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 Actinomadura mexicana DSM 44485, 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_FZNP010000018988659241,005,176RefSeq:NZ_FZNP01000001
NZ_FZNP010000028127891013899,176RefSeq:NZ_FZNP01000002
NZ_FZNP01000003573558510647,359RefSeq:NZ_FZNP01000003
NZ_FZNP01000004513484722603,827RefSeq:NZ_FZNP01000004
NZ_FZNP0100000549147849540,343RefSeq:NZ_FZNP01000005
NZ_FZNP01000006453428619483,966RefSeq:NZ_FZNP01000006
NZ_FZNP01000007448432412464,425RefSeq:NZ_FZNP01000007
NZ_FZNP01000008394376513434,053RefSeq:NZ_FZNP01000008
NZ_FZNP0100000937836927403,096RefSeq:NZ_FZNP01000009
NZ_FZNP0100001032431626338,285RefSeq:NZ_FZNP01000010
NZ_FZNP01000011248235013276,092RefSeq:NZ_FZNP01000011
NZ_FZNP0100001224223705256,285RefSeq:NZ_FZNP01000012
NZ_FZNP0100001325725007254,006RefSeq:NZ_FZNP01000013
NZ_FZNP0100001415214705199,583RefSeq:NZ_FZNP01000014
NZ_FZNP0100001519018046191,217RefSeq:NZ_FZNP01000015
NZ_FZNP0100001616516005170,264RefSeq:NZ_FZNP01000016
NZ_FZNP0100001713112704157,070RefSeq:NZ_FZNP01000017
NZ_FZNP0100001813913306154,797RefSeq:NZ_FZNP01000018
NZ_FZNP0100001913213101151,783RefSeq:NZ_FZNP01000019
NZ_FZNP0100002010910414140,856RefSeq:NZ_FZNP01000020
NZ_FZNP0100002112512311128,370RefSeq:NZ_FZNP01000021
NZ_FZNP0100002211110515118,689RefSeq:NZ_FZNP01000022
NZ_FZNP0100002391863295,906RefSeq:NZ_FZNP01000023
NZ_FZNP0100002495900595,834RefSeq:NZ_FZNP01000024
NZ_FZNP0100002583770684,592RefSeq:NZ_FZNP01000025
NZ_FZNP0100002656530366,091RefSeq:NZ_FZNP01000026
NZ_FZNP0100002752490363,027RefSeq:NZ_FZNP01000027
NZ_FZNP0100002860571258,272RefSeq:NZ_FZNP01000028
NZ_FZNP0100002946440251,982RefSeq:NZ_FZNP01000029
NZ_FZNP0100003049451347,957RefSeq:NZ_FZNP01000030
NZ_FZNP0100003147450245,463RefSeq:NZ_FZNP01000031
NZ_FZNP0100003240391044,111RefSeq:NZ_FZNP01000032
NZ_FZNP0100003336332139,425RefSeq:NZ_FZNP01000033
NZ_FZNP0100003513120113,566RefSeq:NZ_FZNP01000035
19 Undisplayed Contigs/Replicons31310761,417
Total:7,9917,688692348,786,361
Ortholog data available?Yes
Database Contents
Genes7,987
Pathways249
Enzymatic Reactions1,539
Transport Reactions70
Polypeptides7,692
Protein Complexes39
Enzymes1,210
Transporters667
Compounds1,322
Transcription Units5,689
tRNAs62
Protein Features8,714
GO Terms22,100
Database Version29.0
Synonyms Actinomadura mexicana Quintana et al. 2004
DSM 44485
JCM 13236
NRRL B-24203
strain A290
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Streptosporangiales
Thermomonosporaceae
Actinomadura
Actinomadura mexicana
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06265355
NCBI BioProjectPRJNA224116
NCBI-Taxonomy134959
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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