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 Actinoplanes ianthinogenes JCM 3249, 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_BMQZ0100000186384599944,771RefSeq:NZ_BMQZ01000001
NZ_BMQZ010000028568271613902,799RefSeq:NZ_BMQZ01000002
NZ_BMQZ01000003923903020893,791RefSeq:NZ_BMQZ01000003
NZ_BMQZ0100000461960919700,341RefSeq:NZ_BMQZ01000004
NZ_BMQZ0100000560059109663,839RefSeq:NZ_BMQZ01000005
NZ_BMQZ01000006517498145574,523RefSeq:NZ_BMQZ01000006
NZ_BMQZ01000007478450226498,882RefSeq:NZ_BMQZ01000007
NZ_BMQZ0100000834634024420,019RefSeq:NZ_BMQZ01000008
NZ_BMQZ0100000936235408368,639RefSeq:NZ_BMQZ01000009
NZ_BMQZ0100001031330904366,260RefSeq:NZ_BMQZ01000010
NZ_BMQZ0100001125324814302,468RefSeq:NZ_BMQZ01000011
NZ_BMQZ0100001223322706251,412RefSeq:NZ_BMQZ01000012
NZ_BMQZ0100001320619466244,761RefSeq:NZ_BMQZ01000013
NZ_BMQZ0100001420619916223,253RefSeq:NZ_BMQZ01000014
NZ_BMQZ0100001518418022221,730RefSeq:NZ_BMQZ01000015
NZ_BMQZ0100001620720205217,943RefSeq:NZ_BMQZ01000016
NZ_BMQZ0100001716616132193,286RefSeq:NZ_BMQZ01000017
NZ_BMQZ0100001815014703183,604RefSeq:NZ_BMQZ01000018
NZ_BMQZ0100001918117803179,828RefSeq:NZ_BMQZ01000019
NZ_BMQZ0100002017216714178,037RefSeq:NZ_BMQZ01000020
NZ_BMQZ0100002114213912165,786RefSeq:NZ_BMQZ01000021
NZ_BMQZ0100002213713601155,787RefSeq:NZ_BMQZ01000022
NZ_BMQZ0100002313413301154,300RefSeq:NZ_BMQZ01000023
NZ_BMQZ0100002414814323154,269RefSeq:NZ_BMQZ01000024
NZ_BMQZ0100002515615411133,336RefSeq:NZ_BMQZ01000025
NZ_BMQZ0100002611711502126,705RefSeq:NZ_BMQZ01000026
NZ_BMQZ01000027706415119,756RefSeq:NZ_BMQZ01000027
NZ_BMQZ010000281019722114,146RefSeq:NZ_BMQZ01000028
NZ_BMQZ0100002977760180,431RefSeq:NZ_BMQZ01000029
NZ_BMQZ0100003063620175,916RefSeq:NZ_BMQZ01000030
NZ_BMQZ0100003162611063,231RefSeq:NZ_BMQZ01000031
NZ_BMQZ0100003248440453,350RefSeq:NZ_BMQZ01000032
NZ_BMQZ0100003346440241,813RefSeq:NZ_BMQZ01000033
NZ_BMQZ0100003423230031,902RefSeq:NZ_BMQZ01000034
NZ_BMQZ0100003532270529,508RefSeq:NZ_BMQZ01000035
NZ_BMQZ0100003623220124,048RefSeq:NZ_BMQZ01000036
69 Undisplayed Contigs/Replicons1612111657,936
Total:9,2538,9819717510,112,406
Ortholog data available?No
Database Contents
Genes9,244
Pathways276
Enzymatic Reactions1,409
Transport Reactions59
Polypeptides9,023
Protein Complexes56
Enzymes1,154
Transporters590
Compounds1,096
Transcription Units6,334
tRNAs82
Protein Features10,136
Database Version29.0
Sequence SourceGCF_014648375.1
Synonyms Actinoplanes sp. DSM 43864
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micromonosporales
Micromonosporaceae
Actinoplanes
Actinoplanes ianthinogenes
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00245339
NCBI BioProjectPRJNA224116
NCBI-Taxonomy122358
Annotation ProviderNCBI RefSeq
Annotation Date2020-11-23
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.13
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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