Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Actinomadura rifamycini DSM 43936, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_KE38430067767034722,828RefSeq:NZ_KE384300
NZ_AULB01000003549532413639,172RefSeq:NZ_AULB01000003
NZ_KE38430141340337473,144RefSeq:NZ_KE384301
NZ_AULB01000007406390511462,906RefSeq:NZ_AULB01000007
NZ_AULB0100000838337427413,724RefSeq:NZ_AULB01000008
NZ_AULB0100000935234705391,266RefSeq:NZ_AULB01000009
NZ_AULB0100001032831459340,880RefSeq:NZ_AULB01000010
NZ_AULB0100001128127119296,603RefSeq:NZ_AULB01000011
NZ_AULB0100001224023244271,747RefSeq:NZ_AULB01000012
NZ_AULB0100001324824323245,427RefSeq:NZ_AULB01000013
NZ_AULB0100001418417923204,461RefSeq:NZ_AULB01000014
NZ_AULB0100001519618907201,397RefSeq:NZ_AULB01000015
NZ_AULB0100001618718223195,041RefSeq:NZ_AULB01000016
NZ_AULB0100001717317012191,805RefSeq:NZ_AULB01000017
NZ_AULB0100001815815305171,743RefSeq:NZ_AULB01000018
NZ_AULB0100001915714926169,342RefSeq:NZ_AULB01000019
NZ_AULB0100002016015307168,411RefSeq:NZ_AULB01000020
NZ_AULB0100002115815134166,345RefSeq:NZ_AULB01000021
NZ_AULB0100002213212309160,350RefSeq:NZ_AULB01000022
NZ_AULB0100002314113803146,156RefSeq:NZ_AULB01000023
NZ_AULB0100002413712755143,492RefSeq:NZ_AULB01000024
NZ_AULB0100002513712836128,707RefSeq:NZ_AULB01000025
NZ_AULB0100002613513401127,630RefSeq:NZ_AULB01000026
NZ_AULB0100002711411301126,917RefSeq:NZ_AULB01000027
NZ_AULB010000281029543122,215RefSeq:NZ_AULB01000028
NZ_AULB0100002911010451120,841RefSeq:NZ_AULB01000029
NZ_AULB0100003011110515120,476RefSeq:NZ_AULB01000030
NZ_AULB0100003112010875114,218RefSeq:NZ_AULB01000031
NZ_AULB01000032878106104,535RefSeq:NZ_AULB01000032
NZ_AULB0100003365600591,280RefSeq:NZ_AULB01000033
NZ_AULB0100003480743387,264RefSeq:NZ_AULB01000034
NZ_AULB0100003553500384,481RefSeq:NZ_AULB01000035
NZ_AULB0100003683821082,428RefSeq:NZ_AULB01000036
NZ_AULB0100003775740178,687RefSeq:NZ_AULB01000037
NZ_AULB0100003868650376,927RefSeq:NZ_AULB01000038
NZ_AULB0100003956520463,674RefSeq:NZ_AULB01000039
NZ_AULB0100004052492158,182RefSeq:NZ_AULB01000040
NZ_AULB0100004154510357,754RefSeq:NZ_AULB01000041
NZ_AULB0100004254540053,241RefSeq:NZ_AULB01000042
NZ_AULB0100004343430043,507RefSeq:NZ_AULB01000043
NZ_AULB0100004434310342,718RefSeq:NZ_AULB01000044
NZ_AULB0100004535300537,294RefSeq:NZ_AULB01000045
NZ_AULB0100004638323336,604RefSeq:NZ_AULB01000046
NZ_AULB0100004730300031,021RefSeq:NZ_AULB01000047
NZ_AULB0100004929280129,776RefSeq:NZ_AULB01000049
NZ_AULB0100004817130429,769RefSeq:NZ_AULB01000048
NZ_AULB0100005021200129,210RefSeq:NZ_AULB01000050
NZ_AULB0100005127260125,032RefSeq:NZ_AULB01000051
NZ_AULB0100005219180122,315RefSeq:NZ_AULB01000052
NZ_AULB0100005417160117,354RefSeq:NZ_AULB01000054
NZ_AULB010000571390413,158RefSeq:NZ_AULB01000057
NZ_AULB0100005914130112,488RefSeq:NZ_AULB01000059
23 Undisplayed Contigs/Replicons3837128139,489
Total:7,6197,315742308,385,432
Ortholog data available?Yes
Database Contents
Genes7,614
Pathways284
Enzymatic Reactions1,470
Transport Reactions81
Polypeptides7,325
Protein Complexes65
Enzymes1,191
Transporters668
Compounds1,213
Transcription Units5,377
tRNAs62
Protein Features8,618
Database Version29.0
Sequence SourceGCF_000425065.1
Synonyms Actinomadura cremea subsp. rifamycini DSM 43936
Actinomadura rifamycini IFO 14183
Actinomadura rifamycini JCM 3309
Actinomadura rifamycini DSM 43936
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Streptosporangiales
Thermomonosporaceae
Actinomadura
Actinomadura rifamycini
Actinomadura rifamycini DSM 43936
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02441154
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120937
EnvironmentSoil
Relationship to Oxygenaerobe
Temperature Rangemesophile
Annotation ProviderNCBI
Annotation Date2017-04-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+
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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