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 Acetivibrio cellulolyticus CD2, 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_JH5566531,8031,73535332,192,750RefSeq:NZ_JH556653
NZ_JH5566591,1201,09110191,349,091RefSeq:NZ_JH556659
NZ_JH5566588127856211,072,651RefSeq:NZ_JH556658
NZ_JH556657722699419946,364RefSeq:NZ_JH556657
NZ_JH55665135033866367,531RefSeq:NZ_JH556651
NZ_JH55665274730176,464RefSeq:NZ_JH556652
NZ_JH556655574213269,690RefSeq:NZ_JH556655
NZ_JH55666032320031,848RefSeq:NZ_JH556660
NZ_JH556656980126,110RefSeq:NZ_JH556656
NZ_JH55665430300024,236RefSeq:NZ_JH556654
Total:5,0094,833741026,156,735
Ortholog data available?Yes
Database Contents
Genes5,007
Pathways194
Enzymatic Reactions1,049
Transport Reactions45
Polypeptides4,908
Protein Complexes75
Enzymes758
Transporters241
Compounds804
Transcription Units3,605
tRNAs59
Protein Features6,282
GO Terms182
Database Version29.0
Sequence SourceGCF_000179595.2
Synonyms Acetivibrio cellulolyticus ATCC 33288
Acetivibrio cellulolyticus DSM 1870
Hungateiclostridium cellulolyticum CD2
Acetivibrio cellulolyticus CD2
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Eubacteriales
Oscillospiraceae
Acetivibrio
Acetivibrio cellulolyticus
Acetivibrio cellulolyticus CD2
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02256541
NCBI BioProjectPRJNA224116
NCBI-Taxonomy509191
Environmentsewage sludge
Geographic LocationCanada
Relationship to Oxygenfacultative
Temperature Rangemesophile
Biotic Relationshipfree-living
Annotation ProviderNCBI RefSeq
Annotation Date2022-01-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17.