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 13-Mar-2021 from the annotated genome of Actinoalloteichus cyanogriseus NRRL B-2194, 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 24.5 [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_JODV010000017026741315802,983RefSeq:NZ_JODV01000001
NZ_JODV01000002406394210468,816RefSeq:NZ_JODV01000002
NZ_JODV0100000738437284409,112RefSeq:NZ_JODV01000007
NZ_JODV0100000830730205369,272RefSeq:NZ_JODV01000008
NZ_JODV0100000334033055365,193RefSeq:NZ_JODV01000003
NZ_JODV01000005311296105337,967RefSeq:NZ_JODV01000005
NZ_JODV0100000627926847320,749RefSeq:NZ_JODV01000006
NZ_JODV0100000420719719285,990RefSeq:NZ_JODV01000004
NZ_JODV0100000922221705278,568RefSeq:NZ_JODV01000009
NZ_JODV0100001319418608220,671RefSeq:NZ_JODV01000013
NZ_JODV0100001014414004204,179RefSeq:NZ_JODV01000010
NZ_JODV0100001416916702200,099RefSeq:NZ_JODV01000014
NZ_JODV0100001116615925191,811RefSeq:NZ_JODV01000011
NZ_JODV01000012747103137,533RefSeq:NZ_JODV01000012
NZ_JODV01000015605712107,005RefSeq:NZ_JODV01000015
NZ_JODV01000016898522106,524RefSeq:NZ_JODV01000016
NZ_JODV01000017706802102,855RefSeq:NZ_JODV01000017
NZ_JODV0100002258550393,867RefSeq:NZ_JODV01000022
NZ_JODV0100001874701392,487RefSeq:NZ_JODV01000018
NZ_JODV0100001978731485,376RefSeq:NZ_JODV01000019
NZ_JODV0100002072671482,568RefSeq:NZ_JODV01000020
NZ_JODV0100002169680176,851RefSeq:NZ_JODV01000021
NZ_JODV0100002457540370,216RefSeq:NZ_JODV01000024
NZ_JODV0100002348460267,768RefSeq:NZ_JODV01000023
NZ_JODV0100002856520465,188RefSeq:NZ_JODV01000028
NZ_JODV0100002524240059,393RefSeq:NZ_JODV01000025
NZ_JODV0100002641370439,587RefSeq:NZ_JODV01000026
NZ_JODV0100002729290035,364RefSeq:NZ_JODV01000027
NZ_JODV0100003020180225,386RefSeq:NZ_JODV01000030
NZ_JODV0100003118160223,264RefSeq:NZ_JODV01000031
NZ_JODV0100003314140018,424RefSeq:NZ_JODV01000033
NZ_JODV0100003512110115,105RefSeq:NZ_JODV01000035
121 Undisplayed Contigs/Replicons5149458266,198
Total:4,9054,666551846,026,369
Ortholog data available?Yes
Database Contents
Genes4,903
Pathways251
Enzymatic Reactions1,261
Transport Reactions60
Polypeptides4,756
Protein Complexes41
Enzymes806
Transporters441
Compounds971
Transcription Units3,832
tRNAs47
Protein Features5,632
GO Terms1
Database Version29.0
Sequence SourceGCF_000718005.1
Synonyms Actinomyces caeruleus
Streptomyces caeruleus
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Actinoalloteichus
Actinoalloteichus cyanogriseus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02645219
NCBI BioProjectPRJNA224116
NCBI-Taxonomy65497
Environmentrice straw
Collection Date2010
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-8
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

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