Summary This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Actinomyces sp. ICM54 ICM54, 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 22.0 [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_JDFI0100007920420031226,411RefSeq:NZ_JDFI01000079
NZ_JDFI0100008019218462205,610RefSeq:NZ_JDFI01000080
NZ_JDFI01000026979115115,801RefSeq:NZ_JDFI01000026
NZ_JDFI0100005910210011107,080RefSeq:NZ_JDFI01000059
NZ_JDFI0100002467631383,843RefSeq:NZ_JDFI01000024
NZ_JDFI0100008258580065,486RefSeq:NZ_JDFI01000082
NZ_JDFI0100003560564064,345RefSeq:NZ_JDFI01000035
NZ_JDFI0100007363602163,477RefSeq:NZ_JDFI01000073
NZ_JDFI0100000753512056,060RefSeq:NZ_JDFI01000007
NZ_JDFI0100002351500155,780RefSeq:NZ_JDFI01000023
NZ_JDFI0100005342390345,659RefSeq:NZ_JDFI01000053
NZ_JDFI0100008931310044,791RefSeq:NZ_JDFI01000089
NZ_JDFI0100003947450243,732RefSeq:NZ_JDFI01000039
NZ_JDFI0100000633321040,641RefSeq:NZ_JDFI01000006
NZ_JDFI0100004437350239,422RefSeq:NZ_JDFI01000044
NZ_JDFI0100003433330038,420RefSeq:NZ_JDFI01000034
NZ_JDFI0100003833294037,691RefSeq:NZ_JDFI01000038
NZ_JDFI0100006932292137,469RefSeq:NZ_JDFI01000069
NZ_JDFI0100005728270137,342RefSeq:NZ_JDFI01000057
NZ_JDFI0100009137351136,214RefSeq:NZ_JDFI01000091
NZ_JDFI0100006330300035,475RefSeq:NZ_JDFI01000063
NZ_JDFI0100007227270034,230RefSeq:NZ_JDFI01000072
NZ_JDFI0100000534331034,196RefSeq:NZ_JDFI01000005
NZ_JDFI0100005825250033,725RefSeq:NZ_JDFI01000058
NZ_JDFI0100001223230032,714RefSeq:NZ_JDFI01000012
NZ_JDFI0100001022210132,582RefSeq:NZ_JDFI01000010
NZ_JDFI0100009420191029,706RefSeq:NZ_JDFI01000094
NZ_JDFI0100005126260028,517RefSeq:NZ_JDFI01000051
NZ_JDFI0100004024185126,977RefSeq:NZ_JDFI01000040
NZ_JDFI0100000419190026,805RefSeq:NZ_JDFI01000004
NZ_JDFI0100008620191026,076RefSeq:NZ_JDFI01000086
NZ_JDFI0100006628260225,088RefSeq:NZ_JDFI01000066
NZ_JDFI0100005622191224,152RefSeq:NZ_JDFI01000056
NZ_JDFI0100001713130022,890RefSeq:NZ_JDFI01000017
NZ_JDFI0100005221201022,311RefSeq:NZ_JDFI01000052
NZ_JDFI0100008822220022,194RefSeq:NZ_JDFI01000088
NZ_JDFI0100004520200017,932RefSeq:NZ_JDFI01000045
NZ_JDFI0100002913130017,439RefSeq:NZ_JDFI01000029
NZ_JDFI0100009015150016,896RefSeq:NZ_JDFI01000090
NZ_JDFI0100004114130116,565RefSeq:NZ_JDFI01000041
NZ_JDFI0100003613110215,952RefSeq:NZ_JDFI01000036
NZ_JDFI0100000214112115,826RefSeq:NZ_JDFI01000002
NZ_JDFI0100001415141015,826RefSeq:NZ_JDFI01000014
NZ_JDFI0100002014121115,589RefSeq:NZ_JDFI01000020
NZ_JDFI0100006512120012,262RefSeq:NZ_JDFI01000065
NZ_JDFI010000111919008,142RefSeq:NZ_JDFI01000011
48 Undisplayed Contigs/Replicons215206915299,706
Total:2,0551,95451502,355,047
Ortholog data available?Yes
Database Contents
Genes2,055
Pathways154
Enzymatic Reactions809
Transport Reactions43
Polypeptides1,966
Protein Complexes24
Enzymes438
Transporters208
Compounds681
Transcription Units1,305
tRNAs46
Protein Features2,371
GO Terms9,861
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces sp. ICM54
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02344581
NCBI BioProjectPRJNA224116
NCBI-Taxonomy936549
Human Microbiome Body Sitenot-specified

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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