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 Acidiphilium angustum ATCC 35903, 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_JNJH0100000120119533218,842RefSeq:NZ_JNJH01000001
NZ_JNJH0100000215014712168,204RefSeq:NZ_JNJH01000002
NZ_JNJH0100000317316643154,694RefSeq:NZ_JNJH01000003
NZ_JNJH0100000411711403143,378RefSeq:NZ_JNJH01000004
NZ_JNJH0100000511311021134,006RefSeq:NZ_JNJH01000005
NZ_JNJH0100000611411103131,137RefSeq:NZ_JNJH01000006
NZ_JNJH0100000710810233118,998RefSeq:NZ_JNJH01000007
NZ_JNJH0100000810510500111,049RefSeq:NZ_JNJH01000008
NZ_JNJH01000009858320102,646RefSeq:NZ_JNJH01000009
NZ_JNJH0100001096883597,808RefSeq:NZ_JNJH01000010
NZ_JNJH0100001186850191,884RefSeq:NZ_JNJH01000011
NZ_JNJH0100001285841089,944RefSeq:NZ_JNJH01000012
NZ_JNJH0100001395940185,415RefSeq:NZ_JNJH01000013
NZ_JNJH0100001475740184,807RefSeq:NZ_JNJH01000014
NZ_JNJH0100001583810282,416RefSeq:NZ_JNJH01000015
NZ_JNJH0100001699961281,519RefSeq:NZ_JNJH01000016
NZ_KL37079573710279,517RefSeq:NZ_KL370795
NZ_JNJH0100001969670272,592RefSeq:NZ_JNJH01000019
NZ_JNJH0100002065611371,968RefSeq:NZ_JNJH01000020
NZ_JNJH0100002172701171,045RefSeq:NZ_JNJH01000021
NZ_JNJH0100002262591261,916RefSeq:NZ_JNJH01000022
NZ_JNJH0100002360591061,263RefSeq:NZ_JNJH01000023
NZ_JNJH0100002447460160,085RefSeq:NZ_JNJH01000024
NZ_JNJH0100002557551159,934RefSeq:NZ_JNJH01000025
NZ_JNJH0100002655541059,244RefSeq:NZ_JNJH01000026
NZ_JNJH0100002740390157,144RefSeq:NZ_JNJH01000027
NZ_JNJH0100002847460155,247RefSeq:NZ_JNJH01000028
NZ_JNJH0100002951490251,999RefSeq:NZ_JNJH01000029
NZ_JNJH0100003047430450,071RefSeq:NZ_JNJH01000030
NZ_JNJH0100003142420046,378RefSeq:NZ_JNJH01000031
NZ_JNJH0100003240400045,720RefSeq:NZ_JNJH01000032
NZ_JNJH0100003343391345,411RefSeq:NZ_JNJH01000033
NZ_JNJH0100003441383043,805RefSeq:NZ_JNJH01000034
NZ_JNJH0100003535341042,705RefSeq:NZ_JNJH01000035
NZ_JNJH0100003634340039,195RefSeq:NZ_JNJH01000036
NZ_JNJH0100003726260037,972RefSeq:NZ_JNJH01000037
NZ_JNJH0100003851501037,360RefSeq:NZ_JNJH01000038
NZ_JNJH0100003930290135,863RefSeq:NZ_JNJH01000039
NZ_JNJH0100004030290133,229RefSeq:NZ_JNJH01000040
NZ_JNJH0100004129281031,980RefSeq:NZ_JNJH01000041
NZ_JNJH0100004231300131,676RefSeq:NZ_JNJH01000042
NZ_JNJH0100004335321230,278RefSeq:NZ_JNJH01000043
NZ_JNJH0100004428262029,605RefSeq:NZ_JNJH01000044
NZ_JNJH0100004522220029,423RefSeq:NZ_JNJH01000045
NZ_JNJH0100004635331128,665RefSeq:NZ_JNJH01000046
NZ_JNJH0100004727240328,060RefSeq:NZ_JNJH01000047
NZ_JNJH0100004830272126,189RefSeq:NZ_JNJH01000048
NZ_JNJH0100004923220125,526RefSeq:NZ_JNJH01000049
NZ_JNJH0100005020200023,144RefSeq:NZ_JNJH01000050
NZ_JNJH0100005123201222,757RefSeq:NZ_JNJH01000051
NZ_JNJH0100005214140021,881RefSeq:NZ_JNJH01000052
NZ_JNJH0100005320200021,452RefSeq:NZ_JNJH01000053
NZ_JNJH0100005421201021,294RefSeq:NZ_JNJH01000054
NZ_JNJH0100005520200020,864RefSeq:NZ_JNJH01000055
NZ_JNJH0100005622220020,125RefSeq:NZ_JNJH01000056
NZ_JNJH0100005718160219,238RefSeq:NZ_JNJH01000057
NZ_JNJH0100005822220018,442RefSeq:NZ_JNJH01000058
NZ_JNJH0100005913121018,194RefSeq:NZ_JNJH01000059
NZ_JNJH0100006020181117,450RefSeq:NZ_JNJH01000060
NZ_JNJH0100006114140016,364RefSeq:NZ_JNJH01000061
NZ_JNJH0100006219190016,278RefSeq:NZ_JNJH01000062
NZ_JNJH010000631476116,182RefSeq:NZ_JNJH01000063
NZ_JNJH0100006418161115,121RefSeq:NZ_JNJH01000064
NZ_JNJH0100006513120114,787RefSeq:NZ_JNJH01000065
NZ_JNJH0100006612120013,881RefSeq:NZ_JNJH01000066
NZ_JNJH0100006713130013,794RefSeq:NZ_JNJH01000067
NZ_JNJH0100006813130013,348RefSeq:NZ_JNJH01000068
NZ_JNJH0100007012120013,061RefSeq:NZ_JNJH01000070
NZ_JNJH0100007116160011,869RefSeq:NZ_JNJH01000071
NZ_JNJH0100007614120210,723RefSeq:NZ_JNJH01000076
NZ_JNJH010000781111009,936RefSeq:NZ_JNJH01000078
NZ_JNJH01000084128138,782RefSeq:NZ_JNJH01000084
NZ_JNJH010000881010007,713RefSeq:NZ_JNJH01000088
133 Undisplayed Contigs/Replicons294289561390,916
Total:3,9213,727561384,175,408
Ortholog data available?Yes
Database Contents
Genes3,919
Pathways295
Enzymatic Reactions1,491
Transport Reactions58
Polypeptides3,819
Protein Complexes64
Enzymes845
Transporters323
Compounds1,053
Transcription Units2,340
tRNAs48
Protein Features4,416
Database Version29.0
Sequence SourceGCF_000701585.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acidiphilium
Acidiphilium angustum
Acidiphilium angustum ATCC 35903
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02841149
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1408418
EnvironmentAcid mine
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-9
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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