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 12-July-2021 from the annotated genome of Actinomadura alba HBUM206468, 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 25.0) [Karp16, Karp11] using MetaCyc version 25.0 [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_JABVEC01000000159357887587,695RefSeq:NZ_JABVEC010000001
NZ_JABVEC01000000252250859578,446RefSeq:NZ_JABVEC010000002
NZ_JABVEC010000003339323511382,273RefSeq:NZ_JABVEC010000003
NZ_JABVEC01000000429529203318,900RefSeq:NZ_JABVEC010000004
NZ_JABVEC01000000524624132279,295RefSeq:NZ_JABVEC010000005
NZ_JABVEC01000000625625123265,104RefSeq:NZ_JABVEC010000006
NZ_JABVEC01000000725725151259,379RefSeq:NZ_JABVEC010000007
NZ_JABVEC01000000822421923251,402RefSeq:NZ_JABVEC010000008
NZ_JABVEC010000009233223010250,941RefSeq:NZ_JABVEC010000009
NZ_JABVEC01000001023522735244,599RefSeq:NZ_JABVEC010000010
NZ_JABVEC01000001122321823238,447RefSeq:NZ_JABVEC010000011
NZ_JABVEC010000012208191512222,389RefSeq:NZ_JABVEC010000012
NZ_JABVEC01000001319318616214,848RefSeq:NZ_JABVEC010000013
NZ_JABVEC01000001419719304210,867RefSeq:NZ_JABVEC010000014
NZ_JABVEC01000001515615114197,840RefSeq:NZ_JABVEC010000015
NZ_JABVEC01000001618217426194,379RefSeq:NZ_JABVEC010000016
NZ_JABVEC01000001716316003190,489RefSeq:NZ_JABVEC010000017
NZ_JABVEC01000001816716412188,896RefSeq:NZ_JABVEC010000018
NZ_JABVEC01000001916415833169,766RefSeq:NZ_JABVEC010000019
NZ_JABVEC01000002013313003163,080RefSeq:NZ_JABVEC010000020
NZ_JABVEC01000002112611934151,059RefSeq:NZ_JABVEC010000021
NZ_JABVEC01000002213813701134,220RefSeq:NZ_JABVEC010000022
NZ_JABVEC01000002313413112125,545RefSeq:NZ_JABVEC010000023
NZ_JABVEC01000002410810611117,122RefSeq:NZ_JABVEC010000024
NZ_JABVEC010000025999603107,020RefSeq:NZ_JABVEC010000025
NZ_JABVEC010000026928624101,074RefSeq:NZ_JABVEC010000026
NZ_JABVEC01000002787822392,641RefSeq:NZ_JABVEC010000027
NZ_JABVEC01000002887850290,880RefSeq:NZ_JABVEC010000028
NZ_JABVEC01000002979753188,105RefSeq:NZ_JABVEC010000029
NZ_JABVEC01000003078770184,625RefSeq:NZ_JABVEC010000030
NZ_JABVEC01000003174740083,517RefSeq:NZ_JABVEC010000031
NZ_JABVEC01000003275750081,520RefSeq:NZ_JABVEC010000032
NZ_JABVEC01000003372635475,693RefSeq:NZ_JABVEC010000033
NZ_JABVEC01000003466660075,535RefSeq:NZ_JABVEC010000034
NZ_JABVEC01000003573672474,321RefSeq:NZ_JABVEC010000035
NZ_JABVEC01000003665610474,099RefSeq:NZ_JABVEC010000036
NZ_JABVEC01000003767660172,603RefSeq:NZ_JABVEC010000037
NZ_JABVEC01000003869670271,124RefSeq:NZ_JABVEC010000038
NZ_JABVEC01000003971690270,676RefSeq:NZ_JABVEC010000039
NZ_JABVEC01000004060580266,987RefSeq:NZ_JABVEC010000040
NZ_JABVEC01000004166610566,339RefSeq:NZ_JABVEC010000041
NZ_JABVEC01000004255540164,790RefSeq:NZ_JABVEC010000042
NZ_JABVEC01000004355550061,485RefSeq:NZ_JABVEC010000043
NZ_JABVEC01000004456560058,123RefSeq:NZ_JABVEC010000044
NZ_JABVEC01000004543400352,541RefSeq:NZ_JABVEC010000045
NZ_JABVEC01000004638380052,316RefSeq:NZ_JABVEC010000046
NZ_JABVEC01000004752490350,374RefSeq:NZ_JABVEC010000047
NZ_JABVEC01000004844430150,362RefSeq:NZ_JABVEC010000048
NZ_JABVEC01000004945420346,203RefSeq:NZ_JABVEC010000049
NZ_JABVEC01000005045431143,073RefSeq:NZ_JABVEC010000050
NZ_JABVEC01000005141410040,747RefSeq:NZ_JABVEC010000051
NZ_JABVEC01000005247460140,481RefSeq:NZ_JABVEC010000052
NZ_JABVEC01000005325240135,950RefSeq:NZ_JABVEC010000053
NZ_JABVEC01000005433320133,060RefSeq:NZ_JABVEC010000054
NZ_JABVEC01000005540370332,743RefSeq:NZ_JABVEC010000055
NZ_JABVEC01000005629290032,004RefSeq:NZ_JABVEC010000056
NZ_JABVEC01000005732320028,972RefSeq:NZ_JABVEC010000057
NZ_JABVEC01000005823230028,428RefSeq:NZ_JABVEC010000058
NZ_JABVEC01000005926213225,679RefSeq:NZ_JABVEC010000059
NZ_JABVEC01000006019140523,215RefSeq:NZ_JABVEC010000060
NZ_JABVEC01000006120190121,194RefSeq:NZ_JABVEC010000061
NZ_JABVEC01000006224240020,871RefSeq:NZ_JABVEC010000062
NZ_JABVEC01000006322210120,374RefSeq:NZ_JABVEC010000063
NZ_JABVEC01000006419190020,094RefSeq:NZ_JABVEC010000064
NZ_JABVEC01000006612110116,255RefSeq:NZ_JABVEC010000066
NZ_JABVEC01000006818180014,160RefSeq:NZ_JABVEC010000068
NZ_JABVEC01000007112110113,050RefSeq:NZ_JABVEC010000071
NZ_JABVEC010000073129219,578RefSeq:NZ_JABVEC010000073
32 Undisplayed Contigs/Replicons7472312132,842
Total:7,7467,482761888,382,704
Ortholog data available?No
Database Contents
Genes7,745
Pathways258
Enzymatic Reactions1,323
Transport Reactions63
Polypeptides7,518
Protein Complexes53
Enzymes979
Transporters527
Compounds1,006
Transcription Units5,750
tRNAs70
Protein Features8,398
Database Version29.0
Sequence SourceGCF_014323705.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Streptosporangiales
Thermomonosporaceae
Actinomadura
Actinomadura alba
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN14775380
NCBI BioProjectPRJNA224116
NCBI-Taxonomy406431
Geographic LocationChina
Collection Date2019-11
Annotation ProviderNCBI RefSeq
Annotation Date2020-08-29
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
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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