Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 03-Nov-2025 from the annotated genome of Pseudomonas amygdali 0893_23, as obtained from RefSeq (annotation date: 05-APR-2025). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 29.5) [Karp11, Karp16] using MetaCyc version 29.5 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_GL384620327326117422,068RefSeq:NZ_GL384620
NZ_GL38462123823445274,108RefSeq:NZ_GL384621
NZ_GL38462221121015258,833RefSeq:NZ_GL384622
NZ_GL384623144144014165,472RefSeq:NZ_GL384623
NZ_GL384624133133012155,259RefSeq:NZ_GL384624
NZ_GL384625121120113154,041RefSeq:NZ_GL384625
NZ_GL38470812612516145,039RefSeq:NZ_GL384708
NZ_GL384626106106010138,748RefSeq:NZ_GL384626
NZ_GL38462711811806136,078RefSeq:NZ_GL384627
NZ_GL38470611811806136,078RefSeq:NZ_GL384706
NZ_GL384707102102014131,022RefSeq:NZ_GL384707
NZ_GL384628909006116,668RefSeq:NZ_GL384628
NZ_GL384629949316114,175RefSeq:NZ_GL384629
NZ_GL384630828204112,588RefSeq:NZ_GL384630
NZ_GL384631818105105,994RefSeq:NZ_GL384631
NZ_GL384632868519103,783RefSeq:NZ_GL384632
NZ_GL384633838307102,053RefSeq:NZ_GL384633
NZ_GL38463481810399,727RefSeq:NZ_GL384634
NZ_GL38463578771392,896RefSeq:NZ_GL384635
NZ_GL38463659590987,809RefSeq:NZ_GL384636
NZ_GL38470566660286,237RefSeq:NZ_GL384705
NZ_GL38463965632781,416RefSeq:NZ_GL384639
NZ_GL38463773721680,613RefSeq:NZ_GL384637
NZ_GL38463866660680,185RefSeq:NZ_GL384638
NZ_GL38464059581777,501RefSeq:NZ_GL384640
NZ_GL38464273730276,682RefSeq:NZ_GL384642
NZ_GL38464371710276,354RefSeq:NZ_GL384643
NZ_GL38464152493475,969RefSeq:NZ_GL384641
NZ_GL38464562620469,746RefSeq:NZ_GL384645
NZ_GL38464462602269,214RefSeq:NZ_GL384644
NZ_GL38464657561564,632RefSeq:NZ_GL384646
NZ_GL38464747470863,852RefSeq:NZ_GL384647
NZ_GL38464846460663,785RefSeq:NZ_GL384648
NZ_GL38464950491362,608RefSeq:NZ_GL384649
NZ_GL38465149490361,678RefSeq:NZ_GL384651
NZ_GL38465258580460,147RefSeq:NZ_GL384652
NZ_GL38465050491258,774RefSeq:NZ_GL384650
NZ_GL38465344440657,354RefSeq:NZ_GL384653
NZ_GL38465442420356,179RefSeq:NZ_GL384654
NZ_GL38465542420255,768RefSeq:NZ_GL384655
NZ_GL38465648480253,693RefSeq:NZ_GL384656
NZ_GL38465736360449,943RefSeq:NZ_GL384657
NZ_GL38465845450149,296RefSeq:NZ_GL384658
NZ_GL38465957534046,743RefSeq:NZ_GL384659
NZ_GL38466024240043,337RefSeq:NZ_GL384660
NZ_GL38466133330341,765RefSeq:NZ_GL384661
NZ_GL38466342411141,341RefSeq:NZ_GL384663
NZ_GL38466223230740,076RefSeq:NZ_GL384662
NZ_GL38466528280339,485RefSeq:NZ_GL384665
NZ_GL38466730300439,297RefSeq:NZ_GL384667
NZ_GL38466428280239,151RefSeq:NZ_GL384664
NZ_GL38466832320038,054RefSeq:NZ_GL384668
NZ_GL38466929290035,292RefSeq:NZ_GL384669
NZ_GL38466624240134,451RefSeq:NZ_GL384666
NZ_GL38467123230333,619RefSeq:NZ_GL384671
NZ_GL38467225241232,457RefSeq:NZ_GL384672
NZ_GL38467019172032,371RefSeq:NZ_GL384670
NZ_AEAD0100042123230129,778RefSeq:NZ_AEAD01000421
NZ_GL38467331310129,391RefSeq:NZ_GL384673
NZ_GL38467418171227,321RefSeq:NZ_GL384674
NZ_GL38467528280027,288RefSeq:NZ_GL384675
NZ_GL38467625250324,984RefSeq:NZ_GL384676
NZ_AEAD0100043422220023,533RefSeq:NZ_AEAD01000434
NZ_GL38467722220222,695RefSeq:NZ_GL384677
NZ_GL38467914140221,651RefSeq:NZ_GL384679
NZ_GL38467820200421,595RefSeq:NZ_GL384678
NZ_GL38468017170421,461RefSeq:NZ_GL384680
NZ_GL38468113130220,644RefSeq:NZ_GL384681
NZ_GL38468219190220,530RefSeq:NZ_GL384682
NZ_GL38468313130219,527RefSeq:NZ_GL384683
NZ_GL38468415150018,472RefSeq:NZ_GL384684
NZ_AEAD0100046113130218,381RefSeq:NZ_AEAD01000461
NZ_AEAD0100046218180118,287RefSeq:NZ_AEAD01000462
NZ_GL38468710100417,240RefSeq:NZ_GL384687
NZ_GL38468615150116,651RefSeq:NZ_GL384686
NZ_AEAD0100047024240116,336RefSeq:NZ_AEAD01000470
NZ_GL38468514140316,127RefSeq:NZ_GL384685
NZ_GL38468817161014,518RefSeq:NZ_GL384688
NZ_AEAD01000473990313,571RefSeq:NZ_AEAD01000473
NZ_AEAD0100047414131013,112RefSeq:NZ_AEAD01000474
NZ_AEAD0100047512111112,202RefSeq:NZ_AEAD01000475
382 Undisplayed Contigs/Replicons1901828126398,868
Total:5,2184,731434446,005,667
Ortholog data available?Yes
Database Contents
Genes4,774
Pathways348
Enzymatic Reactions1,908
Transport Reactions147
Polypeptides5,296
Protein Complexes157
Enzymes1,141
Transporters512
Compounds1,608
Transcription Units4,070
tRNAs36
GO Annotations8,483
Database Version29.6
Sequence SourceGCF_000145685.1
Synonyms Pseudomonas syringae pv. aesculi str. 0893_23
Pseudomonas syringae pv. aesculi strain 0893_23
Pseudomonas amygdali pv. aesculi str. 0893_23
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae
Pseudomonas
Pseudomonas syringae group
Pseudomonas syringae group genomosp. 2
Pseudomonas amygdali
Pseudomonas amygdali pv. aesculi
Pseudomonas amygdali pv. aesculi str. 0893_23
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471319
NCBI BioProjectPRJNA224116
NCBI-Taxonomy629258
Annotation ProviderNCBI RefSeq
Annotation Date2025-04-4
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.10
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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