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 Actinophytocola xinjiangensis CGMCC 4.4663, 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_MSIF010000019789594151,134,410RefSeq:NZ_MSIF01000001
NZ_MSIF0100000261961207693,018RefSeq:NZ_MSIF01000002
NZ_MSIF01000003510497013581,851RefSeq:NZ_MSIF01000003
NZ_MSIF0100000441139948469,009RefSeq:NZ_MSIF01000004
NZ_MSIF0100000542541096442,288RefSeq:NZ_MSIF01000005
NZ_MSIF01000006323306611386,368RefSeq:NZ_MSIF01000006
NZ_MSIF0100000731731412369,992RefSeq:NZ_MSIF01000007
NZ_MSIF0100000823823503342,701RefSeq:NZ_MSIF01000008
NZ_MSIF0100000931831017320,825RefSeq:NZ_MSIF01000009
NZ_MSIF0100001023923333301,259RefSeq:NZ_MSIF01000010
NZ_MSIF0100001125024433261,143RefSeq:NZ_MSIF01000011
NZ_MSIF0100001226225444259,187RefSeq:NZ_MSIF01000012
NZ_MSIF0100001324023712249,030RefSeq:NZ_MSIF01000013
NZ_MSIF0100001419818837215,329RefSeq:NZ_MSIF01000014
NZ_MSIF0100001519719052201,024RefSeq:NZ_MSIF01000015
NZ_MSIF0100001614013703196,961RefSeq:NZ_MSIF01000016
NZ_MSIF0100001720720403194,600RefSeq:NZ_MSIF01000017
NZ_MSIF0100001812812431168,913RefSeq:NZ_MSIF01000018
NZ_MSIF0100001914314102167,458RefSeq:NZ_MSIF01000019
NZ_MSIF0100002013212804159,275RefSeq:NZ_MSIF01000020
NZ_MSIF0100002115915702157,286RefSeq:NZ_MSIF01000021
NZ_MSIF0100002215014343156,648RefSeq:NZ_MSIF01000022
NZ_MSIF0100002314714403150,753RefSeq:NZ_MSIF01000023
NZ_MSIF0100002411811404148,691RefSeq:NZ_MSIF01000024
NZ_MSIF0100002513913513135,298RefSeq:NZ_MSIF01000025
NZ_MSIF0100002612412202134,612RefSeq:NZ_MSIF01000026
NZ_MSIF01000027999900131,587RefSeq:NZ_MSIF01000027
NZ_MSIF0100002810110001111,301RefSeq:NZ_MSIF01000028
NZ_MSIF0100003093920193,822RefSeq:NZ_MSIF01000030
NZ_MSIF0100003175694289,854RefSeq:NZ_MSIF01000031
NZ_MSIF0100003257550275,409RefSeq:NZ_MSIF01000032
NZ_MSIF0100003375740175,392RefSeq:NZ_MSIF01000033
NZ_MSIF0100003465610470,249RefSeq:NZ_MSIF01000034
NZ_MSIF0100003567650269,203RefSeq:NZ_MSIF01000035
NZ_MSIF0100003661600166,380RefSeq:NZ_MSIF01000036
NZ_MSIF0100003745440161,064RefSeq:NZ_MSIF01000037
NZ_MSIF0100003866611460,567RefSeq:NZ_MSIF01000038
NZ_MSIF0100003963592258,590RefSeq:NZ_MSIF01000039
NZ_MSIF0100004047470056,615RefSeq:NZ_MSIF01000040
NZ_MSIF0100004156530355,735RefSeq:NZ_MSIF01000041
NZ_MSIF0100004254530155,717RefSeq:NZ_MSIF01000042
NZ_MSIF0100004347460141,689RefSeq:NZ_MSIF01000043
NZ_MSIF0100004434312140,992RefSeq:NZ_MSIF01000044
NZ_MSIF0100004520190134,074RefSeq:NZ_MSIF01000045
NZ_MSIF0100004631310033,837RefSeq:NZ_MSIF01000046
NZ_MSIF0100004731310033,689RefSeq:NZ_MSIF01000047
NZ_MSIF0100004815150021,969RefSeq:NZ_MSIF01000048
NZ_MSIF0100004918170120,298RefSeq:NZ_MSIF01000049
NZ_MSIF0100005017170016,249RefSeq:NZ_MSIF01000050
23 Undisplayed Contigs/Replicons3734312163,325
Total:8,3988,170641649,535,536
Ortholog data available?Yes
Database Contents
Genes8,398
Pathways292
Enzymatic Reactions1,536
Transport Reactions45
Polypeptides8,221
Protein Complexes224
Enzymes1,072
Transporters502
Compounds1,176
Transcription Units4,978
tRNAs58
Protein Features10,242
GO Terms547
Database Version29.0
Sequence SourceGCF_001921215.1
Synonyms Actinophytocola sp. QAIII60
Amycolatopsis sp. QAIII60
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Actinophytocola
Actinophytocola xinjiangensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05942565
NCBI BioProjectPRJNA224116
NCBI-Taxonomy485602
Environmentvirgin forest soil
Geographic LocationChina
Collection Date2008
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-19
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
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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