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 Actinoplanes philippinensis DSM 43019, 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_FONV010000017086741123805,299RefSeq:NZ_FONV01000001
NZ_FONV01000002695667523789,403RefSeq:NZ_FONV01000002
NZ_FONV01000003641620021746,613RefSeq:NZ_FONV01000003
NZ_FONV01000004645634110708,589RefSeq:NZ_FONV01000004
NZ_FONV01000005555527721658,467RefSeq:NZ_FONV01000005
NZ_FONV01000006513501012557,734RefSeq:NZ_FONV01000006
NZ_FONV01000007476457217551,867RefSeq:NZ_FONV01000007
NZ_FONV01000008444418323527,412RefSeq:NZ_FONV01000008
NZ_FONV01000009509498011527,201RefSeq:NZ_FONV01000009
NZ_FONV01000010466447712497,204RefSeq:NZ_FONV01000010
NZ_FONV0100001143742377487,119RefSeq:NZ_FONV01000011
NZ_FONV01000012355337513357,307RefSeq:NZ_FONV01000012
NZ_FONV0100001329629204323,721RefSeq:NZ_FONV01000013
NZ_FONV0100001427026424287,771RefSeq:NZ_FONV01000014
NZ_FONV01000015219200811224,308RefSeq:NZ_FONV01000015
NZ_FONV0100001621020316221,151RefSeq:NZ_FONV01000016
NZ_FONV0100001718417473195,785RefSeq:NZ_FONV01000017
NZ_FONV0100001816215534187,747RefSeq:NZ_FONV01000018
NZ_FONV0100001916616402184,020RefSeq:NZ_FONV01000019
NZ_FONV0100002013612835148,368RefSeq:NZ_FONV01000020
NZ_FONV0100002112712403128,044RefSeq:NZ_FONV01000021
NZ_FONV010000221019506104,127RefSeq:NZ_FONV01000022
NZ_FONV0100002392910195,172RefSeq:NZ_FONV01000023
NZ_FONV0100002486830390,164RefSeq:NZ_FONV01000024
NZ_FONV0100002573720183,388RefSeq:NZ_FONV01000025
NZ_FONV0100002672710171,416RefSeq:NZ_FONV01000026
NZ_FONV0100002769680170,910RefSeq:NZ_FONV01000027
NZ_FONV0100002869650470,431RefSeq:NZ_FONV01000028
NZ_FONV0100002946440267,705RefSeq:NZ_FONV01000029
NZ_FONV0100003056540265,921RefSeq:NZ_FONV01000030
NZ_FONV0100003160550560,413RefSeq:NZ_FONV01000031
NZ_FONV0100003252500254,915RefSeq:NZ_FONV01000032
NZ_FONV0100003347460154,475RefSeq:NZ_FONV01000033
NZ_FONV0100003448480054,130RefSeq:NZ_FONV01000034
NZ_FONV0100003535330240,199RefSeq:NZ_FONV01000035
NZ_FONV0100003639353139,176RefSeq:NZ_FONV01000036
NZ_FONV0100003741390239,167RefSeq:NZ_FONV01000037
NZ_FONV0100003836310538,616RefSeq:NZ_FONV01000038
NZ_FONV0100003940391037,449RefSeq:NZ_FONV01000039
NZ_FONV0100004031256024,989RefSeq:NZ_FONV01000040
NZ_FONV0100004123230023,385RefSeq:NZ_FONV01000041
18 Undisplayed Contigs/Replicons51512879,952
Total:9,3919,0258428210,381,230
Ortholog data available?Yes
Database Contents
Genes9,386
Pathways255
Enzymatic Reactions1,496
Transport Reactions77
Polypeptides9,026
Protein Complexes37
Enzymes1,307
Transporters741
Compounds1,300
Transcription Units6,516
tRNAs75
Protein Features10,175
GO Terms26,184
Database Version29.0
Synonyms ATCC 12427
Actinoplanes philippinensis Couch 1950
DSM 43019
HAMBI 1927
IFO 13878
JCM 3001
NBRC 13878
NRRL 2506
VKM Ac-842
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micromonosporales
Micromonosporaceae
Actinoplanes
Actinoplanes philippinensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05421541
NCBI BioProjectPRJNA224116
NCBI-Taxonomy35752
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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