Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Acetobacter okinawensis JCM 25146, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_BAJU01000001282218460293,529RefSeq:NZ_BAJU01000001
NZ_BAJU01000002192149241233,807RefSeq:NZ_BAJU01000002
NZ_BAJU01000003151116035171,961RefSeq:NZ_BAJU01000003
NZ_BAJU01000004136103231144,968RefSeq:NZ_BAJU01000004
NZ_BAJU0100000512893332137,914RefSeq:NZ_BAJU01000005
NZ_BAJU01000006937212095,451RefSeq:NZ_BAJU01000006
NZ_BAJU01000007916422594,932RefSeq:NZ_BAJU01000007
NZ_BAJU01000008776021588,170RefSeq:NZ_BAJU01000008
NZ_BAJU01000009865912685,565RefSeq:NZ_BAJU01000009
NZ_BAJU01000010684911870,301RefSeq:NZ_BAJU01000010
NZ_BAJU01000011795551968,236RefSeq:NZ_BAJU01000011
NZ_BAJU01000012654901667,082RefSeq:NZ_BAJU01000012
NZ_BAJU01000013594411466,162RefSeq:NZ_BAJU01000013
NZ_BAJU01000014502921953,318RefSeq:NZ_BAJU01000014
NZ_BAJU01000015433101252,039RefSeq:NZ_BAJU01000015
NZ_BAJU01000016412701451,608RefSeq:NZ_BAJU01000016
NZ_BAJU01000017523821251,134RefSeq:NZ_BAJU01000017
NZ_BAJU0100001859570250,276RefSeq:NZ_BAJU01000018
NZ_BAJU01000019443211148,812RefSeq:NZ_BAJU01000019
NZ_BAJU01000020564511045,505RefSeq:NZ_BAJU01000020
NZ_BAJU01000021423011145,240RefSeq:NZ_BAJU01000021
NZ_BAJU01000022523531443,739RefSeq:NZ_BAJU01000022
NZ_BAJU01000023433111142,313RefSeq:NZ_BAJU01000023
NZ_BAJU0100002435270840,061RefSeq:NZ_BAJU01000024
NZ_BAJU01000025422911239,665RefSeq:NZ_BAJU01000025
NZ_BAJU0100002636271839,635RefSeq:NZ_BAJU01000026
NZ_BAJU0100002728240434,560RefSeq:NZ_BAJU01000027
NZ_BAJU0100002836280833,751RefSeq:NZ_BAJU01000028
NZ_BAJU0100002933232833,630RefSeq:NZ_BAJU01000029
NZ_BAJU0100003025210433,424RefSeq:NZ_BAJU01000030
NZ_BAJU0100003125220328,108RefSeq:NZ_BAJU01000031
NZ_BAJU0100003228190927,563RefSeq:NZ_BAJU01000032
NZ_BAJU01000033261401227,439RefSeq:NZ_BAJU01000033
NZ_BAJU0100003431230824,833RefSeq:NZ_BAJU01000034
NZ_BAJU0100003522140824,423RefSeq:NZ_BAJU01000035
NZ_BAJU0100003624200424,178RefSeq:NZ_BAJU01000036
NZ_BAJU0100003735271724,020RefSeq:NZ_BAJU01000037
NZ_BAJU0100003827210621,801RefSeq:NZ_BAJU01000038
NZ_BAJU0100003919150421,271RefSeq:NZ_BAJU01000039
NZ_BAJU0100004020170321,196RefSeq:NZ_BAJU01000040
NZ_BAJU0100004120190120,401RefSeq:NZ_BAJU01000041
NZ_BAJU0100004218160220,093RefSeq:NZ_BAJU01000042
NZ_BAJU0100004315110419,838RefSeq:NZ_BAJU01000043
NZ_BAJU010000441461718,726RefSeq:NZ_BAJU01000044
NZ_BAJU0100004517150217,815RefSeq:NZ_BAJU01000045
NZ_BAJU0100004617151116,965RefSeq:NZ_BAJU01000046
NZ_BAJU0100004717101616,935RefSeq:NZ_BAJU01000047
NZ_BAJU0100004817111516,925RefSeq:NZ_BAJU01000048
NZ_BAJU0100004915130215,848RefSeq:NZ_BAJU01000049
NZ_BAJU0100005012100215,771RefSeq:NZ_BAJU01000050
NZ_BAJU0100005116101515,533RefSeq:NZ_BAJU01000051
NZ_BAJU010000521390415,139RefSeq:NZ_BAJU01000052
NZ_BAJU0100005320180214,913RefSeq:NZ_BAJU01000053
NZ_BAJU010000541380514,764RefSeq:NZ_BAJU01000054
NZ_BAJU0100005520701314,619RefSeq:NZ_BAJU01000055
NZ_BAJU0100005617110614,326RefSeq:NZ_BAJU01000056
NZ_BAJU010000591390413,756RefSeq:NZ_BAJU01000059
NZ_BAJU0100006014110313,617RefSeq:NZ_BAJU01000060
NZ_BAJU010000611050513,188RefSeq:NZ_BAJU01000061
NZ_BAJU01000063128049,704RefSeq:NZ_BAJU01000063
NZ_BAJU010000721111006,287RefSeq:NZ_BAJU01000072
66 Undisplayed Contigs/Replicons128121794239,461
Total:3,0242,211527613,166,244
Ortholog data available?Yes
Database Contents
Genes3,024
Pathways175
Enzymatic Reactions923
Transport Reactions39
Polypeptides2,271
Protein Complexes22
Enzymes459
Transporters171
Compounds768
Transcription Units2,053
tRNAs45
Protein Features2,409
Database Version29.0
Sequence SourceGCF_000613865.1
Synonyms Acetobacter okinawensis 1-35
Acetobacter okinawensis LMG 26457
Acetobacter sp. 1-35
Acetobacter sp. JCM 25146
Acetobacter okinawensis JCM 25146
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter okinawensis
Acetobacter okinawensis JCM 25146
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00009357
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1236501
Annotation ProviderNCBI RefSeq
Annotation Date2019-08-27
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.9
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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