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 Actinocatenispora sera NRRL B-24477, 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_JOEG01000001661637321699,218RefSeq:NZ_JOEG01000001
NZ_JOEG0100000338537438480,373RefSeq:NZ_JOEG01000003
NZ_JOEG0100000440939559419,632RefSeq:NZ_JOEG01000004
NZ_JOEG0100000535935009402,994RefSeq:NZ_JOEG01000005
NZ_JOEG0100001232031217375,267RefSeq:NZ_JOEG01000012
NZ_JOEG0100000937536456373,891RefSeq:NZ_JOEG01000009
NZ_JOEG0100001131230138342,707RefSeq:NZ_JOEG01000011
NZ_JOEG0100001428828035327,219RefSeq:NZ_JOEG01000014
NZ_JOEG0100000228127245294,276RefSeq:NZ_JOEG01000002
NZ_JOEG0100000823422905256,629RefSeq:NZ_JOEG01000008
NZ_JOEG0100001920620303219,621RefSeq:NZ_JOEG01000019
NZ_JOEG0100001323222363218,224RefSeq:NZ_JOEG01000013
NZ_JOEG0100000619519014209,315RefSeq:NZ_JOEG01000006
NZ_JOEG01000018188161243180,744RefSeq:NZ_JOEG01000018
NZ_JOEG0100000716315913172,993RefSeq:NZ_JOEG01000007
NZ_JOEG0100001015815314165,124RefSeq:NZ_JOEG01000010
NZ_JOEG0100002813613105139,598RefSeq:NZ_JOEG01000028
NZ_JOEG0100002711811215135,586RefSeq:NZ_JOEG01000027
NZ_JOEG0100001511911531135,287RefSeq:NZ_JOEG01000015
NZ_JOEG0100002111411400123,252RefSeq:NZ_JOEG01000021
NZ_JOEG0100001610910612121,249RefSeq:NZ_JOEG01000016
NZ_JOEG010000251009901114,277RefSeq:NZ_JOEG01000025
NZ_JOEG0100002310610024114,217RefSeq:NZ_JOEG01000023
NZ_JOEG0100001712612123113,372RefSeq:NZ_JOEG01000017
NZ_JOEG01000022898702103,446RefSeq:NZ_JOEG01000022
NZ_JOEG0100002085840192,709RefSeq:NZ_JOEG01000020
NZ_JOEG0100002478741381,345RefSeq:NZ_JOEG01000024
NZ_JOEG0100002669642371,802RefSeq:NZ_JOEG01000026
NZ_JOEG0100003468633266,505RefSeq:NZ_JOEG01000034
NZ_JOEG0100002948461154,275RefSeq:NZ_JOEG01000029
NZ_JOEG0100003353511148,399RefSeq:NZ_JOEG01000033
NZ_JOEG0100003542391246,750RefSeq:NZ_JOEG01000035
NZ_JOEG0100003040381145,659RefSeq:NZ_JOEG01000030
NZ_JOEG0100003131300140,217RefSeq:NZ_JOEG01000031
NZ_JOEG0100003236360039,545RefSeq:NZ_JOEG01000032
NZ_JOEG0100003812120011,361RefSeq:NZ_JOEG01000038
NZ_JOEG010000401211018,712RefSeq:NZ_JOEG01000040
41 Undisplayed Contigs/Replicons7168313101,446
Total:6,4416,204821556,947,236
Ortholog data available?Yes
Database Contents
Genes6,439
Pathways257
Enzymatic Reactions1,297
Transport Reactions60
Polypeptides6,219
Protein Complexes58
Enzymes874
Transporters539
Compounds998
Transcription Units4,948
tRNAs74
Protein Features7,122
Database Version29.0
Sequence SourceGCF_000720965.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micromonosporales
Micromonosporaceae
Actinocatenispora
Actinocatenispora sera
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02645231
NCBI BioProjectPRJNA224116
NCBI-Taxonomy390989
Environmentsoil
Geographic LocationJapan
Collection Date2010
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-16
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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