Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 27-Feb-2018 from the annotated genome of Actinomyces nasicola KPR-1, 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 22.0) [Karp16, Karp11] using MetaCyc version 21.5 [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_FNQV0100000124623925267,033RefSeq:NZ_FNQV01000001
NZ_FNQV01000002219206103244,401RefSeq:NZ_FNQV01000002
NZ_FNQV0100000321820783224,324RefSeq:NZ_FNQV01000003
NZ_FNQV0100000420719719211,626RefSeq:NZ_FNQV01000004
NZ_FNQV0100000519118803201,903RefSeq:NZ_FNQV01000005
NZ_FNQV0100000617416275186,289RefSeq:NZ_FNQV01000006
NZ_FNQV0100000713412329143,699RefSeq:NZ_FNQV01000007
NZ_FNQV0100000813412824139,566RefSeq:NZ_FNQV01000008
NZ_FNQV0100000910610312133,298RefSeq:NZ_FNQV01000009
NZ_FNQV0100001012211912128,208RefSeq:NZ_FNQV01000010
NZ_FNQV01000011107986399,549RefSeq:NZ_FNQV01000011
NZ_FNQV01000012877341087,465RefSeq:NZ_FNQV01000012
NZ_FNQV0100001380772181,408RefSeq:NZ_FNQV01000013
NZ_FNQV0100001468670175,658RefSeq:NZ_FNQV01000014
NZ_FNQV0100001558540458,303RefSeq:NZ_FNQV01000015
NZ_FNQV0100001651500154,104RefSeq:NZ_FNQV01000016
NZ_FNQV0100001728271033,586RefSeq:NZ_FNQV01000017
NZ_FNQV0100001833280530,558RefSeq:NZ_FNQV01000018
NZ_FNQV0100001925212227,264RefSeq:NZ_FNQV01000019
NZ_FNQV0100002026201526,843RefSeq:NZ_FNQV01000020
NZ_FNQV0100002118162017,672RefSeq:NZ_FNQV01000021
NZ_FNQV0100002218160217,211RefSeq:NZ_FNQV01000022
NZ_FNQV010000241611239,756RefSeq:NZ_FNQV01000024
6 Undisplayed Contigs/Replicons25232532,511
Total:2,3962,25356872,532,235
Ortholog data available?Yes
Database Contents
Genes2,395
Pathways176
Enzymatic Reactions962
Transport Reactions56
Polypeptides2,254
Protein Complexes13
Enzymes500
Transporters189
Compounds757
Transcription Units1,409
tRNAs47
Protein Features2,773
GO Terms9,454
Database Version29.0
Synonyms Actinomyces nasico
Actinomyces nasicola Hall et al. 2003
CCUG 46092
CIP 107668
strain R2014
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces nasicola
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02910418
NCBI BioProjectPRJNA224116
NCBI-Taxonomy208480

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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