Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 27-Feb-2018 from the annotated genome of Actinopolymorpha cephalotaxi CPCC 202808, 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 22.0) [Karp16, Karp11] using MetaCyc version 21.5 [Caspi18]. 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 Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_FOOI01000001569544322635,070RefSeq:NZ_FOOI01000001
NZ_FOOI01000002531508419589,841RefSeq:NZ_FOOI01000002
NZ_FOOI01000003465449610483,112RefSeq:NZ_FOOI01000003
NZ_FOOI0100000440839549443,557RefSeq:NZ_FOOI01000004
NZ_FOOI0100000537136308426,719RefSeq:NZ_FOOI01000005
NZ_FOOI01000006297279315353,209RefSeq:NZ_FOOI01000006
NZ_FOOI0100000730229723347,313RefSeq:NZ_FOOI01000007
NZ_FOOI0100000829528348325,160RefSeq:NZ_FOOI01000008
NZ_FOOI0100000930629448319,791RefSeq:NZ_FOOI01000009
NZ_FOOI0100001024724115281,814RefSeq:NZ_FOOI01000010
NZ_FOOI0100001120520302238,706RefSeq:NZ_FOOI01000011
NZ_FOOI0100001221920739234,445RefSeq:NZ_FOOI01000012
NZ_FOOI01000013217205210227,607RefSeq:NZ_FOOI01000013
NZ_FOOI0100001420319427218,428RefSeq:NZ_FOOI01000014
NZ_FOOI0100001520219516217,661RefSeq:NZ_FOOI01000015
NZ_FOOI0100001617917225189,231RefSeq:NZ_FOOI01000016
NZ_FOOI0100001714513807169,955RefSeq:NZ_FOOI01000017
NZ_FOOI0100001814113605169,775RefSeq:NZ_FOOI01000018
NZ_FOOI0100001912812242135,296RefSeq:NZ_FOOI01000019
NZ_FOOI0100002079674888,695RefSeq:NZ_FOOI01000020
NZ_FOOI0100002178760287,732RefSeq:NZ_FOOI01000021
NZ_FOOI0100002277760183,199RefSeq:NZ_FOOI01000022
NZ_FOOI0100002372700280,060RefSeq:NZ_FOOI01000023
NZ_FOOI0100002468620672,220RefSeq:NZ_FOOI01000024
NZ_FOOI0100002551491168,167RefSeq:NZ_FOOI01000025
NZ_FOOI0100002639360364,904RefSeq:NZ_FOOI01000026
NZ_FOOI0100002758551255,012RefSeq:NZ_FOOI01000027
NZ_FOOI0100002845430249,181RefSeq:NZ_FOOI01000028
NZ_FOOI0100002927250240,797RefSeq:NZ_FOOI01000029
NZ_FOOI0100003035340134,474RefSeq:NZ_FOOI01000030
NZ_FOOI0100003126220433,261RefSeq:NZ_FOOI01000031
NZ_FOOI0100003214140017,603RefSeq:NZ_FOOI01000032
NZ_FOOI010000331190215,980RefSeq:NZ_FOOI01000033
7 Undisplayed Contigs/Replicons14140524,886
Total:6,1295,877512016,822,861
Ortholog data available?Yes
Database Contents
Genes6,130
Pathways215
Enzymatic Reactions1,275
Transport Reactions62
Polypeptides5,880
Protein Complexes26
Enzymes909
Transporters546
Compounds1,056
Transcription Units4,513
tRNAs46
Protein Features6,762
GO Terms17,097
Database Version29.0
Synonyms CCM 7466
DSM 45117
JCM 17964
KCTC 19293
strain I06-2230
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Propionibacteriales
Nocardioidaceae
Actinopolymorpha
Actinopolymorpha cephalotaxi
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05421678
NCBI BioProjectPRJNA224116
NCBI-Taxonomy504797
NCBI Genome Typerepresentative

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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