Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Actinomyces israelii DSM 43320, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_JONS0100000123922847275,560RefSeq:NZ_JONS01000001
NZ_JONS0100000218117416215,524RefSeq:NZ_JONS01000002
NZ_JONS0100000311010532171,234RefSeq:NZ_JONS01000003
NZ_JONS0100000414013208167,077RefSeq:NZ_JONS01000004
NZ_JONS0100000514112759155,849RefSeq:NZ_JONS01000005
NZ_JONS0100000611610736147,867RefSeq:NZ_JONS01000006
NZ_KL5440031079953139,329RefSeq:NZ_KL544003
NZ_JONS0100000912611709138,467RefSeq:NZ_JONS01000009
NZ_JONS0100001010510104123,521RefSeq:NZ_JONS01000010
NZ_KL54400411410932123,472RefSeq:NZ_KL544004
NZ_JONS010000131019506109,497RefSeq:NZ_JONS01000013
NZ_JONS01000014857717105,415RefSeq:NZ_JONS01000014
NZ_JONS0100001572680498,100RefSeq:NZ_JONS01000015
NZ_JONS0100001682760694,589RefSeq:NZ_JONS01000016
NZ_JONS0100001771622788,578RefSeq:NZ_JONS01000017
NZ_JONS0100001863525676,237RefSeq:NZ_JONS01000018
NZ_JONS01000019675701072,599RefSeq:NZ_JONS01000019
NZ_JONS0100002066630372,002RefSeq:NZ_JONS01000020
NZ_JONS0100002145390670,717RefSeq:NZ_JONS01000021
NZ_JONS0100002253501268,166RefSeq:NZ_JONS01000022
NZ_JONS0100002367573768,009RefSeq:NZ_JONS01000023
NZ_JONS0100002449462161,471RefSeq:NZ_JONS01000024
NZ_JONS0100002537351157,700RefSeq:NZ_JONS01000025
NZ_JONS0100002637340352,968RefSeq:NZ_JONS01000026
NZ_JONS0100002736340251,295RefSeq:NZ_JONS01000027
NZ_JONS0100002833320149,147RefSeq:NZ_JONS01000028
NZ_JONS0100002943380549,029RefSeq:NZ_JONS01000029
NZ_JONS0100003035313140,064RefSeq:NZ_JONS01000030
NZ_JONS0100003135300539,964RefSeq:NZ_JONS01000031
NZ_JONS0100003239370236,735RefSeq:NZ_JONS01000032
NZ_JONS0100003329251336,053RefSeq:NZ_JONS01000033
NZ_JONS0100003433282335,162RefSeq:NZ_JONS01000034
NZ_JONS0100003533291335,159RefSeq:NZ_JONS01000035
NZ_JONS0100003626230333,704RefSeq:NZ_JONS01000036
NZ_JONS0100003726240231,037RefSeq:NZ_JONS01000037
NZ_JONS0100003825230230,872RefSeq:NZ_JONS01000038
NZ_JONS0100003926250130,285RefSeq:NZ_JONS01000039
NZ_JONS0100004022210129,233RefSeq:NZ_JONS01000040
NZ_JONS0100004121170429,120RefSeq:NZ_JONS01000041
NZ_JONS0100004220190127,318RefSeq:NZ_JONS01000042
NZ_JONS0100004317150226,954RefSeq:NZ_JONS01000043
NZ_JONS0100004421180325,886RefSeq:NZ_JONS01000044
NZ_JONS0100004520200025,425RefSeq:NZ_JONS01000045
NZ_JONS0100004620181124,703RefSeq:NZ_JONS01000046
NZ_JONS0100004723221024,604RefSeq:NZ_JONS01000047
NZ_JONS0100004818180022,261RefSeq:NZ_JONS01000048
NZ_JONS0100004921180321,432RefSeq:NZ_JONS01000049
NZ_JONS0100005017150220,902RefSeq:NZ_JONS01000050
NZ_JONS0100005120180220,667RefSeq:NZ_JONS01000051
NZ_JONS0100005220190120,441RefSeq:NZ_JONS01000052
NZ_JONS0100005315140120,111RefSeq:NZ_JONS01000053
NZ_JONS0100005412120018,633RefSeq:NZ_JONS01000054
NZ_JONS0100005518150318,395RefSeq:NZ_JONS01000055
NZ_JONS0100005615132018,338RefSeq:NZ_JONS01000056
NZ_JONS0100005718160218,085RefSeq:NZ_JONS01000057
NZ_JONS0100005821161417,761RefSeq:NZ_JONS01000058
NZ_JONS0100005913100317,521RefSeq:NZ_JONS01000059
NZ_JONS0100006015132017,110RefSeq:NZ_JONS01000060
NZ_JONS0100006115130217,017RefSeq:NZ_JONS01000061
NZ_JONS0100006216150116,625RefSeq:NZ_JONS01000062
NZ_JONS010000631190216,469RefSeq:NZ_JONS01000063
NZ_JONS0100006413120115,985RefSeq:NZ_JONS01000064
NZ_JONS0100006511100115,508RefSeq:NZ_JONS01000065
NZ_JONS0100006813111113,297RefSeq:NZ_JONS01000068
NZ_JONS0100007015132012,277RefSeq:NZ_JONS01000070
NZ_JONS0100007112110112,162RefSeq:NZ_JONS01000071
36 Undisplayed Contigs/Replicons127126217189,078
Total:3,3313,056582174,025,772
Ortholog data available?Yes
Database Contents
Genes3,327
Pathways204
Enzymatic Reactions1,010
Transport Reactions73
Polypeptides3,085
Protein Complexes39
Enzymes577
Transporters374
Compounds760
Transcription Units2,410
tRNAs49
Protein Features3,590
Database Version29.0
Sequence SourceGCF_000711965.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces israelii
Actinomyces israelii DSM 43320
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02745698
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120944
EnvironmentHost; Human
Geographic LocationUSA
Latitude/Longitude44.028866 N 92.46855 W
Relationship to Oxygenanaerobe
Temperature Rangemesophile
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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