Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Actinomyces urogenitalis S6-C4, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_JRMT0100006217216444207,310RefSeq:NZ_JRMT01000062
NZ_JRMT0100002214814710174,505RefSeq:NZ_JRMT01000022
NZ_JRMT0100006312812413151,860RefSeq:NZ_JRMT01000063
NZ_JRMT0100003312311751140,924RefSeq:NZ_JRMT01000033
NZ_JRMT0100005811510933135,279RefSeq:NZ_JRMT01000058
NZ_JRMT010000611019902120,279RefSeq:NZ_JRMT01000061
NZ_JRMT0100005910610150117,465RefSeq:NZ_JRMT01000059
NZ_JRMT0100002083811195,596RefSeq:NZ_JRMT01000020
NZ_JRMT0100003474704094,474RefSeq:NZ_JRMT01000034
NZ_JRMT0100004877761092,396RefSeq:NZ_JRMT01000048
NZ_JRMT0100004079745090,575RefSeq:NZ_JRMT01000040
NZ_JRMT0100004964621182,981RefSeq:NZ_JRMT01000049
NZ_JRMT0100006459563079,819RefSeq:NZ_JRMT01000064
NZ_JRMT0100003975740179,693RefSeq:NZ_JRMT01000039
NZ_JRMT0100005065590679,015RefSeq:NZ_JRMT01000050
NZ_JRMT0100003862591270,287RefSeq:NZ_JRMT01000038
NZ_JRMT0100001564586065,054RefSeq:NZ_JRMT01000015
NZ_JRMT0100000353530063,064RefSeq:NZ_JRMT01000003
NZ_JRMT0100001860562257,090RefSeq:NZ_JRMT01000018
NZ_JRMT0100002651480354,828RefSeq:NZ_JRMT01000026
NZ_JRMT0100003640390147,710RefSeq:NZ_JRMT01000036
NZ_JRMT0100002142420043,276RefSeq:NZ_JRMT01000021
NZ_JRMT0100002934330142,110RefSeq:NZ_JRMT01000029
NZ_JRMT0100000430291042,096RefSeq:NZ_JRMT01000004
NZ_JRMT0100000131273141,505RefSeq:NZ_JRMT01000001
NZ_JRMT0100000535330241,339RefSeq:NZ_JRMT01000005
NZ_JRMT0100000830300041,222RefSeq:NZ_JRMT01000008
NZ_JRMT0100005537343040,162RefSeq:NZ_JRMT01000055
NZ_JRMT0100003223230034,932RefSeq:NZ_JRMT01000032
NZ_JRMT0100005626260032,424RefSeq:NZ_JRMT01000056
NZ_JRMT0100001920180226,670RefSeq:NZ_JRMT01000019
NZ_JRMT0100002824222025,102RefSeq:NZ_JRMT01000028
NZ_JRMT0100005119190024,879RefSeq:NZ_JRMT01000051
NZ_JRMT0100004121210023,307RefSeq:NZ_JRMT01000041
NZ_JRMT0100001714140023,140RefSeq:NZ_JRMT01000017
NZ_JRMT0100004216140213,810RefSeq:NZ_JRMT01000042
NZ_JRMT0100000613130013,683RefSeq:NZ_JRMT01000006
28 Undisplayed Contigs/Replicons625394103,583
Total:2,2802,17761422,713,444
Ortholog data available?No
Database Contents
Genes2,280
Pathways181
Enzymatic Reactions902
Transport Reactions37
Polypeptides2,194
Protein Complexes86
Enzymes544
Transporters203
Compounds643
Transcription Units1,568
tRNAs52
Protein Features2,889
GO Terms217
Database Version29.0
Sequence SourceGCF_000758745.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces urogenitalis
Actinomyces urogenitalis S6-C4
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02850922
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1284679
Environmentvagina
HostHomo sapiens
Human Microbiome Body Siteurogenital-tract
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-11
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

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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