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 R055a, 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_AMOX010000024984601226504,272RefSeq:NZ_AMOX01000002
NZ_AMOX01000004299276320313,674RefSeq:NZ_AMOX01000004
NZ_AMOX01000005184170311178,507RefSeq:NZ_AMOX01000005
NZ_AMOX0100000311294612125,861RefSeq:NZ_AMOX01000003
NZ_AMOX010000121161110594,626RefSeq:NZ_AMOX01000012
NZ_AMOX0100001063550874,287RefSeq:NZ_AMOX01000010
NZ_AMOX01000011826381174,104RefSeq:NZ_AMOX01000011
NZ_AMOX01000007584061256,462RefSeq:NZ_AMOX01000007
NZ_AMOX0100000639342346,956RefSeq:NZ_AMOX01000006
NZ_AMOX0100000846403346,794RefSeq:NZ_AMOX01000008
NZ_AMOX0100001536273633,585RefSeq:NZ_AMOX01000015
NZ_AMOX0100000933281427,885RefSeq:NZ_AMOX01000009
NZ_AMOX0100001423172426,222RefSeq:NZ_AMOX01000014
NZ_AMOX0100001315150018,425RefSeq:NZ_AMOX01000013
NZ_AMOX010000161312018,993RefSeq:NZ_AMOX01000016
NZ_AMOX010000011100437RefSeq:NZ_AMOX01000001
Total:1,6181,443491261,631,090
Ortholog data available?Yes
Database Contents
Genes1,616
Pathways140
Enzymatic Reactions794
Transport Reactions58
Polypeptides1,447
Protein Complexes49
Enzymes441
Transporters99
Compounds642
Transcription Units790
tRNAs36
GO Terms5,523
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Campylobacterota
Epsilonproteobacteria
Campylobacterales
Helicobacteraceae
Helicobacter
Helicobacter pylori
Helicobacter pylori R055a
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00997711
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1145117
Geographic LocationCanada
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-03-23
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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