Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 12-July-2021 from the annotated genome of Pseudomonadaceae bacterium P4C P4C, 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 25.0) [Karp16, Karp11] using MetaCyc version 25.0 [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_QJUO0100000132231138369,899RefSeq:NZ_QJUO01000001
NZ_QJUO01000002250233116280,458RefSeq:NZ_QJUO01000002
NZ_QJUO0100000318017424208,115RefSeq:NZ_QJUO01000003
NZ_QJUO0100000416516104170,812RefSeq:NZ_QJUO01000004
NZ_QJUO0100000512011820155,814RefSeq:NZ_QJUO01000005
NZ_QJUO0100000613012811152,233RefSeq:NZ_QJUO01000006
NZ_QJUO0100000713212534137,215RefSeq:NZ_QJUO01000007
NZ_QJUO0100000810910423132,148RefSeq:NZ_QJUO01000008
NZ_QJUO01000009737012121,480RefSeq:NZ_QJUO01000009
NZ_QJUO01000010989710118,934RefSeq:NZ_QJUO01000010
NZ_QJUO01000011999261118,393RefSeq:NZ_QJUO01000011
NZ_QJUO010000121009811112,484RefSeq:NZ_QJUO01000012
NZ_QJUO01000013878700103,701RefSeq:NZ_QJUO01000013
NZ_QJUO01000014928804101,356RefSeq:NZ_QJUO01000014
NZ_QJUO0100001590880299,071RefSeq:NZ_QJUO01000015
NZ_QJUO0100001697910694,640RefSeq:NZ_QJUO01000016
NZ_QJUO0100001776720491,988RefSeq:NZ_QJUO01000017
NZ_QJUO0100001879770285,577RefSeq:NZ_QJUO01000018
NZ_QJUO0100001980781184,128RefSeq:NZ_QJUO01000019
NZ_QJUO0100002076740281,566RefSeq:NZ_QJUO01000020
NZ_QJUO0100002166650178,924RefSeq:NZ_QJUO01000021
NZ_QJUO0100002257560178,821RefSeq:NZ_QJUO01000022
NZ_QJUO0100002361581269,897RefSeq:NZ_QJUO01000023
NZ_QJUO0100002468613469,111RefSeq:NZ_QJUO01000024
NZ_QJUO0100002546460060,883RefSeq:NZ_QJUO01000025
NZ_QJUO0100002648451260,729RefSeq:NZ_QJUO01000026
NZ_QJUO0100002753521060,684RefSeq:NZ_QJUO01000027
NZ_QJUO0100002865641058,234RefSeq:NZ_QJUO01000028
NZ_QJUO0100002955550058,214RefSeq:NZ_QJUO01000029
NZ_QJUO0100003042400257,950RefSeq:NZ_QJUO01000030
NZ_QJUO0100003138353057,362RefSeq:NZ_QJUO01000031
NZ_QJUO0100003250500053,181RefSeq:NZ_QJUO01000032
NZ_QJUO0100003354522053,124RefSeq:NZ_QJUO01000033
NZ_QJUO0100003436360044,230RefSeq:NZ_QJUO01000034
NZ_QJUO0100003533330043,573RefSeq:NZ_QJUO01000035
NZ_QJUO0100003633330042,929RefSeq:NZ_QJUO01000036
NZ_QJUO0100003740370339,703RefSeq:NZ_QJUO01000037
NZ_QJUO0100003837370038,305RefSeq:NZ_QJUO01000038
NZ_QJUO0100003929290035,788RefSeq:NZ_QJUO01000039
NZ_QJUO0100004034322035,072RefSeq:NZ_QJUO01000040
NZ_QJUO0100004127270034,198RefSeq:NZ_QJUO01000041
NZ_QJUO0100004230290134,191RefSeq:NZ_QJUO01000042
NZ_QJUO0100004343411131,755RefSeq:NZ_QJUO01000043
NZ_QJUO0100004427240331,720RefSeq:NZ_QJUO01000044
NZ_QJUO0100004515150025,195RefSeq:NZ_QJUO01000045
NZ_QJUO0100004619180124,821RefSeq:NZ_QJUO01000046
NZ_QJUO0100004721210024,369RefSeq:NZ_QJUO01000047
NZ_QJUO0100004821191122,601RefSeq:NZ_QJUO01000048
NZ_QJUO0100004922171422,426RefSeq:NZ_QJUO01000049
NZ_QJUO0100005015150021,024RefSeq:NZ_QJUO01000050
NZ_QJUO0100005115150017,102RefSeq:NZ_QJUO01000051
NZ_QJUO0100005312120015,470RefSeq:NZ_QJUO01000053
NZ_QJUO0100005411110013,948RefSeq:NZ_QJUO01000054
NZ_QJUO0100005512120013,238RefSeq:NZ_QJUO01000055
31 Undisplayed Contigs/Replicons5851118104,844
Total:3,7603,60962894,353,628
Ortholog data available?Yes
Database Contents
Genes3,755
Pathways274
Enzymatic Reactions1,309
Transport Reactions80
Polypeptides3,663
Protein Complexes58
Enzymes835
Transporters449
Compounds940
Transcription Units2,395
tRNAs51
Protein Features5,135
GO Terms12
Database Version29.0
Sequence SourceGCF_004327335.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae
unclassified Pseudomonadaceae
Pseudomonadaceae bacterium P4C
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN09280092
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2211392
EnvironmentSymptomatic Inner Bark
Geographic LocationUnited Kingdom
Collection Date2012-01-27
HostQuercus robur
Annotation ProviderNCBI RefSeq
Annotation Date2020-08-9
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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