Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Actinoalloteichus cyanogriseus DSM 43889, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_AUBJ01000001697676147792,029RefSeq:NZ_AUBJ01000001
NZ_KE38685464763395709,341RefSeq:NZ_KE386854
NZ_KE38685547846729562,200RefSeq:NZ_KE386855
NZ_AUBJ01000006444424128503,346RefSeq:NZ_AUBJ01000006
NZ_AUBJ0100000733532528490,193RefSeq:NZ_AUBJ01000007
NZ_KE38685629028712419,495RefSeq:NZ_KE386856
NZ_AUBJ0100001035033659375,129RefSeq:NZ_AUBJ01000010
NZ_KE38685727426707361,430RefSeq:NZ_KE386857
NZ_AUBJ0100001326625844314,603RefSeq:NZ_AUBJ01000013
NZ_AUBJ0100001422922603277,602RefSeq:NZ_AUBJ01000014
NZ_KE38685815014604220,970RefSeq:NZ_KE386858
NZ_AUBJ0100001718217813215,146RefSeq:NZ_AUBJ01000017
NZ_AUBJ0100001817516834200,772RefSeq:NZ_AUBJ01000018
NZ_KE386859908901106,792RefSeq:NZ_KE386859
NZ_AUBJ0100002145440167,466RefSeq:NZ_AUBJ01000021
NZ_AUBJ0100002256531266,590RefSeq:NZ_AUBJ01000022
NZ_KE38686023210230,761RefSeq:NZ_KE386860
NZ_AUBJ0100002819180125,961RefSeq:NZ_AUBJ01000028
NZ_AUBJ0100002924230125,630RefSeq:NZ_AUBJ01000029
NZ_AUBJ0100003014140021,770RefSeq:NZ_AUBJ01000030
32 Undisplayed Contigs/Replicons2927410181,737
Total:4,8294,68058915,968,963
Ortholog data available?Yes
Database Contents
Genes4,827
Pathways247
Enzymatic Reactions1,285
Transport Reactions42
Polypeptides4,725
Protein Complexes3
Enzymes845
Transporters466
Compounds990
Transcription Units3,710
tRNAs48
Protein Features5,776
GO Terms312
Database Version29.0
Sequence SourceGCF_000429185.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Actinoalloteichus
Actinoalloteichus cyanogriseus
Actinoalloteichus cyanogriseus DSM 43889
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02441196
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120930
EnvironmentSoil
Geographic LocationChina
Relationship to Oxygenaerobe
Temperature Rangemesophile
Annotation ProviderNCBI RefSeq
Annotation Date2021-05-4
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.1
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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