Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-Nov-2024 from the annotated genome of Acetobacter tropicalis NBRC 101654, as obtained from RefSeq (annotation date: 23-FEB-2023). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [Karp11, Karp16] using MetaCyc version 28.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_BABS01000001868600102,592RefSeq:NZ_BABS01000001
NZ_BABS0100000262601162,248RefSeq:NZ_BABS01000002
NZ_BABS0100000340400059,890RefSeq:NZ_BABS01000003
NZ_BABS0100000452520059,192RefSeq:NZ_BABS01000004
NZ_BABS0100000539390057,366RefSeq:NZ_BABS01000005
NZ_BABS0100000648480057,240RefSeq:NZ_BABS01000006
NZ_BABS0100000749472057,107RefSeq:NZ_BABS01000007
NZ_BABS0100000847441254,273RefSeq:NZ_BABS01000008
NZ_BABS0100000952511051,987RefSeq:NZ_BABS01000009
NZ_BABS0100001043421050,011RefSeq:NZ_BABS01000010
NZ_BABS0100001149472049,778RefSeq:NZ_BABS01000011
NZ_BABS0100001235341048,158RefSeq:NZ_BABS01000012
NZ_BABS0100001342402048,039RefSeq:NZ_BABS01000013
NZ_BABS0100001447470046,323RefSeq:NZ_BABS01000014
NZ_BABS0100001542393045,285RefSeq:NZ_BABS01000015
NZ_BABS0100001638380044,635RefSeq:NZ_BABS01000016
NZ_BABS0100001742420044,167RefSeq:NZ_BABS01000017
NZ_BABS0100001835323041,204RefSeq:NZ_BABS01000018
NZ_BABS0100001925250038,909RefSeq:NZ_BABS01000019
NZ_BABS0100002030300038,350RefSeq:NZ_BABS01000020
NZ_BABS0100002132320037,336RefSeq:NZ_BABS01000021
NZ_BABS0100002224240035,740RefSeq:NZ_BABS01000022
NZ_BABS0100002325240135,702RefSeq:NZ_BABS01000023
NZ_BABS0100002429281035,321RefSeq:NZ_BABS01000024
NZ_BABS0100002533312033,908RefSeq:NZ_BABS01000025
NZ_BABS0100002626250133,136RefSeq:NZ_BABS01000026
NZ_BABS0100002729290031,688RefSeq:NZ_BABS01000027
NZ_BABS0100002823220131,173RefSeq:NZ_BABS01000028
NZ_BABS0100002924231030,088RefSeq:NZ_BABS01000029
NZ_BABS0100003028261128,782RefSeq:NZ_BABS01000030
NZ_BABS0100003127270028,333RefSeq:NZ_BABS01000031
NZ_BABS0100003219190027,804RefSeq:NZ_BABS01000032
NZ_BABS0100003318180027,480RefSeq:NZ_BABS01000033
NZ_BABS0100003419190026,612RefSeq:NZ_BABS01000034
NZ_BABS0100003521210025,989RefSeq:NZ_BABS01000035
NZ_BABS0100003725240125,976RefSeq:NZ_BABS01000037
NZ_BABS0100003621200125,976RefSeq:NZ_BABS01000036
NZ_BABS0100003815150025,827RefSeq:NZ_BABS01000038
NZ_BABS0100003918170125,280RefSeq:NZ_BABS01000039
NZ_BABS0100004021200125,262RefSeq:NZ_BABS01000040
NZ_BABS0100004115150024,725RefSeq:NZ_BABS01000041
NZ_BABS0100004221210024,365RefSeq:NZ_BABS01000042
NZ_BABS0100004321201022,866RefSeq:NZ_BABS01000043
NZ_BABS0100004419180122,863RefSeq:NZ_BABS01000044
NZ_BABS0100004516150122,783RefSeq:NZ_BABS01000045
NZ_BABS0100004619190022,309RefSeq:NZ_BABS01000046
NZ_BABS0100004717170022,226RefSeq:NZ_BABS01000047
NZ_BABS0100004820190122,058RefSeq:NZ_BABS01000048
NZ_BABS0100004918180021,860RefSeq:NZ_BABS01000049
NZ_BABS0100005021210021,851RefSeq:NZ_BABS01000050
NZ_BABS0100005125232021,569RefSeq:NZ_BABS01000051
NZ_BABS0100005217170021,152RefSeq:NZ_BABS01000052
NZ_BABS0100005317160121,144RefSeq:NZ_BABS01000053
NZ_BABS0100005419181020,645RefSeq:NZ_BABS01000054
NZ_BABS0100005512120020,588RefSeq:NZ_BABS01000055
