Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 13-Mar-2021 from the annotated genome of Acinetobacter rudis DSM 24031, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [Caspi20]. 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 Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_BBRX0100000115115001177,545RefSeq:NZ_BBRX01000001
NZ_BBRX0100001712912243141,190RefSeq:NZ_BBRX01000017
NZ_BBRX0100001812111722139,938RefSeq:NZ_BBRX01000018
NZ_BBRX0100001912812701132,731RefSeq:NZ_BBRX01000019
NZ_BBRX0100002010310021122,069RefSeq:NZ_BBRX01000020
NZ_BBRX0100002110510203121,571RefSeq:NZ_BBRX01000021
NZ_BBRX0100002210310201117,392RefSeq:NZ_BBRX01000022
NZ_BBRX0100002311911540115,402RefSeq:NZ_BBRX01000023
NZ_BBRX0100002480772194,369RefSeq:NZ_BBRX01000024
NZ_BBRX0100002587824188,784RefSeq:NZ_BBRX01000025
NZ_BBRX0100002666640275,585RefSeq:NZ_BBRX01000026
NZ_BBRX0100002767625075,363RefSeq:NZ_BBRX01000027
NZ_BBRX0100002868635073,387RefSeq:NZ_BBRX01000028
NZ_BBRX0100002966620473,360RefSeq:NZ_BBRX01000029
NZ_BBRX0100003064620272,326RefSeq:NZ_BBRX01000030
NZ_BBRX0100003164593268,490RefSeq:NZ_BBRX01000031
NZ_BBRX0100003258580067,535RefSeq:NZ_BBRX01000032
NZ_BBRX0100003367660167,396RefSeq:NZ_BBRX01000033
NZ_BBRX0100000860590167,321RefSeq:NZ_BBRX01000008
NZ_BBRX0100003463620167,193RefSeq:NZ_BBRX01000034
NZ_BBRX0100000346460054,642RefSeq:NZ_BBRX01000003
NZ_BBRX0100003553493153,631RefSeq:NZ_BBRX01000035
NZ_BBRX0100000950460447,954RefSeq:NZ_BBRX01000009
NZ_BBRX0100003645450045,440RefSeq:NZ_BBRX01000036
NZ_BBRX0100003740400043,836RefSeq:NZ_BBRX01000037
NZ_BBRX0100001137350241,924RefSeq:NZ_BBRX01000011
NZ_BBRX0100003828280041,287RefSeq:NZ_BBRX01000038
NZ_BBRX0100003938360239,614RefSeq:NZ_BBRX01000039
NZ_BBRX0100004037360139,583RefSeq:NZ_BBRX01000040
NZ_BBRX0100004129290036,835RefSeq:NZ_BBRX01000041
NZ_BBRX0100004235330234,688RefSeq:NZ_BBRX01000042
NZ_BBRX0100004334340034,460RefSeq:NZ_BBRX01000043
NZ_BBRX0100004426231233,471RefSeq:NZ_BBRX01000044
NZ_BBRX0100004528280032,629RefSeq:NZ_BBRX01000045
NZ_BBRX0100000428262032,464RefSeq:NZ_BBRX01000004
NZ_BBRX0100001020190131,579RefSeq:NZ_BBRX01000010
NZ_BBRX0100004627252029,539RefSeq:NZ_BBRX01000046
NZ_BBRX0100004722220029,478RefSeq:NZ_BBRX01000047
NZ_BBRX0100004827261029,157RefSeq:NZ_BBRX01000048
NZ_BBRX0100004924240029,149RefSeq:NZ_BBRX01000049
NZ_BBRX0100005027270028,330RefSeq:NZ_BBRX01000050
NZ_BBRX0100000534302227,947RefSeq:NZ_BBRX01000005
NZ_BBRX0100005122210127,241RefSeq:NZ_BBRX01000051
NZ_BBRX0100005230240626,785RefSeq:NZ_BBRX01000052
NZ_BBRX0100005324191426,712RefSeq:NZ_BBRX01000053
NZ_BBRX0100005424230126,623RefSeq:NZ_BBRX01000054
NZ_BBRX0100005524176125,361RefSeq:NZ_BBRX01000055
NZ_BBRX0100005621210025,224RefSeq:NZ_BBRX01000056
NZ_BBRX0100005721190224,580RefSeq:NZ_BBRX01000057
