Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 13-Mar-2021 from the annotated genome of Thermincola ferriacetica Z-0001, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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_LGTE01000001324311132317,748RefSeq:NZ_LGTE01000001
NZ_LGTE0100000228528503265,702RefSeq:NZ_LGTE01000002
NZ_LGTE0100000321320850210,588RefSeq:NZ_LGTE01000003
NZ_LGTE0100000416015733156,513RefSeq:NZ_LGTE01000004
NZ_LGTE0100000514514320153,282RefSeq:NZ_LGTE01000005
NZ_LGTE0100000611911901127,275RefSeq:NZ_LGTE01000006
NZ_LGTE0100000711911721122,948RefSeq:NZ_LGTE01000007
NZ_LGTE0100000810210200106,581RefSeq:NZ_LGTE01000008
NZ_LGTE01000009959233100,471RefSeq:NZ_LGTE01000009
NZ_LGTE010000101031021397,917RefSeq:NZ_LGTE01000010
NZ_LGTE0100001195878097,771RefSeq:NZ_LGTE01000011
NZ_LGTE01000012103985097,611RefSeq:NZ_LGTE01000012
NZ_LGTE0100001388880096,627RefSeq:NZ_LGTE01000013
NZ_LGTE0100001468680088,378RefSeq:NZ_LGTE01000014
NZ_LGTE0100001581801385,661RefSeq:NZ_LGTE01000015
NZ_LGTE0100001678780070,230RefSeq:NZ_LGTE01000016
NZ_LGTE0100001757570164,883RefSeq:NZ_LGTE01000017
NZ_LGTE0100001855541060,308RefSeq:NZ_LGTE01000018
NZ_LGTE0100001967670259,459RefSeq:NZ_LGTE01000019
NZ_LGTE0100002054540158,477RefSeq:NZ_LGTE01000020
NZ_LGTE0100002151510055,889RefSeq:NZ_LGTE01000021
NZ_LGTE0100002259572254,145RefSeq:NZ_LGTE01000022
NZ_LGTE0100002345450250,132RefSeq:NZ_LGTE01000023
NZ_LGTE0100002444440143,326RefSeq:NZ_LGTE01000024
NZ_LGTE0100002534340040,479RefSeq:NZ_LGTE01000025
NZ_LGTE0100002644440039,672RefSeq:NZ_LGTE01000026
NZ_LGTE0100002733321137,495RefSeq:NZ_LGTE01000027
NZ_LGTE0100002829290136,844RefSeq:NZ_LGTE01000028
NZ_LGTE0100002935305035,169RefSeq:NZ_LGTE01000029
NZ_LGTE0100003031302033,835RefSeq:NZ_LGTE01000030
NZ_LGTE0100003125250031,204RefSeq:NZ_LGTE01000031
NZ_LGTE0100003236360029,779RefSeq:NZ_LGTE01000032
NZ_LGTE0100003319190122,693RefSeq:NZ_LGTE01000033
NZ_LGTE0100003424240222,641RefSeq:NZ_LGTE01000034
NZ_LGTE0100003520200022,003RefSeq:NZ_LGTE01000035
NZ_LGTE0100003619190219,018RefSeq:NZ_LGTE01000036
NZ_LGTE0100003715150017,700RefSeq:NZ_LGTE01000037
NZ_LGTE0100003815150015,944RefSeq:NZ_LGTE01000038
NZ_LGTE0100003912120015,382RefSeq:NZ_LGTE01000039
NZ_LGTE0100004013130114,206RefSeq:NZ_LGTE01000040
NZ_LGTE0100004212120011,735RefSeq:NZ_LGTE01000042
NZ_LGTE0100004313130010,783RefSeq:NZ_LGTE01000043
36 Undisplayed Contigs/Replicons524851680,223
Total:3,1433,03459523,178,727
Ortholog data available?Yes
Database Contents
Genes3,091
Pathways202
Enzymatic Reactions1,027
Transport Reactions58
Polypeptides3,067
Protein Complexes38
Enzymes636
Transporters259
Compounds774
Transcription Units1,901
tRNAs49
Protein Features3,955
GO Annotations1
Database Version29.6
Sequence SourceGCF_001263415.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Bacillati
Bacillota
Clostridia
Eubacteriales
Thermincolaceae
Thermincola
Thermincola ferriacetica
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03840759
NCBI BioProjectPRJNA224116
NCBI-Taxonomy281456
EnvironmentMicrobial Fuel Cell
Geographic LocationRussia
Collection Date2013
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-18
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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