Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Actinokineospora iranica IBRC-M 10403, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_FMZZ010000011,0871,0632221,146,341RefSeq:NZ_FMZZ01000001
NZ_FMZZ01000002517506110540,718RefSeq:NZ_FMZZ01000002
NZ_FMZZ0100000341340148441,665RefSeq:NZ_FMZZ01000003
NZ_FMZZ0100000439938595412,771RefSeq:NZ_FMZZ01000004
NZ_FMZZ0100000537836558392,129RefSeq:NZ_FMZZ01000005
NZ_FMZZ0100000635534447384,203RefSeq:NZ_FMZZ01000006
NZ_FMZZ0100000731330724360,745RefSeq:NZ_FMZZ01000007
NZ_FMZZ0100000831430806326,584RefSeq:NZ_FMZZ01000008
NZ_FMZZ0100000927726827295,689RefSeq:NZ_FMZZ01000009
NZ_FMZZ0100001023623402291,113RefSeq:NZ_FMZZ01000010
NZ_FMZZ0100001123823341229,901RefSeq:NZ_FMZZ01000011
NZ_FMZZ0100001216615853199,265RefSeq:NZ_FMZZ01000012
NZ_FMZZ0100001319118407194,509RefSeq:NZ_FMZZ01000013
NZ_FMZZ0100001412611907169,590RefSeq:NZ_FMZZ01000014
NZ_FMZZ0100001515715511158,530RefSeq:NZ_FMZZ01000015
NZ_FMZZ0100001613212714139,332RefSeq:NZ_FMZZ01000016
NZ_FMZZ0100001710710322114,497RefSeq:NZ_FMZZ01000017
NZ_FMZZ010000181039643112,326RefSeq:NZ_FMZZ01000018
NZ_FMZZ01000019928813102,524RefSeq:NZ_FMZZ01000019
NZ_FMZZ01000020101972291,431RefSeq:NZ_FMZZ01000020
NZ_FMZZ0100002180706474,649RefSeq:NZ_FMZZ01000021
NZ_FMZZ0100002271682163,281RefSeq:NZ_FMZZ01000022
NZ_FMZZ0100002347450259,572RefSeq:NZ_FMZZ01000023
NZ_FMZZ0100002462581354,573RefSeq:NZ_FMZZ01000024
NZ_FMZZ0100002541410052,368RefSeq:NZ_FMZZ01000025
NZ_FMZZ0100002638380046,988RefSeq:NZ_FMZZ01000026
NZ_FMZZ0100002725240136,008RefSeq:NZ_FMZZ01000027
NZ_FMZZ0100002824230126,350RefSeq:NZ_FMZZ01000028
11 Undisplayed Contigs/Replicons43433761,111
Total:6,1435,951611316,578,763
Ortholog data available?Yes
Database Contents
Genes6,135
Pathways268
Enzymatic Reactions1,411
Transport Reactions47
Polypeptides5,983
Protein Complexes100
Enzymes931
Transporters261
Compounds1,047
Transcription Units4,245
tRNAs47
Protein Features6,596
GO Terms257
Database Version29.0
Sequence SourceGCF_900101685.1
Synonyms Alloactinosynnema iranicum
Alloactinosynnema sp. Chem10
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Actinokineospora
Actinokineospora iranica
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05216174
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1271860
Annotation ProviderNCBI RefSeq
Annotation Date2021-11-16
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

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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