NZ_BABS0100005625250019,945RefSeq:NZ_BABS01000056
NZ_BABS0100005717170019,619RefSeq:NZ_BABS01000057
NZ_BABS0100005810100019,206RefSeq:NZ_BABS01000058
NZ_BABS0100005916160018,789RefSeq:NZ_BABS01000059
NZ_BABS0100006017150218,276RefSeq:NZ_BABS01000060
NZ_BABS0100006115150018,027RefSeq:NZ_BABS01000061
NZ_BABS0100006217140317,772RefSeq:NZ_BABS01000062
NZ_BABS0100006317142117,542RefSeq:NZ_BABS01000063
NZ_BABS0100006417141216,926RefSeq:NZ_BABS01000064
NZ_BABS0100006614140016,369RefSeq:NZ_BABS01000066
NZ_BABS0100006812120016,067RefSeq:NZ_BABS01000068
NZ_BABS0100006914131015,824RefSeq:NZ_BABS01000069
NZ_BABS0100007017142115,747RefSeq:NZ_BABS01000070
NZ_BABS0100007115131115,681RefSeq:NZ_BABS01000071
NZ_BABS0100007213130015,238RefSeq:NZ_BABS01000072
NZ_BABS0100007319180115,188RefSeq:NZ_BABS01000073
NZ_BABS0100007413130014,870RefSeq:NZ_BABS01000074
NZ_BABS0100007512120014,650RefSeq:NZ_BABS01000075
NZ_BABS0100007615150014,606RefSeq:NZ_BABS01000076
NZ_BABS0100007712110114,520RefSeq:NZ_BABS01000077
NZ_BABS0100007811110014,414RefSeq:NZ_BABS01000078
NZ_BABS0100007913120114,410RefSeq:NZ_BABS01000079
NZ_BABS0100008018180014,133RefSeq:NZ_BABS01000080
NZ_BABS0100008111110014,079RefSeq:NZ_BABS01000081
NZ_BABS010000821290314,024RefSeq:NZ_BABS01000082
NZ_BABS0100008312120013,782RefSeq:NZ_BABS01000083
NZ_BABS0100008414130113,756RefSeq:NZ_BABS01000084
NZ_BABS0100008511110013,642RefSeq:NZ_BABS01000085
NZ_BABS0100008913120112,831RefSeq:NZ_BABS01000089
NZ_BABS0100009212120012,761RefSeq:NZ_BABS01000092
NZ_BABS0100009411110012,736RefSeq:NZ_BABS01000094
NZ_BABS0100009513130012,729RefSeq:NZ_BABS01000095
NZ_BABS0100009815150012,387RefSeq:NZ_BABS01000098
NZ_BABS0100010115140112,188RefSeq:NZ_BABS01000101
NZ_BABS0100010411100111,990RefSeq:NZ_BABS01000104
NZ_BABS0100010713111111,565RefSeq:NZ_BABS01000107
NZ_BABS0100011014130110,866RefSeq:NZ_BABS01000110
NZ_BABS0100011214130110,616RefSeq:NZ_BABS01000112
NZ_BABS0100011312120010,324RefSeq:NZ_BABS01000113
NZ_BABS010001301514018,704RefSeq:NZ_BABS01000130
NZ_BABS010001321212008,486RefSeq:NZ_BABS01000132
677 Undisplayed Contigs/Replicons760749111531,136,082
Total:3,1492,912451923,718,538
Ortholog data available?No
Database Contents
Genes3,149
Pathways284
Enzymatic Reactions1,573
Transport Reactions60
Polypeptides3,242
Protein Complexes76
Enzymes767
Transporters313
Compounds1,374
Transcription Units2,545
tRNAs38
Protein Features3,649
GO Terms4,138
Database Version29.0
Sequence SourceGCF_000225485.1
Synonyms Acetobacter tropicalis SKU1100
Acetobacter tropicalis strain NBRC 101654
Acetobacter tropicalis str. NBRC 101654
Acetobacter tropicalis NBRC 101654
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter tropicalis
Acetobacter tropicalis NBRC 101654
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00015735
NCBI BioProjectPRJNA224116
NCBI-Taxonomy749388
Annotation ProviderNCBI RefSeq
Annotation Date2023-09-10
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.6
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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