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 johnsonii F0542, 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_KE9520961089981126,736RefSeq:NZ_KE952096
NZ_KE95188273683284,758RefSeq:NZ_KE951882
NZ_KE95208279770281,537RefSeq:NZ_KE952082
NZ_KE95192874731078,459RefSeq:NZ_KE951928
NZ_KE95203566650174,980RefSeq:NZ_KE952035
NZ_KE95193557560167,355RefSeq:NZ_KE951935
NZ_KE95195257543056,643RefSeq:NZ_KE951952
NZ_KE95207233320152,378RefSeq:NZ_KE952072
NZ_KE95184041410049,829RefSeq:NZ_KE951840
NZ_KE95184751473149,396RefSeq:NZ_KE951847
NZ_KE95189639381046,254RefSeq:NZ_KE951896
NZ_KE95205036351045,347RefSeq:NZ_KE952050
NZ_KE95189732320042,595RefSeq:NZ_KE951897
NZ_KE95200428270141,751RefSeq:NZ_KE952004
NZ_KE95202131282139,048RefSeq:NZ_KE952021
NZ_KE95184836301537,888RefSeq:NZ_KE951848
NZ_KE95209534302237,404RefSeq:NZ_KE952095
NZ_KE95208629290037,328RefSeq:NZ_KE952086
NZ_KE95190923230033,425RefSeq:NZ_KE951909
NZ_KE95196627240333,347RefSeq:NZ_KE951966
NZ_KE95196321210031,396RefSeq:NZ_KE951963
NZ_KE95185329290030,702RefSeq:NZ_KE951853
NZ_KE95201522200230,239RefSeq:NZ_KE952015
NZ_KE95195427261030,161RefSeq:NZ_KE951954
NZ_KE95184424221129,416RefSeq:NZ_KE951844
NZ_KE95191125240129,152RefSeq:NZ_KE951911
NZ_KE95192618160228,815RefSeq:NZ_KE951926
NZ_KE95205220200028,263RefSeq:NZ_KE952052
NZ_KE95197630263128,075RefSeq:NZ_KE951976
NZ_KE95199924220227,868RefSeq:NZ_KE951999
NZ_KE95185227270027,462RefSeq:NZ_KE951852
NZ_KE95192732293027,096RefSeq:NZ_KE951927
NZ_KE95200224200427,039RefSeq:NZ_KE952002
NZ_KE95184523220125,210RefSeq:NZ_KE951845
NZ_KE95206123211125,120RefSeq:NZ_KE952061
NZ_KE95198818180025,043RefSeq:NZ_KE951988
NZ_KE95199023210224,998RefSeq:NZ_KE951990
NZ_KE95190121200124,848RefSeq:NZ_KE951901
NZ_KE95201719190024,678RefSeq:NZ_KE952017
NZ_KE95203416160024,214RefSeq:NZ_KE952034
NZ_KE95198423230024,187RefSeq:NZ_KE951984
NZ_KE95184321210024,141RefSeq:NZ_KE951843
NZ_KE95204020200023,925RefSeq:NZ_KE952040
NZ_KE95186319190023,597RefSeq:NZ_KE951863
NZ_KE95203120190123,101RefSeq:NZ_KE952031
NZ_KE95202724222021,840RefSeq:NZ_KE952027
NZ_KE95204222210121,426RefSeq:NZ_KE952042
NZ_KE95209114131021,220RefSeq:NZ_KE952091
NZ_KE95188917170021,059RefSeq:NZ_KE951889
NZ_KE95195517150220,816RefSeq:NZ_KE951955
NZ_KE95187217160120,341RefSeq:NZ_KE951872
NZ_KE95186217170020,137RefSeq:NZ_KE951862
NZ_KE95185014130119,702RefSeq:NZ_KE951850
NZ_KE95183914130119,137RefSeq:NZ_KE951839
NZ_KE95203216150119,088RefSeq:NZ_KE952032
NZ_KE95200915150018,924RefSeq:NZ_KE952009
NZ_KE95188020200018,814RefSeq:NZ_KE951880
NZ_KE95185518180018,562RefSeq:NZ_KE951855
NZ_KE95208812100218,006RefSeq:NZ_KE952088
NZ_KE95207813120117,974RefSeq:NZ_KE952078
NZ_KE95183216160017,691RefSeq:NZ_KE951832
NZ_KE95199815140117,610RefSeq:NZ_KE951998
NZ_KE95183413120117,474RefSeq:NZ_KE951834
NZ_KE95184217150217,469RefSeq:NZ_KE951842
NZ_KE95188515150016,714RefSeq:NZ_KE951885
NZ_KE95199112110116,537RefSeq:NZ_KE951991
NZ_KE95194711110016,231RefSeq:NZ_KE951947
NZ_KE9519391191115,687RefSeq:NZ_KE951939
NZ_KE95189510100015,481RefSeq:NZ_KE951895
NZ_KE95185413130015,042RefSeq:NZ_KE951854
NZ_KE95185911110014,481RefSeq:NZ_KE951859
NZ_KE95193111101014,402RefSeq:NZ_KE951931
NZ_KE95192911110013,937RefSeq:NZ_KE951929
NZ_KE95194411101013,420RefSeq:NZ_KE951944
NZ_KE95201114120213,210RefSeq:NZ_KE952011
NZ_KE95190813120113,099RefSeq:NZ_KE951908
NZ_KE95186013121012,981RefSeq:NZ_KE951860
NZ_KE95197013120112,759RefSeq:NZ_KE951970
NZ_KE95207014130112,126RefSeq:NZ_KE952070
NZ_KE95184618170112,037RefSeq:NZ_KE951846
NZ_KE95186910100011,958RefSeq:NZ_KE951869
NZ_KE95196810100011,884RefSeq:NZ_KE951968
NZ_KE95202313130011,046RefSeq:NZ_KE952023
NZ_KE95200111110010,978RefSeq:NZ_KE952001
NZ_KE95209211110010,448RefSeq:NZ_KE952092
NZ_KE9518901111009,651RefSeq:NZ_KE951890
NZ_KE9519231515008,939RefSeq:NZ_KE951923
179 Undisplayed Contigs/Replicons5215091297872,169
Total:2,7342,522531593,327,711
Ortholog data available?No
Database Contents
Genes2,734
Pathways190
Enzymatic Reactions942
Transport Reactions53
Polypeptides2,754
Protein Complexes91
Enzymes532
Transporters226
Compounds726
Transcription Units2,202
tRNAs47
Protein Features2,864
GO Terms199
Database Version29.0
Sequence SourceGCF_000466245.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces johnsonii
Actinomyces johnsonii F0542
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436817
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1321818
Environmentoral cavity- mouth
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-9
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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