Database Authors
Carol A Fulcher1, Anamika Kothari1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp10, Karp11, Caspi14] component of Pathway Tools software version 21.0 and MetaCyc version 20.5 on 12-Dec-2016 13:12:46.

The primary data source for this dataset was the whole genome shotgun sequencing project for Collinsella aerofaciens ATCC 25986 derived from NCBI Reference Sequence: NZ_AAVN00000000.

The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AAVN02000001439418147478,714RefSeq:NZ_AAVN02000001
NZ_AAVN02000002332313316386,275RefSeq:NZ_AAVN02000002
NZ_AAVN0200000323622178280,878RefSeq:NZ_AAVN02000003
NZ_AAVN0200000415614961184,100RefSeq:NZ_AAVN02000004
NZ_AAVN0200000515214624183,388RefSeq:NZ_AAVN02000005
NZ_AAVN0200000617216444169,609RefSeq:NZ_AAVN02000006
NZ_AAVN0200000712010794145,096RefSeq:NZ_AAVN02000007
NZ_AAVN020000081089936121,015RefSeq:NZ_AAVN02000008
NZ_AAVN02000009938652105,018RefSeq:NZ_AAVN02000009
NZ_AAVN0200001078722477,635RefSeq:NZ_AAVN02000010
NZ_AAVN0200001172652574,115RefSeq:NZ_AAVN02000011
NZ_AAVN0200001240373049,431RefSeq:NZ_AAVN02000012
NZ_AAVN0200001337315144,709RefSeq:NZ_AAVN02000013
NZ_AAVN0200001423210235,550RefSeq:NZ_AAVN02000014
NZ_AAVN0200001535331132,993RefSeq:NZ_AAVN02000015
NZ_AAVN0200001622210129,625RefSeq:NZ_AAVN02000016
NZ_AAVN0200001726240222,286RefSeq:NZ_AAVN02000017
NZ_AAVN0200001864024,270RefSeq:NZ_AAVN02000018
NZ_AAVN0200001964113,244RefSeq:NZ_AAVN02000019
NZ_AAVN0200002033002,949RefSeq:NZ_AAVN02000020
NZ_AAVN0200002122002,932RefSeq:NZ_AAVN02000021
NZ_AAVN0200002221012,111RefSeq:NZ_AAVN02000022
NZ_AAVN0200002521011,667RefSeq:NZ_AAVN02000025
NZ_AAVN0200002400001,185RefSeq:NZ_AAVN02000024
NZ_AAVN0200002320021,074RefSeq:NZ_AAVN02000023
Total:2,1642,02267752,439,869
Ortholog data available?Yes
Database Contents
Genes2,161
Pathways137
Enzymatic Reactions790
Transport Reactions79
Polypeptides2,027
Protein Complexes22
Enzymes503
Transporters172
Compounds693
Transcription Units1,463
tRNAs50
Growth Media19
Protein Features2,548
GO Terms12,198
Database Version29.0
Synonyms Collinsella aerofaciens ATCC 25986
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Coriobacteriia
Coriobacteriales
Coriobacteriaceae
Collinsella
Collinsella aerofaciens
Collinsella aerofaciens ATCC 25986
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA224116
NCBI-Taxonomy411903
Environmentbiological product [ENVO:02000043]
Relationship to Oxygenanaerobe
Temperature Rangemesophile
HostHomo sapiens
Copyright SRI International 2016. All Rights Reserved.

References

Caspi14: Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (2014). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases." Nucleic Acids Res. 42(1):D459-D471. PMID: 24225315

Karp10: Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R (2010). "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology." Brief Bioinform 11(1);40-79. PMID: 19955237

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC14.