Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Actinokineospora enzanensis DSM 44649, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [Caspi20]. 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 Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_KB89440355053659671,370RefSeq:NZ_KB894403
NZ_KB89440439638709572,116RefSeq:NZ_KB894404
NZ_KB89440538237507516,406RefSeq:NZ_KB894405
NZ_KB89440626926603294,529RefSeq:NZ_KB894406
NZ_KB89440725224903294,464RefSeq:NZ_KB894407
NZ_KB89440827727025277,759RefSeq:NZ_KB894408
NZ_KB89440921621321234,673RefSeq:NZ_KB894409
NZ_KB89441020620213227,543RefSeq:NZ_KB894410
NZ_KB89441122421932221,851RefSeq:NZ_KB894411
NZ_KB89441212512104201,885RefSeq:NZ_KB894412
NZ_KB89441319518834189,745RefSeq:NZ_KB894413
NZ_KB89441417616943179,568RefSeq:NZ_KB894414
NZ_KB89441516816062169,873RefSeq:NZ_KB894415
NZ_KB89441616515519164,672RefSeq:NZ_KB894416
NZ_KB89441712612204161,170RefSeq:NZ_KB894417
NZ_KB89441814213642155,366RefSeq:NZ_KB894418
NZ_KB89441915315201152,050RefSeq:NZ_KB894419
NZ_KB89442012912045148,780RefSeq:NZ_KB894420
NZ_KB89442113112830143,286RefSeq:NZ_KB894421
NZ_KB89442211510807141,395RefSeq:NZ_KB894422
NZ_KB89442313413202140,567RefSeq:NZ_KB894423
NZ_KB89442413012901137,752RefSeq:NZ_KB894424
NZ_KB89442513113001136,778RefSeq:NZ_KB894425
NZ_KB89442612211903132,917RefSeq:NZ_KB894426
NZ_KB89442711511122132,449RefSeq:NZ_KB894427
NZ_KB89442811610664130,371RefSeq:NZ_KB894428
NZ_KB89442912312102124,075RefSeq:NZ_KB894429
NZ_KB89443013313003115,910RefSeq:NZ_KB894430
NZ_KB894431838102114,489RefSeq:NZ_KB894431
NZ_KB89443210210101108,950RefSeq:NZ_KB894432
NZ_KB89443310810701101,885RefSeq:NZ_KB894433
NZ_KB89443482810190,100RefSeq:NZ_KB894434
NZ_KB89443579762188,107RefSeq:NZ_KB894435
NZ_KB89443684830185,877RefSeq:NZ_KB894436
NZ_KB89443782811082,590RefSeq:NZ_KB894437
NZ_KB89443874720281,244RefSeq:NZ_KB894438
NZ_KB89443973711174,786RefSeq:NZ_KB894439
NZ_KB89444062620074,454RefSeq:NZ_KB894440
NZ_KB89444155502368,953RefSeq:NZ_KB894441
NZ_KB89444267621463,066RefSeq:NZ_KB894442
NZ_KB89444356511459,427RefSeq:NZ_KB894443
NZ_KB89444446440253,279RefSeq:NZ_KB894444
NZ_KB89444566650152,226RefSeq:NZ_KB894445
NZ_KB89444647433144,800RefSeq:NZ_KB894446
NZ_KB89444743402143,889RefSeq:NZ_KB894447
NZ_KB89444851452442,508RefSeq:NZ_KB894448
NZ_KB89444941400142,054RefSeq:NZ_KB894449
NZ_KB89445042400239,395RefSeq:NZ_KB894450
NZ_KB89445138380037,791RefSeq:NZ_KB894451
NZ_KB89445234300433,872RefSeq:NZ_KB894452
NZ_KB89445329250433,699RefSeq:NZ_KB894453
NZ_KB89445434340033,514RefSeq:NZ_KB894454
NZ_KB89445521210027,535RefSeq:NZ_KB894455
NZ_KB89445628261127,151RefSeq:NZ_KB894456
NZ_KB89445732310126,513RefSeq:NZ_KB894457
NZ_KB89445819180123,929RefSeq:NZ_KB894458
NZ_KB89445936350122,990RefSeq:NZ_KB894459
NZ_KB89446019180119,653RefSeq:NZ_KB894460
NZ_KB89446223191318,218RefSeq:NZ_KB894462
NZ_KB89446318170117,947RefSeq:NZ_KB894463
NZ_KB89446413130017,245RefSeq:NZ_KB894464
NZ_KB89446615140115,896RefSeq:NZ_KB894466
NZ_KB89446717160115,678RefSeq:NZ_KB894467
NZ_KB89446916132114,477RefSeq:NZ_KB894469
NZ_KB8944741610429,340RefSeq:NZ_KB894474
23 Undisplayed Contigs/Replicons777539143,011
Total:7,2397,002721658,119,858
Ortholog data available?Yes
Database Contents
Genes7,232
Pathways268
Enzymatic Reactions1,337
Transport Reactions54
Polypeptides7,047
Protein Complexes56
Enzymes964
Transporters484
Compounds1,011
Transcription Units4,960
tRNAs57
Protein Features7,920
GO Terms1
Database Version29.0
Sequence SourceGCF_000374445.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Actinokineospora
Actinokineospora enzanensis
Actinokineospora enzanensis DSM 44649
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02441015
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120934
EnvironmentSoil
Geographic LocationJapan
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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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