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 02-Nov-2024 from the annotated genome of Campylobacter coli Z163, as obtained from RefSeq (annotation date: 01-AUG-2023). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [Karp11, Karp16] using MetaCyc version 28.1 [Caspi19]. It has not undergone any manual curation or review, and may contain errors.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AIMK0100001415814882156,969RefSeq:NZ_AIMK01000014
NZ_AIMK0100001110910315109,079RefSeq:NZ_AIMK01000011
NZ_AIMK01000009959320101,802RefSeq:NZ_AIMK01000009
NZ_AIMK0100001210510500101,465RefSeq:NZ_AIMK01000012
NZ_AIMK0100000192920088,909RefSeq:NZ_AIMK01000001
NZ_AIMK0100000699907285,381RefSeq:NZ_AIMK01000006
NZ_AIMK0100002285850081,607RefSeq:NZ_AIMK01000022
NZ_AIMK0100001574693268,309RefSeq:NZ_AIMK01000015
NZ_AIMK0100000577741266,835RefSeq:NZ_AIMK01000005
NZ_AIMK0100000275730266,557RefSeq:NZ_AIMK01000002
NZ_AIMK0100003363630060,748RefSeq:NZ_AIMK01000033
NZ_AIMK0100002549480150,265RefSeq:NZ_AIMK01000025
NZ_AIMK0100002745450044,997RefSeq:NZ_AIMK01000027
NZ_AIMK0100003844430140,085RefSeq:NZ_AIMK01000038
NZ_AIMK0100000333330038,606RefSeq:NZ_AIMK01000003
NZ_AIMK0100003239370237,535RefSeq:NZ_AIMK01000032
NZ_AIMK0100001039370235,161RefSeq:NZ_AIMK01000010
NZ_AIMK0100003934340033,064RefSeq:NZ_AIMK01000039
NZ_AIMK0100002630290128,772RefSeq:NZ_AIMK01000026
NZ_AIMK0100001728270127,975RefSeq:NZ_AIMK01000017
NZ_AIMK0100001624220227,015RefSeq:NZ_AIMK01000016
NZ_AIMK0100000822220021,416RefSeq:NZ_AIMK01000008
NZ_AIMK0100002129281021,054RefSeq:NZ_AIMK01000021
NZ_AIMK0100000418171020,405RefSeq:NZ_AIMK01000004
NZ_AIMK0100003021191120,318RefSeq:NZ_AIMK01000030
NZ_AIMK0100004516160020,083RefSeq:NZ_AIMK01000045
NZ_AIMK0100002418180018,555RefSeq:NZ_AIMK01000024
NZ_AIMK0100000718170114,737RefSeq:NZ_AIMK01000007
NZ_AIMK0100001316150113,416RefSeq:NZ_AIMK01000013
NZ_AIMK0100005813120112,621RefSeq:NZ_AIMK01000058
NZ_AIMK0100002912110111,539RefSeq:NZ_AIMK01000029
NZ_AIMK010000371414009,965RefSeq:NZ_AIMK01000037
NZ_AIMK010000311010009,611RefSeq:NZ_AIMK01000031
NZ_AIMK010000401212009,192RefSeq:NZ_AIMK01000040
NZ_AIMK010000571111004,831RefSeq:NZ_AIMK01000057
70 Undisplayed Contigs/Replicons104911530118,414
Total:1,7631,66340601,677,293
Ortholog data available?No
Database Contents
Genes1,761
Pathways191
Enzymatic Reactions1,085
Transport Reactions50
Polypeptides1,719
Protein Complexes51
Enzymes510
Transporters178
Compounds956
Transcription Units882
tRNAs33
Protein Features2,051
GO Terms3,051
Database Version29.0
Sequence SourceGCF_000253455.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Campylobacterota
Epsilonproteobacteria
Campylobacterales
Campylobacteraceae
Campylobacter
Campylobacter coli
Campylobacter coli Z163
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02429053
NCBI BioProjectPRJNA224116
NCBI-Taxonomy887314
Geographic LocationSwitzerland
Collection Date2002-06
HostGallus gallus
Annotation ProviderNCBI RefSeq
Annotation Date2023-08-1
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.5
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

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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