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 bangkokensis 44EHW, 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_MKQR010000268998661023931,456RefSeq:NZ_MKQR01000026
NZ_MKQR01000009564546117815,172RefSeq:NZ_MKQR01000009
NZ_MKQR010000287256961217804,127RefSeq:NZ_MKQR01000028
NZ_MKQR01000007703691111743,901RefSeq:NZ_MKQR01000007
NZ_MKQR01000016472451021522,999RefSeq:NZ_MKQR01000016
NZ_MKQR0100001126926207411,225RefSeq:NZ_MKQR01000011
NZ_MKQR0100001728928306382,781RefSeq:NZ_MKQR01000017
NZ_MKQR0100001324324012311,653RefSeq:NZ_MKQR01000013
NZ_MKQR01000018245232112307,652RefSeq:NZ_MKQR01000018
NZ_MKQR0100000521821341236,619RefSeq:NZ_MKQR01000005
NZ_MKQR0100000222021442219,029RefSeq:NZ_MKQR01000002
NZ_MKQR0100003221821044217,111RefSeq:NZ_MKQR01000032
NZ_MKQR0100002119018622209,220RefSeq:NZ_MKQR01000021
NZ_MKQR0100002515515023174,904RefSeq:NZ_MKQR01000025
NZ_MKQR0100000814714403160,919RefSeq:NZ_MKQR01000008
NZ_MKQR0100000612812404158,902RefSeq:NZ_MKQR01000006
NZ_MKQR0100000411811800139,258RefSeq:NZ_MKQR01000004
NZ_MKQR01000001969141101,296RefSeq:NZ_MKQR01000001
NZ_MKQR0100001580790195,422RefSeq:NZ_MKQR01000015
NZ_MKQR0100002392866094,617RefSeq:NZ_MKQR01000023
NZ_MKQR0100001977760189,476RefSeq:NZ_MKQR01000019
NZ_MKQR0100000375712277,547RefSeq:NZ_MKQR01000003
NZ_MKQR0100002050500055,085RefSeq:NZ_MKQR01000020
NZ_MKQR0100002234330137,274RefSeq:NZ_MKQR01000022
NZ_MKQR0100001235350036,998RefSeq:NZ_MKQR01000012
NZ_MKQR01000010320135,881RefSeq:NZ_MKQR01000010
NZ_MKQR0100001418170120,939RefSeq:NZ_MKQR01000014
NZ_MKQR0100003017151120,853RefSeq:NZ_MKQR01000030
NZ_MKQR0100002916150118,199RefSeq:NZ_MKQR01000029
NZ_MKQR0100002413130014,539RefSeq:NZ_MKQR01000024
NZ_MKQR0100003166007,914RefSeq:NZ_MKQR01000031
NZ_MKQR010000271001745RefSeq:NZ_MKQR01000027
Total:6,4166,215551467,453,713
Ortholog data available?Yes
Database Contents
Genes6,416
Pathways264
Enzymatic Reactions1,387
Transport Reactions41
Polypeptides6,250
Protein Complexes122
Enzymes937
Transporters335
Compounds1,002
Transcription Units4,470
tRNAs50
Protein Features7,664
GO Terms343
Database Version29.0
Sequence SourceGCF_001940455.1
Synonyms Actinokineospora sp. 44EHW
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Actinokineospora
Actinokineospora bangkokensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05860870
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1193682
Environmentrhizospheric soil under an elephant ear plant (Colocasia esculenta)
Geographic LocationThailand
Latitude/Longitude13.943309 N 100.51465 E
Collection Date2012
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-30
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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