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 sp. ICM47 ICM47, 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_ALCA0100010068680072,260RefSeq:NZ_ALCA01000100
NZ_ALCA0100011157525069,142RefSeq:NZ_ALCA01000111
NZ_ALCA0100012562611068,672RefSeq:NZ_ALCA01000125
NZ_ALCA0100011064594167,072RefSeq:NZ_ALCA01000110
NZ_ALCA0100012748452152,144RefSeq:NZ_ALCA01000127
NZ_ALCA0100008539380148,242RefSeq:NZ_ALCA01000085
NZ_ALCA0100010543420147,955RefSeq:NZ_ALCA01000105
NZ_ALCA0100006438380047,266RefSeq:NZ_ALCA01000064
NZ_ALCA0100009840382045,292RefSeq:NZ_ALCA01000098
NZ_ALCA0100002337370041,895RefSeq:NZ_ALCA01000023
NZ_ALCA0100004734340040,172RefSeq:NZ_ALCA01000047
NZ_ALCA0100003437340340,111RefSeq:NZ_ALCA01000034
NZ_ALCA0100003727270037,441RefSeq:NZ_ALCA01000037
NZ_ALCA0100000327270037,345RefSeq:NZ_ALCA01000003
NZ_ALCA0100008629271137,034RefSeq:NZ_ALCA01000086
NZ_ALCA0100002436323136,677RefSeq:NZ_ALCA01000024
NZ_ALCA0100007834330135,622RefSeq:NZ_ALCA01000078
NZ_ALCA0100013636360035,597RefSeq:NZ_ALCA01000136
NZ_ALCA0100010622190334,167RefSeq:NZ_ALCA01000106
NZ_ALCA0100002633330033,852RefSeq:NZ_ALCA01000026
NZ_ALCA0100003326250132,341RefSeq:NZ_ALCA01000033
NZ_ALCA0100001427252032,043RefSeq:NZ_ALCA01000014
NZ_ALCA0100008434290530,992RefSeq:NZ_ALCA01000084
NZ_ALCA0100007727270030,941RefSeq:NZ_ALCA01000077
NZ_ALCA0100008822200230,513RefSeq:NZ_ALCA01000088
NZ_ALCA0100009222202029,640RefSeq:NZ_ALCA01000092
NZ_ALCA0100006516160028,896RefSeq:NZ_ALCA01000065
NZ_ALCA0100002713130028,697RefSeq:NZ_ALCA01000027
NZ_ALCA0100004125232028,084RefSeq:NZ_ALCA01000041
NZ_ALCA0100006620200025,020RefSeq:NZ_ALCA01000066
NZ_ALCA0100010122220024,899RefSeq:NZ_ALCA01000101
NZ_ALCA0100000616140224,767RefSeq:NZ_ALCA01000006
NZ_ALCA0100002919172024,610RefSeq:NZ_ALCA01000029
NZ_ALCA0100002215140124,544RefSeq:NZ_ALCA01000022
NZ_ALCA0100002819171123,847RefSeq:NZ_ALCA01000028
NZ_ALCA0100008014130123,701RefSeq:NZ_ALCA01000080
NZ_ALCA0100007020190123,530RefSeq:NZ_ALCA01000070
NZ_ALCA0100005218180023,496RefSeq:NZ_ALCA01000052
NZ_ALCA0100001822191223,183RefSeq:NZ_ALCA01000018
NZ_ALCA0100013318161122,568RefSeq:NZ_ALCA01000133
NZ_ALCA0100012021201021,982RefSeq:NZ_ALCA01000120
NZ_ALCA0100003920191021,883RefSeq:NZ_ALCA01000039
NZ_ALCA0100014022193021,551RefSeq:NZ_ALCA01000140
NZ_ALCA0100009314140021,234RefSeq:NZ_ALCA01000093
NZ_ALCA0100009417160121,200RefSeq:NZ_ALCA01000094
NZ_ALCA0100012422220021,062RefSeq:NZ_ALCA01000124
NZ_ALCA0100011917160120,798RefSeq:NZ_ALCA01000119
NZ_ALCA0100002513121020,642RefSeq:NZ_ALCA01000025
NZ_ALCA0100005620191019,786RefSeq:NZ_ALCA01000056
NZ_ALCA0100008123203019,769RefSeq:NZ_ALCA01000081
NZ_ALCA0100007520190119,688RefSeq:NZ_ALCA01000075
NZ_ALCA0100010819171119,641RefSeq:NZ_ALCA01000108
NZ_ALCA0100001713121019,586RefSeq:NZ_ALCA01000017
NZ_ALCA0100013514121119,130RefSeq:NZ_ALCA01000135
NZ_ALCA0100013717161018,804RefSeq:NZ_ALCA01000137
NZ_ALCA0100000820200018,689RefSeq:NZ_ALCA01000008
NZ_ALCA010001181190217,739RefSeq:NZ_ALCA01000118
NZ_ALCA0100008312120017,215RefSeq:NZ_ALCA01000083
NZ_ALCA0100007412120016,909RefSeq:NZ_ALCA01000074
NZ_ALCA0100010411110015,746RefSeq:NZ_ALCA01000104
NZ_ALCA0100003612110115,501RefSeq:NZ_ALCA01000036
NZ_ALCA0100000915130215,003RefSeq:NZ_ALCA01000009
NZ_ALCA0100003513130014,500RefSeq:NZ_ALCA01000035
NZ_ALCA0100012812120013,857RefSeq:NZ_ALCA01000128
NZ_ALCA010000551064013,715RefSeq:NZ_ALCA01000055
NZ_ALCA0100001911110013,705RefSeq:NZ_ALCA01000019
NZ_ALCA0100008916160013,339RefSeq:NZ_ALCA01000089
NZ_ALCA0100009612111012,635RefSeq:NZ_ALCA01000096
NZ_ALCA0100009012111011,865RefSeq:NZ_ALCA01000090
NZ_ALCA0100001212110111,575RefSeq:NZ_ALCA01000012
NZ_ALCA0100009511110010,460RefSeq:NZ_ALCA01000095
72 Undisplayed Contigs/Replicons290286513440,626
Total:2,0041,89654542,444,105
Ortholog data available?No
Database Contents
Genes2,002
Pathways170
Enzymatic Reactions892
Transport Reactions32
Polypeptides1,978
Protein Complexes68
Enzymes444
Transporters147
Compounds612
Transcription Units1,364
tRNAs47
Protein Features2,428
GO Terms148
Database Version29.0
Sequence SourceGCF_000278725.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. ICM47
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00828776
NCBI BioProjectPRJNA224116
NCBI-Taxonomy936548
Environmentbiological product [ENVO:02000043]
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-18
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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