes3,001
Pathways191
Enzymatic Reactions1,234
Transport Reactions51
Polypeptides2,528
Protein Complexes27
Enzymes581
Transporters182
Compounds1,033
Transcription Units2,173
tRNAs65
GO Terms2,586
Database Version29.0
Synonyms Acinetobacter parvus CIP 108168
Acinetobacter parvus CIP 108168 = DSM 16617
Acinetobacter parvus DSM 16617
Acinetobacter parvus DSM 16617 = CIP 108168
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter parvus
Acinetobacter parvus DSM 16617 = CIP 108168
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471588
NCBI BioProjectPRJNA224116
NCBI-Taxonomy981333
Environmentear from patient with otitis media
Geographic LocationCzech Republic
HostHomo sapiens
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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