Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acidaminobacter hydrogenoformans DSM 2784, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_FMWL0100000137636862412,578RefSeq:NZ_FMWL01000001
NZ_FMWL0100000237436662405,394RefSeq:NZ_FMWL01000002
NZ_FMWL0100000328428112311,183RefSeq:NZ_FMWL01000003
NZ_FMWL0100000423323003260,202RefSeq:NZ_FMWL01000004
NZ_FMWL0100000522822161255,803RefSeq:NZ_FMWL01000005
NZ_FMWL0100000615114902180,922RefSeq:NZ_FMWL01000006
NZ_FMWL0100000714614402161,486RefSeq:NZ_FMWL01000007
NZ_FMWL0100000810510401136,697RefSeq:NZ_FMWL01000008
NZ_FMWL0100000999980199,851RefSeq:NZ_FMWL01000009
NZ_FMWL0100001099980198,845RefSeq:NZ_FMWL01000010
NZ_FMWL0100001181800198,734RefSeq:NZ_FMWL01000011
NZ_FMWL0100001286850196,245RefSeq:NZ_FMWL01000012
NZ_FMWL0100001386860095,804RefSeq:NZ_FMWL01000013
NZ_FMWL0100001482820094,824RefSeq:NZ_FMWL01000014
NZ_FMWL0100001577761092,462RefSeq:NZ_FMWL01000015
NZ_FMWL0100001678770191,343RefSeq:NZ_FMWL01000016
NZ_FMWL0100001769670276,888RefSeq:NZ_FMWL01000017
NZ_FMWL01000018816219076,180RefSeq:NZ_FMWL01000018
NZ_FMWL0100001967660170,545RefSeq:NZ_FMWL01000019
NZ_FMWL0100002043410256,229RefSeq:NZ_FMWL01000020
NZ_FMWL01000021584315048,292RefSeq:NZ_FMWL01000021
NZ_FMWL0100002244430144,978RefSeq:NZ_FMWL01000022
NZ_FMWL0100002334330140,294RefSeq:NZ_FMWL01000023
NZ_FMWL0100002439370239,713RefSeq:NZ_FMWL01000024
NZ_FMWL0100002533330038,544RefSeq:NZ_FMWL01000025
NZ_FMWL0100002652511034,080RefSeq:NZ_FMWL01000026
NZ_FMWL0100002729281031,246RefSeq:NZ_FMWL01000027
NZ_FMWL0100002824222024,096RefSeq:NZ_FMWL01000028
NZ_FMWL0100002920190123,622RefSeq:NZ_FMWL01000029
NZ_FMWL0100003017161020,791RefSeq:NZ_FMWL01000030
NZ_FMWL0100003120200019,637RefSeq:NZ_FMWL01000031
NZ_FMWL0100003220190119,363RefSeq:NZ_FMWL01000032
NZ_FMWL0100003314130114,995RefSeq:NZ_FMWL01000033
NZ_FMWL01000034291612113,642RefSeq:NZ_FMWL01000034
NZ_FMWL0100003510100012,397RefSeq:NZ_FMWL01000035
6 Undisplayed Contigs/Replicons19190017,704
Total:3,3073,20371333,615,609
Ortholog data available?Yes
Database Contents
Genes3,301
Pathways203
Enzymatic Reactions1,092
Transport Reactions48
Polypeptides3,232
Protein Complexes78
Enzymes685
Transporters336
Compounds817
Transcription Units2,112
tRNAs59
Protein Features4,324
GO Terms304
Database Version29.0
Sequence SourceGCF_900103005.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Eubacteriales
Eubacteriales incertae sedis
Eubacteriales Family XII. Incertae Sedis
Acidaminobacter
Acidaminobacter hydrogenoformans
Acidaminobacter hydrogenoformans DSM 2784
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03080599
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120920
Annotation ProviderNCBI RefSeq
Annotation Date2022-03-31
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17A.