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 ruminicola KPR-7B, 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_FNHU0100000137636349450,626RefSeq:NZ_FNHU01000001
NZ_FNHU0100000226625835308,457RefSeq:NZ_FNHU01000002
NZ_FNHU0100000322722061272,134RefSeq:NZ_FNHU01000003
NZ_FNHU0100000421620673251,284RefSeq:NZ_FNHU01000004
NZ_FNHU0100000517116344220,460RefSeq:NZ_FNHU01000005
NZ_FNHU0100000618717359212,836RefSeq:NZ_FNHU01000006
NZ_FNHU0100000717116353191,499RefSeq:NZ_FNHU01000007
NZ_FNHU0100000812111461163,551RefSeq:NZ_FNHU01000008
NZ_FNHU0100000914013613163,396RefSeq:NZ_FNHU01000009
NZ_FNHU0100001011410923142,723RefSeq:NZ_FNHU01000010
NZ_FNHU01000011999333117,082RefSeq:NZ_FNHU01000011
NZ_FNHU0100001258580084,322RefSeq:NZ_FNHU01000012
NZ_FNHU0100001375721280,998RefSeq:NZ_FNHU01000013
NZ_FNHU0100001468670176,255RefSeq:NZ_FNHU01000014
NZ_FNHU0100001562573273,501RefSeq:NZ_FNHU01000015
NZ_FNHU0100001655530267,538RefSeq:NZ_FNHU01000016
NZ_FNHU0100001754492362,382RefSeq:NZ_FNHU01000017
NZ_FNHU0100001851490260,478RefSeq:NZ_FNHU01000018
NZ_FNHU0100001938361150,816RefSeq:NZ_FNHU01000019
NZ_FNHU0100002040352345,300RefSeq:NZ_FNHU01000020
NZ_FNHU0100002136360043,861RefSeq:NZ_FNHU01000021
NZ_FNHU0100002235340139,321RefSeq:NZ_FNHU01000022
NZ_FNHU0100002327260127,152RefSeq:NZ_FNHU01000023
NZ_FNHU0100002419190023,024RefSeq:NZ_FNHU01000024
NZ_FNHU0100002511100117,900RefSeq:NZ_FNHU01000025
NZ_FNHU0100002612100213,903RefSeq:NZ_FNHU01000026
12 Undisplayed Contigs/Replicons242131038,628
Total:2,7632,63058753,299,427
Ortholog data available?Yes
Database Contents
Genes2,761
Pathways168
Enzymatic Reactions992
Transport Reactions79
Polypeptides2,634
Protein Complexes22
Enzymes576
Transporters299
Compounds819
Transcription Units1,939
tRNAs48
Protein Features3,127
GO Terms10,085
Database Version29.0
Synonyms CGMCC 1.5030
JCM 13352
strain B71
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces ruminicola
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04487766
NCBI BioProjectPRJNA224116
NCBI-Taxonomy332524

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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