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 25-Oct-2020 from the annotated genome of Acidomonas methanolica MB58, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_BAND0100003817516933182,472RefSeq:NZ_BAND01000038
NZ_BAND0100000515715232166,945RefSeq:NZ_BAND01000005
NZ_BAND0100001111010811125,242RefSeq:NZ_BAND01000011
NZ_BAND0100003188870195,300RefSeq:NZ_BAND01000031
NZ_BAND0100001588852193,151RefSeq:NZ_BAND01000015
NZ_BAND0100006085804192,715RefSeq:NZ_BAND01000060
NZ_BAND0100001385850088,137RefSeq:NZ_BAND01000013
NZ_BAND0100008578762084,459RefSeq:NZ_BAND01000085
NZ_BAND0100005986850182,555RefSeq:NZ_BAND01000059
NZ_BAND0100004177751181,712RefSeq:NZ_BAND01000041
NZ_BAND0100001852492163,165RefSeq:NZ_BAND01000018
NZ_BAND0100002054530162,436RefSeq:NZ_BAND01000020
NZ_BAND0100000660564056,140RefSeq:NZ_BAND01000006
NZ_BAND0100003543410255,944RefSeq:NZ_BAND01000035
NZ_BAND0100010346450151,624RefSeq:NZ_BAND01000103
NZ_BAND0100002749471150,048RefSeq:NZ_BAND01000027
NZ_BAND0100002338370148,033RefSeq:NZ_BAND01000023
NZ_BAND0100003635350047,735RefSeq:NZ_BAND01000036
NZ_BAND0100003039390047,123RefSeq:NZ_BAND01000030
NZ_BAND0100019644410344,984RefSeq:NZ_BAND01000196
NZ_BAND0100012038370143,527RefSeq:NZ_BAND01000120
NZ_BAND0100001643421042,855RefSeq:NZ_BAND01000016
NZ_BAND0100004043394041,036RefSeq:NZ_BAND01000040
NZ_BAND0100003235321239,489RefSeq:NZ_BAND01000032
NZ_BAND0100007658541339,344RefSeq:NZ_BAND01000076
NZ_BAND0100004845440139,009RefSeq:NZ_BAND01000048
NZ_BAND0100006839390038,717RefSeq:NZ_BAND01000068
NZ_BAND0100011040371238,313RefSeq:NZ_BAND01000110
NZ_BAND0100006344440037,633RefSeq:NZ_BAND01000063
NZ_BAND0100005430280236,160RefSeq:NZ_BAND01000054
NZ_BAND0100008345430235,690RefSeq:NZ_BAND01000083
NZ_BAND0100000328260235,014RefSeq:NZ_BAND01000003
NZ_BAND0100010123230034,424RefSeq:NZ_BAND01000101
NZ_BAND0100000828280034,424RefSeq:NZ_BAND01000008
NZ_BAND0100005731310033,260RefSeq:NZ_BAND01000057
NZ_BAND0100013526240232,262RefSeq:NZ_BAND01000135
NZ_BAND0100016428270132,101RefSeq:NZ_BAND01000164
NZ_BAND0100006433302131,463RefSeq:NZ_BAND01000064
NZ_BAND0100007524230130,207RefSeq:NZ_BAND01000075
NZ_BAND0100011323220129,219RefSeq:NZ_BAND01000113
NZ_BAND0100006722220028,825RefSeq:NZ_BAND01000067
NZ_BAND0100009322220027,905RefSeq:NZ_BAND01000093
NZ_BAND0100005028271027,645RefSeq:NZ_BAND01000050
NZ_BAND0100008129270227,635RefSeq:NZ_BAND01000081
NZ_BAND0100009925240127,371RefSeq:NZ_BAND01000099
NZ_BAND0100001230271225,056RefSeq:NZ_BAND01000012
NZ_BAND0100000923230024,798RefSeq:NZ_BAND01000009
NZ_BAND0100007224211223,016RefSeq:NZ_BAND01000072
NZ_BAND0100010819171122,484RefSeq:NZ_BAND01000108
NZ_BAND0100000227260122,475RefSeq:NZ_BAND01000002
NZ_BAND0100009821190220,490RefSeq:NZ_BAND01000098
NZ_BAND0100011216151020,480RefSeq:NZ_BAND01000112
NZ_BAND0100007817161019,561RefSeq:NZ_BAND01000078
NZ_BAND0100004715130218,837RefSeq:NZ_BAND01000047
NZ_BAND0100011118161118,492RefSeq:NZ_BAND01000111
NZ_BAND0100002117170017,690RefSeq:NZ_BAND01000021
NZ_BAND0100013820170317,366RefSeq:NZ_BAND01000138
NZ_BAND0100004616150117,365RefSeq:NZ_BAND01000046
NZ_BAND0100028815130216,431RefSeq:NZ_BAND01000288
NZ_BAND0100010614130116,162RefSeq:NZ_BAND01000106
NZ_BAND0100012813130015,690RefSeq:NZ_BAND01000128
NZ_BAND0100001719181015,563RefSeq:NZ_BAND01000017
NZ_BAND0100012115150015,493RefSeq:NZ_BAND01000121
NZ_BAND0100011814130115,332RefSeq:NZ_BAND01000118
NZ_BAND0100013319160315,120RefSeq:NZ_BAND01000133
NZ_BAND0100006512110114,908RefSeq:NZ_BAND01000065
NZ_BAND0100007412110114,012RefSeq:NZ_BAND01000074
NZ_BAND0100008016160013,903RefSeq:NZ_BAND01000080
NZ_BAND0100014012100213,533RefSeq:NZ_BAND01000140
NZ_BAND0100001413100313,219RefSeq:NZ_BAND01000014
NZ_BAND0100007316160012,869RefSeq:NZ_BAND01000073
NZ_BAND0100005613130012,819RefSeq:NZ_BAND01000056
NZ_BAND0100004212120011,557RefSeq:NZ_BAND01000042
NZ_BAND0100016812110111,213RefSeq:NZ_BAND01000168
NZ_BAND0100007112100210,550RefSeq:NZ_BAND01000071
NZ_BAND0100004911110010,314RefSeq:NZ_BAND01000049
NZ_BAND010000101313007,161RefSeq:NZ_BAND01000010
469 Undisplayed Contigs/Replicons4764688138682,624
Total:3,4593,195492153,690,031
Ortholog data available?No
Database Contents
Genes3,459
Pathways220
Enzymatic Reactions1,127
Transport Reactions52
Polypeptides3,341
Protein Complexes31
Enzymes685
Transporters252
Compounds840
Transcription Units2,280
tRNAs42
Protein Features3,842
GO Terms10,766
Database Version29.0
Sequence SourceGCF_000617865.1
Synonyms Acidomonas methanolica MB58
Acidomonas methanolica NBRC 104435
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acidomonas
Acidomonas methanolica
Acidomonas methanolica NBRC 104435
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00036639
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1231351
EnvironmentG_DNA_Vaginal introitus
Annotation ProviderNCBI RefSeq
Annotation Date2020-04-9
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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