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 Paenibacillus polymyxa ZF129, 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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0408294,9914,777157575,703,931RefSeq:NZ_CP040829
pAP1101970479,020RefSeq:NZ_CP040830
pAP241410037,602RefSeq:NZ_CP040831
Total:5,1334,915157615,820,553
Ortholog data available?No
Database Contents
Genes5,133
Pathways271
Enzymatic Reactions1,307
Transport Reactions73
Polypeptides4,915
Protein Complexes161
Enzymes847
Transporters501
Compounds996
Transcription Units3,610
tRNAs111
Protein Features6,493
GO Terms1,754
Database Version29.0
Sequence SourceGCF_006274405.1
Synonyms Aerobacillus polymyxa
Bacillus polymyxa
Bacillus sp. NCIM 2538
Bacillus sp. NCIM 2540
Bacillus sp. NCIM 2726
Bacillus sp. RP 2.2
Clostridium polymyxa
Granulobacter polymyxa
Paenibacillus sp. JCM 8035
Paenibacillus sp. JCM 8036
Paenibacillus sp. JCM 8037
Paenibacillus sp. JCM 8038
Paenibacillus sp. JCM 8039
Paenibacillus sp. WLY78
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Bacillales
Paenibacillaceae
Paenibacillus
Paenibacillus polymyxa
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN11890480
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1406
EnvironmentSoil
Geographic LocationChina
Latitude/Longitude41.67 N 115.69 E
Collection Date2018-09-10
HostSolanum tuberosum
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-14
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 Thu Apr 24, 2025, BIOCYC14B.