Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 25-Oct-2020 from the annotated genome of Actinomyces polynesiensis MS2, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_CCXH0100009464562678,271RefSeq:NZ_CCXH01000094
NZ_CCXH0100011172633671,772RefSeq:NZ_CCXH01000111
NZ_CCXH0100009030290143,105RefSeq:NZ_CCXH01000090
NZ_CCXH0100009130270339,140RefSeq:NZ_CCXH01000091
NZ_CCXH0100029834331037,982RefSeq:NZ_CCXH01000298
NZ_CCXH0100000220180236,551RefSeq:NZ_CCXH01000002
NZ_CCXH0100002734310336,095RefSeq:NZ_CCXH01000027
NZ_CCXH0100007824240034,387RefSeq:NZ_CCXH01000078
NZ_CCXH0100030241350632,881RefSeq:NZ_CCXH01000302
NZ_CCXH0100001928212532,146RefSeq:NZ_CCXH01000019
NZ_CCXH0100024234320231,052RefSeq:NZ_CCXH01000242
NZ_CCXH0100020629271130,772RefSeq:NZ_CCXH01000206
NZ_CCXH0100024628261129,075RefSeq:NZ_CCXH01000246
NZ_CCXH0100010525240126,070RefSeq:NZ_CCXH01000105
NZ_CCXH0100007322191225,705RefSeq:NZ_CCXH01000073
NZ_CCXH0100022625220325,488RefSeq:NZ_CCXH01000226
NZ_CCXH0100023118170123,430RefSeq:NZ_CCXH01000231
NZ_CCXH0100021019162122,837RefSeq:NZ_CCXH01000210
NZ_CCXH0100020919180122,743RefSeq:NZ_CCXH01000209
NZ_CCXH0100029015140121,841RefSeq:NZ_CCXH01000290
NZ_CCXH0100018326213221,520RefSeq:NZ_CCXH01000183
NZ_CCXH0100026514140021,360RefSeq:NZ_CCXH01000265
NZ_CCXH0100011919171121,221RefSeq:NZ_CCXH01000119
NZ_CCXH0100029119170221,171RefSeq:NZ_CCXH01000291
NZ_CCXH0100025521200120,566RefSeq:NZ_CCXH01000255
NZ_CCXH0100010915130220,403RefSeq:NZ_CCXH01000109
NZ_CCXH0100005316150120,198RefSeq:NZ_CCXH01000053
NZ_CCXH0100004321180320,162RefSeq:NZ_CCXH01000043
NZ_CCXH0100012717161020,046RefSeq:NZ_CCXH01000127
NZ_CCXH0100008615140119,001RefSeq:NZ_CCXH01000086
NZ_CCXH0100006814140018,725RefSeq:NZ_CCXH01000068
NZ_CCXH0100019518133218,686RefSeq:NZ_CCXH01000195
NZ_CCXH0100008311110018,069RefSeq:NZ_CCXH01000083
NZ_CCXH0100018712100217,735RefSeq:NZ_CCXH01000187
NZ_CCXH0100009615140117,606RefSeq:NZ_CCXH01000096
NZ_CCXH0100022915140117,466RefSeq:NZ_CCXH01000229
NZ_CCXH0100028317140317,402RefSeq:NZ_CCXH01000283
NZ_CCXH0100003615130216,900RefSeq:NZ_CCXH01000036
NZ_CCXH0100014115140116,738RefSeq:NZ_CCXH01000141
NZ_CCXH0100024512110116,339RefSeq:NZ_CCXH01000245
NZ_CCXH0100005116150116,315RefSeq:NZ_CCXH01000051
NZ_CCXH0100007116160016,069RefSeq:NZ_CCXH01000071
NZ_CCXH0100028912111015,794RefSeq:NZ_CCXH01000289
NZ_CCXH0100023719144115,542RefSeq:NZ_CCXH01000237
NZ_CCXH0100010712120015,518RefSeq:NZ_CCXH01000107
NZ_CCXH0100009216160015,363RefSeq:NZ_CCXH01000092
NZ_CCXH0100017716150115,246RefSeq:NZ_CCXH01000177
NZ_CCXH0100006915130215,202RefSeq:NZ_CCXH01000069
NZ_CCXH0100019114111214,920RefSeq:NZ_CCXH01000191
NZ_CCXH0100001614113014,791RefSeq:NZ_CCXH01000016
NZ_CCXH0100019411110014,677RefSeq:NZ_CCXH01000194
NZ_CCXH0100010412111014,487RefSeq:NZ_CCXH01000104
NZ_CCXH0100019813120114,255RefSeq:NZ_CCXH01000198
NZ_CCXH0100013414100413,832RefSeq:NZ_CCXH01000134
NZ_CCXH0100007216141113,453RefSeq:NZ_CCXH01000072
NZ_CCXH010002821290312,424RefSeq:NZ_CCXH01000282
NZ_CCXH0100020313130011,906RefSeq:NZ_CCXH01000203
NZ_CCXH010001841271410,295RefSeq:NZ_CCXH01000184
NZ_CCXH010001931091010,265RefSeq:NZ_CCXH01000193
NZ_CCXH010003071212008,614RefSeq:NZ_CCXH01000307
NZ_CCXH010002411616008,275RefSeq:NZ_CCXH01000241
248 Undisplayed Contigs/Replicons995976191741,508,549
Total:2,3982,079532662,878,449
Ortholog data available?Yes
Database Contents
Genes2,398
Pathways162
Enzymatic Reactions842
Transport Reactions51
Polypeptides2,266
Protein Complexes35
Enzymes475
Transporters257
Compounds670
Transcription Units1,860
tRNAs48
Protein Features2,471
Database Version29.0
Sequence SourceGCF_000820725.1
Synonyms Actinomyces sp. MS2
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces polynesiensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA2769926
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1325934
EnvironmentInvitro plant
Geographic LocationColombia
Collection Date2011-12
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-10
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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