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 sp. LMG 1636 LMG 1636, 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_WOSX01000001422403118484,166RefSeq:NZ_WOSX01000001
NZ_WOSX0100000213312805178,114RefSeq:NZ_WOSX01000002
NZ_WOSX0100000316515933174,268RefSeq:NZ_WOSX01000003
NZ_WOSX0100000412412103162,003RefSeq:NZ_WOSX01000004
NZ_WOSX0100000512812404147,104RefSeq:NZ_WOSX01000005
NZ_WOSX0100000612912234146,178RefSeq:NZ_WOSX01000006
NZ_WOSX0100000712311913140,308RefSeq:NZ_WOSX01000007
NZ_WOSX0100000810410112121,423RefSeq:NZ_WOSX01000008
NZ_WOSX010000091049806116,063RefSeq:NZ_WOSX01000009
NZ_WOSX01000010938904113,930RefSeq:NZ_WOSX01000010
NZ_WOSX0100001180742495,315RefSeq:NZ_WOSX01000011
NZ_WOSX0100001283784191,159RefSeq:NZ_WOSX01000012
NZ_WOSX0100001370680289,702RefSeq:NZ_WOSX01000013
NZ_WOSX0100001479714488,078RefSeq:NZ_WOSX01000014
NZ_WOSX0100001574721182,530RefSeq:NZ_WOSX01000015
NZ_WOSX0100001663591378,140RefSeq:NZ_WOSX01000016
NZ_WOSX0100001760560476,811RefSeq:NZ_WOSX01000017
NZ_WOSX0100001862560672,063RefSeq:NZ_WOSX01000018
NZ_WOSX0100001960551469,699RefSeq:NZ_WOSX01000019
NZ_WOSX0100002070682068,587RefSeq:NZ_WOSX01000020
NZ_WOSX0100002155530261,225RefSeq:NZ_WOSX01000021
NZ_WOSX0100002245411352,957RefSeq:NZ_WOSX01000022
NZ_WOSX0100002341380352,011RefSeq:NZ_WOSX01000023
NZ_WOSX0100002444430151,440RefSeq:NZ_WOSX01000024
NZ_WOSX0100002563591349,837RefSeq:NZ_WOSX01000025
NZ_WOSX0100002663630048,582RefSeq:NZ_WOSX01000026
NZ_WOSX0100002750481148,070RefSeq:NZ_WOSX01000027
NZ_WOSX0100002841380345,879RefSeq:NZ_WOSX01000028
NZ_WOSX0100002942381343,933RefSeq:NZ_WOSX01000029
NZ_WOSX0100003035311343,641RefSeq:NZ_WOSX01000030
NZ_WOSX0100003139330640,494RefSeq:NZ_WOSX01000031
NZ_WOSX0100003235322137,789RefSeq:NZ_WOSX01000032
NZ_WOSX0100003337331337,413RefSeq:NZ_WOSX01000033
NZ_WOSX0100003442390337,158RefSeq:NZ_WOSX01000034
NZ_WOSX0100003529260333,505RefSeq:NZ_WOSX01000035
NZ_WOSX0100003637360133,136RefSeq:NZ_WOSX01000036
NZ_WOSX0100003728270132,869RefSeq:NZ_WOSX01000037
NZ_WOSX0100003830270332,600RefSeq:NZ_WOSX01000038
NZ_WOSX0100003921210032,477RefSeq:NZ_WOSX01000039
NZ_WOSX0100004029280128,752RefSeq:NZ_WOSX01000040
NZ_WOSX0100004121200128,341RefSeq:NZ_WOSX01000041
NZ_WOSX0100004225240128,180RefSeq:NZ_WOSX01000042
NZ_WOSX0100004324201328,149RefSeq:NZ_WOSX01000043
NZ_WOSX0100004423220127,138RefSeq:NZ_WOSX01000044
NZ_WOSX0100004527260125,762RefSeq:NZ_WOSX01000045
NZ_WOSX0100004614140024,143RefSeq:NZ_WOSX01000046
NZ_WOSX0100004717170023,768RefSeq:NZ_WOSX01000047
NZ_WOSX0100004816150122,472RefSeq:NZ_WOSX01000048
NZ_WOSX0100004925210421,733RefSeq:NZ_WOSX01000049
NZ_WOSX0100005024220220,416RefSeq:NZ_WOSX01000050
NZ_WOSX0100005112110120,125RefSeq:NZ_WOSX01000051
NZ_WOSX0100005214130118,720RefSeq:NZ_WOSX01000052
NZ_WOSX0100005316160018,690RefSeq:NZ_WOSX01000053
NZ_WOSX0100005419170217,953RefSeq:NZ_WOSX01000054
NZ_WOSX0100005516140217,232RefSeq:NZ_WOSX01000055
NZ_WOSX0100005614130115,198RefSeq:NZ_WOSX01000056
NZ_WOSX0100005720151414,549RefSeq:NZ_WOSX01000057
NZ_WOSX0100005818150314,168RefSeq:NZ_WOSX01000058
NZ_WOSX0100005921190214,101RefSeq:NZ_WOSX01000059
NZ_WOSX0100006213110213,161RefSeq:NZ_WOSX01000062
NZ_WOSX0100006415140112,626RefSeq:NZ_WOSX01000064
NZ_WOSX010000681390410,231RefSeq:NZ_WOSX01000068
NZ_WOSX01000074117048,572RefSeq:NZ_WOSX01000074
100 Undisplayed Contigs/Replicons234227763332,168
Total:3,7473,477512194,217,005
Ortholog data available?No
Database Contents
Genes3,747
Pathways241
Enzymatic Reactions1,238
Transport Reactions49
Polypeptides3,530
Protein Complexes45
Enzymes769
Transporters281
Compounds916
Transcription Units2,653
tRNAs44
Protein Features4,119
GO Terms3
Database Version29.0
Sequence SourceGCF_011516735.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
unclassified Acetobacter
Acetobacter sp. LMG 1636
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN13343657
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1737473
EnvironmentCider fermentation
Geographic LocationUnited Kingdom
Collection Date1900
Annotation ProviderNCBI RefSeq
Annotation Date2020-12-29
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17.