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 Actinoplanes utahensis NRRL 12052, 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_JRTT01000137635611717659,685RefSeq:NZ_JRTT01000137
NZ_JRTT01000001293283010355,119RefSeq:NZ_JRTT01000001
NZ_JRTT01000002305288710330,437RefSeq:NZ_JRTT01000002
NZ_JRTT0100000323022325261,594RefSeq:NZ_JRTT01000003
NZ_JRTT0100000422622213246,841RefSeq:NZ_JRTT01000004
NZ_JRTT0100013321120308242,775RefSeq:NZ_JRTT01000133
NZ_JRTT0100000517817413221,936RefSeq:NZ_JRTT01000005
NZ_JRTT0100000621720809221,340RefSeq:NZ_JRTT01000006
NZ_JRTT0100012821420257218,291RefSeq:NZ_JRTT01000128
NZ_JRTT0100000719819107214,577RefSeq:NZ_JRTT01000007
NZ_JRTT0100000817517005213,911RefSeq:NZ_JRTT01000008
NZ_JRTT0100000918418013210,652RefSeq:NZ_JRTT01000009
NZ_JRTT0100001021620808204,213RefSeq:NZ_JRTT01000010
NZ_JRTT0100013118918504204,035RefSeq:NZ_JRTT01000131
NZ_JRTT0100013917917504201,317RefSeq:NZ_JRTT01000139
NZ_JRTT0100001118618015199,102RefSeq:NZ_JRTT01000011
NZ_JRTT01000012185174110198,760RefSeq:NZ_JRTT01000012
NZ_JRTT0100001318217237194,522RefSeq:NZ_JRTT01000013
NZ_JRTT0100001416716205182,109RefSeq:NZ_JRTT01000014
NZ_JRTT0100001512712403177,638RefSeq:NZ_JRTT01000015
NZ_JRTT0100001615715304175,081RefSeq:NZ_JRTT01000016
NZ_JRTT0100001715114326165,803RefSeq:NZ_JRTT01000017
NZ_JRTT010000181721461511164,466RefSeq:NZ_JRTT01000018
NZ_JRTT0100001915514546163,386RefSeq:NZ_JRTT01000019
NZ_JRTT01000130167154013159,012RefSeq:NZ_JRTT01000130
NZ_JRTT0100013211610907155,235RefSeq:NZ_JRTT01000132
NZ_JRTT0100002014213804151,025RefSeq:NZ_JRTT01000020
NZ_JRTT0100002112812323149,086RefSeq:NZ_JRTT01000021
NZ_JRTT0100002212511861132,397RefSeq:NZ_JRTT01000022
NZ_JRTT01000129999207131,116RefSeq:NZ_JRTT01000129
NZ_JRTT0100002310810602123,028RefSeq:NZ_JRTT01000023
NZ_JRTT01000024133122011114,665RefSeq:NZ_JRTT01000024
NZ_JRTT010000251009703111,436RefSeq:NZ_JRTT01000025
NZ_JRTT0100002611811008110,923RefSeq:NZ_JRTT01000026
NZ_JRTT010000271019236110,549RefSeq:NZ_JRTT01000027
NZ_JRTT01000028999306107,266RefSeq:NZ_JRTT01000028
NZ_JRTT01000029999306106,700RefSeq:NZ_JRTT01000029
NZ_JRTT01000141908505101,232RefSeq:NZ_JRTT01000141
NZ_JRTT01000135103993197,066RefSeq:NZ_JRTT01000135
NZ_JRTT01000030101943496,838RefSeq:NZ_JRTT01000030
NZ_JRTT0100003189830694,694RefSeq:NZ_JRTT01000031
NZ_JRTT0100003282770591,444RefSeq:NZ_JRTT01000032
NZ_JRTT0100003384762689,879RefSeq:NZ_JRTT01000033
NZ_JRTT0100003481760587,118RefSeq:NZ_JRTT01000034
NZ_JRTT0100003573670678,266RefSeq:NZ_JRTT01000035
NZ_JRTT0100013462600273,487RefSeq:NZ_JRTT01000134
NZ_JRTT0100003661560571,872RefSeq:NZ_JRTT01000036
NZ_JRTT0100003765630268,407RefSeq:NZ_JRTT01000037
NZ_JRTT0100003855540167,330RefSeq:NZ_JRTT01000038
NZ_JRTT0100003957550264,965RefSeq:NZ_JRTT01000039
NZ_JRTT0100004054520264,646RefSeq:NZ_JRTT01000040
NZ_JRTT0100004149420764,187RefSeq:NZ_JRTT01000041
NZ_JRTT0100004249490064,003RefSeq:NZ_JRTT01000042
NZ_JRTT0100014050490159,284RefSeq:NZ_JRTT01000140
NZ_JRTT0100004353530051,807RefSeq:NZ_JRTT01000043
NZ_JRTT0100004450432550,469RefSeq:NZ_JRTT01000044
NZ_JRTT0100004539340549,959RefSeq:NZ_JRTT01000045
NZ_JRTT0100004639380149,915RefSeq:NZ_JRTT01000046
NZ_JRTT0100004748450348,524RefSeq:NZ_JRTT01000047
NZ_JRTT0100004845421247,390RefSeq:NZ_JRTT01000048
NZ_JRTT0100004948430546,005RefSeq:NZ_JRTT01000049
NZ_JRTT0100013841390242,923RefSeq:NZ_JRTT01000138
NZ_JRTT0100013626260034,726RefSeq:NZ_JRTT01000136
NZ_JRTT0100005129250433,643RefSeq:NZ_JRTT01000051
NZ_JRTT0100005230290130,626RefSeq:NZ_JRTT01000052
NZ_JRTT0100005328271027,751RefSeq:NZ_JRTT01000053
NZ_JRTT0100005422210126,373RefSeq:NZ_JRTT01000054
NZ_JRTT0100005526213225,353RefSeq:NZ_JRTT01000055
NZ_JRTT0100005621200124,146RefSeq:NZ_JRTT01000056
NZ_JRTT0100005716160022,364RefSeq:NZ_JRTT01000057
NZ_JRTT0100005815150019,585RefSeq:NZ_JRTT01000058
NZ_JRTT0100005915140118,239RefSeq:NZ_JRTT01000059
NZ_JRTT0100006018171017,817RefSeq:NZ_JRTT01000060
NZ_JRTT0100006122160617,251RefSeq:NZ_JRTT01000061
NZ_JRTT0100006211100114,033RefSeq:NZ_JRTT01000062
NZ_JRTT0100006512120011,120RefSeq:NZ_JRTT01000065
65 Undisplayed Contigs/Replicons8380520155,078
Total:8,6318,192823579,489,843
Ortholog data available?Yes
Database Contents
Genes8,629
Pathways292
Enzymatic Reactions1,459
Transport Reactions63
Polypeptides8,269
Protein Complexes59
Enzymes1,105
Transporters636
Compounds1,061
Transcription Units6,083
tRNAs73
Protein Features9,211
GO Terms20,130
Database Version29.0
Sequence SourceGCF_000785985.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micromonosporales
Micromonosporaceae
Actinoplanes
Actinoplanes utahensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03078836
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1869
EnvironmentLiberty Park
Geographic LocationUSA
Latitude/Longitude40.44 N 111.52 W
Collection Date2000-01-24
Annotation ProviderNCBI RefSeq
Annotation Date2020-06-8
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.