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 12-July-2021 from the annotated genome of Acetobacter persici JCM 25330, 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 25.0 [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_BAJW0100000110378223119,499RefSeq:NZ_BAJW01000001
NZ_BAJW0100000210678127104,335RefSeq:NZ_BAJW01000002
NZ_BAJW01000003997422389,661RefSeq:NZ_BAJW01000003
NZ_BAJW01000004735501884,202RefSeq:NZ_BAJW01000004
NZ_BAJW01000005715301877,894RefSeq:NZ_BAJW01000005
NZ_BAJW01000006604301775,087RefSeq:NZ_BAJW01000006
NZ_BAJW01000007705011973,837RefSeq:NZ_BAJW01000007
NZ_BAJW01000008705801270,627RefSeq:NZ_BAJW01000008
NZ_BAJW01000009705211767,777RefSeq:NZ_BAJW01000009
NZ_BAJW01000010533022166,405RefSeq:NZ_BAJW01000010
NZ_BAJW0100001165552864,048RefSeq:NZ_BAJW01000011
NZ_BAJW0100001277680963,840RefSeq:NZ_BAJW01000012
NZ_BAJW01000013604002063,375RefSeq:NZ_BAJW01000013
NZ_BAJW01000014695031660,115RefSeq:NZ_BAJW01000014
NZ_BAJW01000015584401457,998RefSeq:NZ_BAJW01000015
NZ_BAJW0100001652422855,347RefSeq:NZ_BAJW01000016
NZ_BAJW01000017422411751,142RefSeq:NZ_BAJW01000017
NZ_BAJW0100001838320649,063RefSeq:NZ_BAJW01000018
NZ_BAJW0100001936290748,232RefSeq:NZ_BAJW01000019
NZ_BAJW0100002043332848,015RefSeq:NZ_BAJW01000020
NZ_BAJW01000022483521147,268RefSeq:NZ_BAJW01000022
NZ_BAJW01000021543801647,264RefSeq:NZ_BAJW01000021
NZ_BAJW01000023462921546,967RefSeq:NZ_BAJW01000023
NZ_BAJW01000024423101146,348RefSeq:NZ_BAJW01000024
NZ_BAJW01000025392701246,096RefSeq:NZ_BAJW01000025
NZ_BAJW01000026412911145,499RefSeq:NZ_BAJW01000026
NZ_BAJW01000027291701244,182RefSeq:NZ_BAJW01000027
NZ_BAJW0100002836320443,643RefSeq:NZ_BAJW01000028
NZ_BAJW0100002939330642,835RefSeq:NZ_BAJW01000029
NZ_BAJW01000030402811142,381RefSeq:NZ_BAJW01000030
NZ_BAJW0100003144360842,363RefSeq:NZ_BAJW01000031
NZ_BAJW0100003246381742,086RefSeq:NZ_BAJW01000032
NZ_BAJW0100003327210637,275RefSeq:NZ_BAJW01000033
NZ_BAJW0100003424190534,797RefSeq:NZ_BAJW01000034
NZ_BAJW0100003527190833,635RefSeq:NZ_BAJW01000035
NZ_BAJW0100003630241532,084RefSeq:NZ_BAJW01000036
NZ_BAJW0100003732241731,981RefSeq:NZ_BAJW01000037
NZ_BAJW0100003825210431,031RefSeq:NZ_BAJW01000038
NZ_BAJW01000039261601031,005RefSeq:NZ_BAJW01000039
NZ_BAJW0100004032230930,984RefSeq:NZ_BAJW01000040
NZ_BAJW01000041281701130,963RefSeq:NZ_BAJW01000041
NZ_BAJW0100004228250330,202RefSeq:NZ_BAJW01000042
NZ_BAJW0100004324180629,943RefSeq:NZ_BAJW01000043
NZ_BAJW0100004429222529,125RefSeq:NZ_BAJW01000044
NZ_BAJW0100004526200628,868RefSeq:NZ_BAJW01000045
NZ_BAJW0100004634281528,391RefSeq:NZ_BAJW01000046
NZ_BAJW0100004723200328,014RefSeq:NZ_BAJW01000047
NZ_BAJW0100004824190527,456RefSeq:NZ_BAJW01000048
NZ_BAJW0100004925190626,815RefSeq:NZ_BAJW01000049
