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 01-June-2020 from the annotated genome of Borrelia hermsii HS1, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP014349866823385922,500RefSeq:NZ_CP014349
megaplasmid16816503182,863RefSeq:NZ_CP014350
lpB5855480758,207RefSeq:NZ_CP014792
lpV47513801346,648RefSeq:NZ_CP015333
lpN3137280931,123RefSeq:NZ_CP015331
cp2842380427,881RefSeq:NZ_CP014351
lpT2831240727,618RefSeq:NZ_CP015332
lpG2729290027,366RefSeq:NZ_CP015334
lpE2726200627,074RefSeq:NZ_CP014871
lpF2730210926,961RefSeq:NZ_CP015336
cp6.577006,540RefSeq:NZ_CP015335
pR66005,225RefSeq:NZ_CP015337
Total:1,3481,24738631,390,006
Ortholog data available?Yes
Database Contents
Genes1,348
Pathways63
Enzymatic Reactions388
Transport Reactions25
Polypeptides1,249
Protein Complexes13
Enzymes219
Transporters77
Compounds346
Transcription Units767
tRNAs32
Protein Features1,340
GO Terms510
Database Version29.0
Sequence SourceGCF_001660005.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Spirochaetota
Spirochaetia
Spirochaetales
Borreliaceae
Borrelia
Borrelia hermsii
Borrelia hermsii HS1
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04481062
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1867252
EnvironmentOrnithodoros hermsi
Geographic LocationWA
Latitude/Longitude47.6007 N 117.3283 W
Altitude (m)949.0
Collection Date1968
HostOrnithodoros hermsi
Annotation ProviderNCBI RefSeq
Annotation Date2020-02-12
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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