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 regularis DSM 43151, 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_FZNR010000011,0681,03114231,209,810RefSeq:NZ_FZNR01000001
NZ_FZNR01000002839806330973,250RefSeq:NZ_FZNR01000002
NZ_FZNR0100000356955379634,152RefSeq:NZ_FZNR01000003
NZ_FZNR01000004534513021578,873RefSeq:NZ_FZNR01000004
NZ_FZNR01000005519500019550,385RefSeq:NZ_FZNR01000005
NZ_FZNR0100000638237138437,782RefSeq:NZ_FZNR01000006
NZ_FZNR0100000737736908434,292RefSeq:NZ_FZNR01000007
NZ_FZNR01000008331313711362,848RefSeq:NZ_FZNR01000008
NZ_FZNR0100000931429789333,242RefSeq:NZ_FZNR01000009
NZ_FZNR01000010299288011316,824RefSeq:NZ_FZNR01000010
NZ_FZNR0100001125524735261,740RefSeq:NZ_FZNR01000011
NZ_FZNR0100001223722908256,298RefSeq:NZ_FZNR01000012
NZ_FZNR0100001321120713240,525RefSeq:NZ_FZNR01000013
NZ_FZNR0100001421420725233,475RefSeq:NZ_FZNR01000014
NZ_FZNR0100001521020604233,045RefSeq:NZ_FZNR01000015
NZ_FZNR0100001616515915191,467RefSeq:NZ_FZNR01000016
NZ_FZNR0100001714614204185,692RefSeq:NZ_FZNR01000017
NZ_FZNR01000018173157016182,645RefSeq:NZ_FZNR01000018
NZ_FZNR0100001915315102158,622RefSeq:NZ_FZNR01000019
NZ_FZNR0100002014313913147,071RefSeq:NZ_FZNR01000020
NZ_FZNR0100002111210903140,730RefSeq:NZ_FZNR01000021
NZ_FZNR01000022133118213139,326RefSeq:NZ_FZNR01000022
NZ_FZNR0100002312311553130,072RefSeq:NZ_FZNR01000023
NZ_FZNR0100002411110632125,147RefSeq:NZ_FZNR01000024
NZ_FZNR0100002512011325121,171RefSeq:NZ_FZNR01000025
NZ_FZNR0100002611110704120,075RefSeq:NZ_FZNR01000026
NZ_FZNR01000027128105203116,167RefSeq:NZ_FZNR01000027
NZ_FZNR010000288371012104,820RefSeq:NZ_FZNR01000028
NZ_FZNR01000029636102102,766RefSeq:NZ_FZNR01000029
NZ_FZNR01000030998901099,516RefSeq:NZ_FZNR01000030
NZ_FZNR0100003173680597,014RefSeq:NZ_FZNR01000031
NZ_FZNR0100003267640380,370RefSeq:NZ_FZNR01000032
NZ_FZNR0100003361590277,676RefSeq:NZ_FZNR01000033
NZ_FZNR0100003449470265,634RefSeq:NZ_FZNR01000034
NZ_FZNR0100003553470665,621RefSeq:NZ_FZNR01000035
NZ_FZNR0100003666610558,275RefSeq:NZ_FZNR01000036
NZ_FZNR0100003742410143,527RefSeq:NZ_FZNR01000037
NZ_FZNR0100003840352341,859RefSeq:NZ_FZNR01000038
NZ_FZNR0100003939370240,259RefSeq:NZ_FZNR01000039
NZ_FZNR0100004027250240,221RefSeq:NZ_FZNR01000040
NZ_FZNR0100004136340238,663RefSeq:NZ_FZNR01000041
NZ_FZNR0100004231300133,559RefSeq:NZ_FZNR01000042
NZ_FZNR0100004327260129,849RefSeq:NZ_FZNR01000043
NZ_FZNR0100004421190226,345RefSeq:NZ_FZNR01000044
NZ_FZNR0100004616120418,354RefSeq:NZ_FZNR01000046
NZ_FZNR0100004716150117,661RefSeq:NZ_FZNR01000047
NZ_FZNR0100004819170214,873RefSeq:NZ_FZNR01000048
29 Undisplayed Contigs/Replicons4139222120,118
Total:8,9688,5558632710,031,706
Ortholog data available?Yes
Database Contents
Genes8,968
Pathways247
Enzymatic Reactions1,538
Transport Reactions78
Polypeptides8,558
Protein Complexes40
Enzymes1,295
Transporters702
Compounds1,261
Transcription Units6,291
tRNAs79
Protein Features9,370
GO Terms24,819
Database Version29.0
Synonyms "Ampullaria regularis" Couch 1963
Actinoplanes regularis (Couch 1963) Stackebrandt and Kroppenstedt 1988
Ampullaria regularis
Ampullariella regularis
Ampullariella regularis (Couch 1963) Couch 1964 (Approved Lists 1980)
DSM 43151
HAMBI 1928
IFO 12514
JCM 3062
NBRC 12514
NRRL B-3347
VKM Ac-650
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micromonosporales
Micromonosporaceae
Actinoplanes
Actinoplanes regularis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06264365
NCBI BioProjectPRJNA224116
NCBI-Taxonomy52697
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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