NZ_BAJW0100005026190725,049RefSeq:NZ_BAJW01000050
NZ_BAJW0100005125161824,103RefSeq:NZ_BAJW01000051
NZ_BAJW0100005221150623,632RefSeq:NZ_BAJW01000052
NZ_BAJW0100005322131822,592RefSeq:NZ_BAJW01000053
NZ_BAJW0100005425201421,620RefSeq:NZ_BAJW01000054
NZ_BAJW0100005521180321,320RefSeq:NZ_BAJW01000055
NZ_BAJW0100005618110720,781RefSeq:NZ_BAJW01000056
NZ_BAJW010000571691619,170RefSeq:NZ_BAJW01000057
NZ_BAJW0100005818100818,664RefSeq:NZ_BAJW01000058
NZ_BAJW0100005920141518,249RefSeq:NZ_BAJW01000059
NZ_BAJW0100006018131417,534RefSeq:NZ_BAJW01000060
NZ_BAJW0100006117111517,496RefSeq:NZ_BAJW01000061
NZ_BAJW0100006215110417,427RefSeq:NZ_BAJW01000062
NZ_BAJW0100006316100617,418RefSeq:NZ_BAJW01000063
NZ_BAJW0100006419140517,280RefSeq:NZ_BAJW01000064
NZ_BAJW0100006514100417,079RefSeq:NZ_BAJW01000065
NZ_BAJW0100006617131316,696RefSeq:NZ_BAJW01000066
NZ_BAJW0100006712100215,516RefSeq:NZ_BAJW01000067
NZ_BAJW0100006817100715,421RefSeq:NZ_BAJW01000068
NZ_BAJW0100006916120414,992RefSeq:NZ_BAJW01000069
NZ_BAJW010000701190214,806RefSeq:NZ_BAJW01000070
NZ_BAJW010000721140714,259RefSeq:NZ_BAJW01000072
NZ_BAJW010000741270513,957RefSeq:NZ_BAJW01000074
NZ_BAJW010000751180313,800RefSeq:NZ_BAJW01000075
NZ_BAJW010000761170413,528RefSeq:NZ_BAJW01000076
NZ_BAJW0100007814130113,320RefSeq:NZ_BAJW01000078
NZ_BAJW0100008013100313,080RefSeq:NZ_BAJW01000080
NZ_BAJW010000831280412,104RefSeq:NZ_BAJW01000083
NZ_BAJW0100008516130311,570RefSeq:NZ_BAJW01000085
NZ_BAJW010000871380511,182RefSeq:NZ_BAJW01000087
NZ_BAJW0100008814112111,041RefSeq:NZ_BAJW01000088
NZ_BAJW010000921180310,759RefSeq:NZ_BAJW01000092
NZ_BAJW010001061210029,140RefSeq:NZ_BAJW01000106
NZ_BAJW01000108129039,105RefSeq:NZ_BAJW01000108
NZ_BAJW01000113136078,598RefSeq:NZ_BAJW01000113
NZ_BAJW010001151211108,290RefSeq:NZ_BAJW01000115
NZ_BAJW01000121129037,438RefSeq:NZ_BAJW01000121
150 Undisplayed Contigs/Replicons38637511189673,939
Total:3,4412,501538873,701,955
Ortholog data available?No
Database Contents
Genes3,441
Pathways173
Enzymatic Reactions946
Transport Reactions45
Polypeptides2,664
Protein Complexes22
Enzymes516
Transporters204
Compounds753
Transcription Units2,444
tRNAs46
Protein Features2,581
GO Terms1
Database Version29.0
Sequence SourceGCF_000613905.1
Synonyms Acetobacter persici LMG 26458
Acetobacter persici T-120
Acetobacter sp. JCM 25330
Acetobacter sp. T-120
Acetobacter persici JCM 25330
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter persici
Acetobacter persici JCM 25330
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00012185
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1236503
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-13
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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