Database Authors
Pallavi Subhraveti1, Peter Midford, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2019 from the annotated genome of Helicobacter pylori Hp H-18, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.0 [Caspi18]. 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 Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AKPD01000006438409623452,803RefSeq:NZ_AKPD01000006
NZ_AKPD01000011224200519212,116RefSeq:NZ_AKPD01000011
NZ_AKPD01000004190165817190,690RefSeq:NZ_AKPD01000004
NZ_AKPD01000018177158712151,048RefSeq:NZ_AKPD01000018
NZ_AKPD0100002114013424150,464RefSeq:NZ_AKPD01000021
NZ_AKPD0100001711089912109,084RefSeq:NZ_AKPD01000017
NZ_AKPD01000009858104100,085RefSeq:NZ_AKPD01000009
NZ_AKPD0100000786728686,423RefSeq:NZ_AKPD01000007
NZ_AKPD01000013755941277,718RefSeq:NZ_AKPD01000013
NZ_AKPD0100000558530558,778RefSeq:NZ_AKPD01000005
NZ_AKPD0100001641381242,865RefSeq:NZ_AKPD01000016
NZ_AKPD0100001222200231,176RefSeq:NZ_AKPD01000012
NZ_AKPD010000081242620,861RefSeq:NZ_AKPD01000008
NZ_AKPD0100000124180620,572RefSeq:NZ_AKPD01000001
NZ_AKPD0100002021210019,422RefSeq:NZ_AKPD01000020
NZ_AKPD010000141490511,207RefSeq:NZ_AKPD01000014
NZ_AKPD010000021080210,791RefSeq:NZ_AKPD01000002
NZ_AKPD01000015108028,665RefSeq:NZ_AKPD01000015
NZ_AKPD0100001041032,915RefSeq:NZ_AKPD01000010
NZ_AKPD0100000321012,191RefSeq:NZ_AKPD01000003
NZ_AKPD010000191001817RefSeq:NZ_AKPD01000019
Total:1,7441,548521441,760,691
Ortholog data available?Yes
Database Contents
Genes1,740
Pathways144
Enzymatic Reactions796
Transport Reactions68
Polypeptides1,554
Protein Complexes51
Enzymes460
Transporters103
Compounds637
Transcription Units869
tRNAs43
GO Terms6,286
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Campylobacterota
Epsilonproteobacteria
Campylobacterales
Helicobacteraceae
Helicobacter
Helicobacter pylori
Helicobacter pylori Hp H-18
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00778853
NCBI BioProjectPRJNA224116
NCBI-Taxonomy992065
Geographic LocationUSA
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-03-22
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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