Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp16, Karp11] component of Pathway Tools software version 23.0 and MetaCyc [Caspi18] version 23.0 on 08-Mar-2019 13:48:15.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_LOJP010000015,4645,117532945,993,166RefSeq:NZ_LOJP01000001
NZ_LOJP010000021,1961,13812461,245,021RefSeq:NZ_LOJP01000002
NZ_LOJP0100001414814125169,466RefSeq:NZ_LOJP01000014
NZ_LOJP0100000979740598,529RefSeq:NZ_LOJP01000009
NZ_LOJP0100001150460474,390RefSeq:NZ_LOJP01000011
NZ_LOJP0100000336350142,037RefSeq:NZ_LOJP01000003
NZ_LOJP0100000724240028,791RefSeq:NZ_LOJP01000007
NZ_LOJP0100002430280227,617RefSeq:NZ_LOJP01000024
NZ_LOJP0100001828270122,987RefSeq:NZ_LOJP01000018
NZ_LOJP010000101270510,576RefSeq:NZ_LOJP01000010
14 Undisplayed Contigs/Replicons292811339,704
Total:7,1096,665683767,752,284
Ortholog data available?Yes
Database Contents
Genes7,109
Pathways251
Enzymatic Reactions1,634
Transport Reactions60
Polypeptides6,730
Protein Complexes59
Enzymes1,108
Transporters525
Compounds1,325
Transcription Units4,819
tRNAs59
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micromonosporales
Micromonosporaceae
Actinoplanes
Actinoplanes sp. TFC3
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03981066
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1710355
Environmentsterile plastic container
Geographic LocationMexico
Latitude/Longitude18.8151 N 99.106 W
Collection Date2013-08-19
HostActinoplanes sp.
Annotation ProviderNCBI
Annotation Date2017-04-11
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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