Database Authors
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Actinomadura macra NBRC 14102, 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_BCQT01000006859836716976,983RefSeq:NZ_BCQT01000006
NZ_BCQT0100000463262048734,083RefSeq:NZ_BCQT01000004
NZ_BCQT0100001068167236710,297RefSeq:NZ_BCQT01000010
NZ_BCQT01000009566548612629,219RefSeq:NZ_BCQT01000009
NZ_BCQT0100001150549564624,385RefSeq:NZ_BCQT01000011
NZ_BCQT01000002512495116519,865RefSeq:NZ_BCQT01000002
NZ_BCQT0100001833733025447,182RefSeq:NZ_BCQT01000018
NZ_BCQT0100001940639439426,140RefSeq:NZ_BCQT01000019
NZ_BCQT0100001737937711407,863RefSeq:NZ_BCQT01000017
NZ_BCQT0100001526926621299,804RefSeq:NZ_BCQT01000015
NZ_BCQT0100000124324201284,002RefSeq:NZ_BCQT01000001
NZ_BCQT0100000524324003265,804RefSeq:NZ_BCQT01000005
NZ_BCQT0100000325224408262,168RefSeq:NZ_BCQT01000003
NZ_BCQT0100002023522834241,114RefSeq:NZ_BCQT01000020
NZ_BCQT0100002321020622232,526RefSeq:NZ_BCQT01000023
NZ_BCQT0100001420920261225,485RefSeq:NZ_BCQT01000014
NZ_BCQT0100002617917270195,276RefSeq:NZ_BCQT01000026
NZ_BCQT0100001616816044185,883RefSeq:NZ_BCQT01000016
NZ_BCQT0100000711010514144,747RefSeq:NZ_BCQT01000007
NZ_BCQT0100002713413004144,581RefSeq:NZ_BCQT01000027
NZ_BCQT0100002813012910134,602RefSeq:NZ_BCQT01000028
NZ_BCQT01000025908622131,283RefSeq:NZ_BCQT01000025
NZ_BCQT0100001392890393,496RefSeq:NZ_BCQT01000013
NZ_BCQT0100002465650077,196RefSeq:NZ_BCQT01000024
NZ_BCQT0100003167660172,968RefSeq:NZ_BCQT01000031
NZ_BCQT0100002157560159,354RefSeq:NZ_BCQT01000021
NZ_BCQT0100003257540358,576RefSeq:NZ_BCQT01000032
NZ_BCQT0100003044421158,066RefSeq:NZ_BCQT01000030
NZ_BCQT0100003353510254,676RefSeq:NZ_BCQT01000033
NZ_BCQT0100003447460149,554RefSeq:NZ_BCQT01000034
NZ_BCQT0100002256504249,213RefSeq:NZ_BCQT01000022
NZ_BCQT0100002945414046,276RefSeq:NZ_BCQT01000029
NZ_BCQT0100003542420043,955RefSeq:NZ_BCQT01000035
NZ_BCQT0100003617170023,172RefSeq:NZ_BCQT01000036
NZ_BCQT0100003727270022,436RefSeq:NZ_BCQT01000037
NZ_BCQT0100003820190119,646RefSeq:NZ_BCQT01000038
NZ_BCQT0100003931300118,728RefSeq:NZ_BCQT01000039
NZ_BCQT0100004020160416,961RefSeq:NZ_BCQT01000040
NZ_BCQT010000431414008,728RefSeq:NZ_BCQT01000043
17 Undisplayed Contigs/Replicons5421050,058
Total:8,1197,906821319,046,351
Ortholog data available?Yes
Database Contents
Genes8,115
Pathways280
Enzymatic Reactions1,498
Transport Reactions48
Polypeptides7,949
Protein Complexes3
Enzymes1,155
Transporters699
Compounds1,166
Transcription Units5,692
tRNAs72
Protein Features9,245
GO Terms484
Database Version29.0
Sequence SourceGCF_001552215.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Streptosporangiales
Thermomonosporaceae
Actinomadura
Actinomadura macra
Actinomadura macra NBRC 14102
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00046507
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1220564
Annotation ProviderNCBI RefSeq
Annotation Date2021-07-10
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative


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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