Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Pleomorphomonas koreensis DSM 23070, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [Caspi19]. 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_AULH0100000134934324404,394RefSeq:NZ_AULH01000001
NZ_KE38432734533645374,525RefSeq:NZ_KE384327
NZ_AULH0100000533332751352,454RefSeq:NZ_AULH01000005
NZ_AULH01000006344330104348,540RefSeq:NZ_AULH01000006
NZ_AULH0100000731931045330,456RefSeq:NZ_AULH01000007
NZ_AULH0100000827126731296,720RefSeq:NZ_AULH01000008
NZ_AULH0100000921320922210,737RefSeq:NZ_AULH01000009
NZ_AULH0100001016516311190,060RefSeq:NZ_AULH01000010
NZ_AULH0100001117817512188,985RefSeq:NZ_AULH01000011
NZ_AULH0100001215415301180,242RefSeq:NZ_AULH01000012
NZ_AULH0100001315915612174,907RefSeq:NZ_AULH01000013
NZ_AULH0100001415515131173,571RefSeq:NZ_AULH01000014
NZ_AULH0100001514614033158,133RefSeq:NZ_AULH01000015
NZ_AULH0100001613513131156,676RefSeq:NZ_AULH01000016
NZ_AULH0100001712712322106,809RefSeq:NZ_AULH01000017
NZ_AULH0100001811411103102,849RefSeq:NZ_AULH01000018
NZ_AULH010000191061021396,888RefSeq:NZ_AULH01000019
NZ_AULH0100002089862194,209RefSeq:NZ_AULH01000020
NZ_AULH0100002176711490,028RefSeq:NZ_AULH01000021
NZ_AULH0100002260590174,603RefSeq:NZ_AULH01000022
NZ_AULH0100002350481151,418RefSeq:NZ_AULH01000023
NZ_AULH0100002445430244,875RefSeq:NZ_AULH01000024
NZ_AULH0100002540371244,660RefSeq:NZ_AULH01000025
NZ_AULH0100002632301135,807RefSeq:NZ_AULH01000026
NZ_AULH0100002721210030,303RefSeq:NZ_AULH01000027
NZ_AULH0100002827240328,026RefSeq:NZ_AULH01000028
NZ_AULH0100002926250127,739RefSeq:NZ_AULH01000029
NZ_AULH0100003018150321,805RefSeq:NZ_AULH01000030
NZ_AULH0100003115150018,763RefSeq:NZ_AULH01000031
NZ_AULH0100003217140316,567RefSeq:NZ_AULH01000032
NZ_AULH0100003315140116,411RefSeq:NZ_AULH01000033
NZ_AULH0100003414130115,379RefSeq:NZ_AULH01000034
NZ_AULH0100003519110813,182RefSeq:NZ_AULH01000035
NZ_AULH0100003611100112,478RefSeq:NZ_AULH01000036
39 Undisplayed Contigs/Replicons9289626137,453
Total:4,3094,152571004,620,652
Ortholog data available?Yes
Database Contents
Genes4,305
Pathways295
Enzymatic Reactions1,309
Transport Reactions85
Polypeptides4,198
Protein Complexes79
Enzymes858
Transporters528
Compounds970
Transcription Units2,876
tRNAs46
Protein Features5,242
Database Version29.0
Sequence SourceGCF_000425185.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Hyphomicrobiales
Methylocystaceae
Pleomorphomonas
Pleomorphomonas koreensis
Pleomorphomonas koreensis DSM 23070
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02440681
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1122962
EnvironmentContaminated culture of the phototrophic bacterium R. palustris
Geographic LocationSouth Africa
Latitude/Longitude36.356 N 127.386 E
Relationship to Oxygenaerobe
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

References

Caspi19: 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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