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. ICM58 ICM58, 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_ALIY0100004882811093,975RefSeq:NZ_ALIY01000048
NZ_ALIY0100001644440042,535RefSeq:NZ_ALIY01000016
NZ_ALIY0100006133330040,903RefSeq:NZ_ALIY01000061
NZ_ALIY0100001439362140,605RefSeq:NZ_ALIY01000014
NZ_ALIY0100021829290039,778RefSeq:NZ_ALIY01000218
NZ_ALIY0100018933321039,705RefSeq:NZ_ALIY01000189
NZ_ALIY0100005630300039,282RefSeq:NZ_ALIY01000056
NZ_ALIY0100014535340137,460RefSeq:NZ_ALIY01000145
NZ_ALIY0100001536341136,531RefSeq:NZ_ALIY01000015
NZ_ALIY0100003435323035,241RefSeq:NZ_ALIY01000034
NZ_ALIY0100005431301035,087RefSeq:NZ_ALIY01000054
NZ_ALIY0100018017170034,622RefSeq:NZ_ALIY01000180
NZ_ALIY0100017121210034,441RefSeq:NZ_ALIY01000171
NZ_ALIY0100011131255132,092RefSeq:NZ_ALIY01000111
NZ_ALIY0100009426260030,018RefSeq:NZ_ALIY01000094
NZ_ALIY0100008227270029,430RefSeq:NZ_ALIY01000082
NZ_ALIY0100009724221129,099RefSeq:NZ_ALIY01000097
NZ_ALIY0100015423212028,719RefSeq:NZ_ALIY01000154
NZ_ALIY0100012318180027,546RefSeq:NZ_ALIY01000123
NZ_ALIY0100005723211126,959RefSeq:NZ_ALIY01000057
NZ_ALIY0100013529254026,349RefSeq:NZ_ALIY01000135
NZ_ALIY0100011713120123,093RefSeq:NZ_ALIY01000117
NZ_ALIY0100012720200022,250RefSeq:NZ_ALIY01000127
NZ_ALIY0100007113103022,217RefSeq:NZ_ALIY01000071
NZ_ALIY0100009519190021,465RefSeq:NZ_ALIY01000095
NZ_ALIY0100022115150021,112RefSeq:NZ_ALIY01000221
NZ_ALIY0100021517170020,375RefSeq:NZ_ALIY01000215
NZ_ALIY0100021319190020,302RefSeq:NZ_ALIY01000213
NZ_ALIY0100015619181020,195RefSeq:NZ_ALIY01000156
NZ_ALIY0100008920200020,070RefSeq:NZ_ALIY01000089
NZ_ALIY0100001914140019,649RefSeq:NZ_ALIY01000019
NZ_ALIY0100000819180118,752RefSeq:NZ_ALIY01000008
NZ_ALIY0100014416160018,645RefSeq:NZ_ALIY01000144
NZ_ALIY0100007016160018,204RefSeq:NZ_ALIY01000070
NZ_ALIY0100008816160018,165RefSeq:NZ_ALIY01000088
NZ_ALIY0100000111110018,142RefSeq:NZ_ALIY01000001
NZ_ALIY0100017828280018,077RefSeq:NZ_ALIY01000178
NZ_ALIY0100002915140116,460RefSeq:NZ_ALIY01000029
NZ_ALIY0100002411110016,197RefSeq:NZ_ALIY01000024
NZ_ALIY0100019316150116,037RefSeq:NZ_ALIY01000193
NZ_ALIY0100012115140116,010RefSeq:NZ_ALIY01000121
NZ_ALIY0100018214140015,896RefSeq:NZ_ALIY01000182
NZ_ALIY0100010914140015,743RefSeq:NZ_ALIY01000109
NZ_ALIY0100007417150215,122RefSeq:NZ_ALIY01000074
NZ_ALIY0100020315122115,019RefSeq:NZ_ALIY01000203
NZ_ALIY0100022913130014,840RefSeq:NZ_ALIY01000229
NZ_ALIY0100007312120014,811RefSeq:NZ_ALIY01000073
NZ_ALIY0100023912101114,403RefSeq:NZ_ALIY01000239
NZ_ALIY0100020111110014,395RefSeq:NZ_ALIY01000201
NZ_ALIY0100006711100114,359RefSeq:NZ_ALIY01000067
NZ_ALIY0100017611110014,315RefSeq:NZ_ALIY01000176
NZ_ALIY0100012413121014,271RefSeq:NZ_ALIY01000124
NZ_ALIY0100011012110114,207RefSeq:NZ_ALIY01000110
NZ_ALIY0100012513121013,886RefSeq:NZ_ALIY01000125
NZ_ALIY0100021113102112,175RefSeq:NZ_ALIY01000211
NZ_ALIY0100006012120010,732RefSeq:NZ_ALIY01000060
NZ_ALIY010001551210029,796RefSeq:NZ_ALIY01000155
NZ_ALIY010001951312019,195RefSeq:NZ_ALIY01000195
NZ_ALIY010001811111009,113RefSeq:NZ_ALIY01000181
180 Undisplayed Contigs/Replicons6436222364982,423
Total:1,9361,79556852,390,495
Ortholog data available?No
Database Contents
Genes1,934
Pathways166
Enzymatic Reactions816
Transport Reactions34
Polypeptides1,987
Protein Complexes64
Enzymes463
Transporters152
Compounds588
Transcription Units1,395
tRNAs45
Protein Features2,272
GO Terms144
Database Version29.0
Sequence SourceGCF_000283035.1
Synonyms Atopobium sp. ICM58
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. ICM58
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00828781
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1105030
Environmentbiological product [ENVO:02000043]
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2022-02-12
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.0
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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