NZ_BBRX0100005821210024,454RefSeq:NZ_BBRX01000058
NZ_BBRX0100005921191124,438RefSeq:NZ_BBRX01000059
NZ_BBRX0100006025250024,140RefSeq:NZ_BBRX01000060
NZ_BBRX0100006122173223,738RefSeq:NZ_BBRX01000061
NZ_BBRX0100006224231023,429RefSeq:NZ_BBRX01000062
NZ_BBRX0100006313130022,184RefSeq:NZ_BBRX01000063
NZ_BBRX0100006421200121,818RefSeq:NZ_BBRX01000064
NZ_BBRX0100001229280121,347RefSeq:NZ_BBRX01000012
NZ_BBRX0100006518170120,987RefSeq:NZ_BBRX01000065
NZ_BBRX0100006621174019,845RefSeq:NZ_BBRX01000066
NZ_BBRX0100006719190019,710RefSeq:NZ_BBRX01000067
NZ_BBRX0100006815130219,207RefSeq:NZ_BBRX01000068
NZ_BBRX0100006913120119,109RefSeq:NZ_BBRX01000069
NZ_BBRX0100007012120018,967RefSeq:NZ_BBRX01000070
NZ_BBRX0100007115150018,909RefSeq:NZ_BBRX01000071
NZ_BBRX0100007222174118,824RefSeq:NZ_BBRX01000072
NZ_BBRX0100007313130018,300RefSeq:NZ_BBRX01000073
NZ_BBRX0100007420190117,927RefSeq:NZ_BBRX01000074
NZ_BBRX0100007519190017,659RefSeq:NZ_BBRX01000075
NZ_BBRX0100007617170017,357RefSeq:NZ_BBRX01000076
NZ_BBRX0100007712110117,334RefSeq:NZ_BBRX01000077
NZ_BBRX0100007819180116,827RefSeq:NZ_BBRX01000078
NZ_BBRX0100007911110016,436RefSeq:NZ_BBRX01000079
NZ_BBRX0100008019180116,372RefSeq:NZ_BBRX01000080
NZ_BBRX0100008212110115,928RefSeq:NZ_BBRX01000082
NZ_BBRX0100008314130115,499RefSeq:NZ_BBRX01000083
NZ_BBRX0100008411110015,243RefSeq:NZ_BBRX01000084
NZ_BBRX0100008514130115,033RefSeq:NZ_BBRX01000085
NZ_BBRX0100008611110014,089RefSeq:NZ_BBRX01000086
NZ_BBRX0100008715121213,883RefSeq:NZ_BBRX01000087
NZ_BBRX0100008813130013,813RefSeq:NZ_BBRX01000088
NZ_BBRX0100009119170213,022RefSeq:NZ_BBRX01000091
NZ_BBRX0100009211110012,647RefSeq:NZ_BBRX01000092
NZ_BBRX0100001310100012,563RefSeq:NZ_BBRX01000013
NZ_BBRX0100009317160112,526RefSeq:NZ_BBRX01000093
NZ_BBRX0100009412120012,046RefSeq:NZ_BBRX01000094
NZ_BBRX0100009911100110,155RefSeq:NZ_BBRX01000099
NZ_BBRX0100010012120010,127RefSeq:NZ_BBRX01000100
NZ_BBRX010000061515009,455RefSeq:NZ_BBRX01000006
NZ_BBRX01000101127059,317RefSeq:NZ_BBRX01000101
62 Undisplayed Contigs/Replicons228222637318,020
Total:3,5853,392691243,961,794
Ortholog data available?Yes
Database Contents
Genes3,584
Pathways269
Enzymatic Reactions1,279
Transport Reactions83
Polypeptides3,505
Protein Complexes43
Enzymes766
Transporters363
Compounds961
Transcription Units2,629
tRNAs62
Protein Features4,156
GO Terms10
Database Version29.0
Sequence SourceGCF_000829675.1
Synonyms Acinetobacter sp. A1PC16
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter rudis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00019984
NCBI BioProjectPRJNA224116
NCBI-Taxonomy632955
Annotation ProviderNCBI RefSeq
Annotation Date2020-06-28
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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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