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 Parageobacillus caldoxylosilyticus NBRC 107762, 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_BAWO0100000416315904169,871RefSeq:NZ_BAWO01000004
NZ_BAWO0100000514914900149,145RefSeq:NZ_BAWO01000005
NZ_BAWO0100000115615510145,032RefSeq:NZ_BAWO01000001
NZ_BAWO0100001312611916130,561RefSeq:NZ_BAWO01000013
NZ_BAWO0100001112412301128,787RefSeq:NZ_BAWO01000011
NZ_BAWO0100000212011118119,875RefSeq:NZ_BAWO01000002
NZ_BAWO0100002210210002111,437RefSeq:NZ_BAWO01000022
NZ_BAWO0100000811310904100,372RefSeq:NZ_BAWO01000008
NZ_BAWO010000291118621494,293RefSeq:NZ_BAWO01000029
NZ_BAWO0100003076740287,145RefSeq:NZ_BAWO01000030
NZ_BAWO0100002471680384,747RefSeq:NZ_BAWO01000024
NZ_BAWO0100001667650284,537RefSeq:NZ_BAWO01000016
NZ_BAWO0100003192891280,433RefSeq:NZ_BAWO01000031
NZ_BAWO0100001074690578,416RefSeq:NZ_BAWO01000010
NZ_BAWO0100002175740170,703RefSeq:NZ_BAWO01000021
NZ_BAWO0100000367640368,864RefSeq:NZ_BAWO01000003
NZ_BAWO0100003271620961,814RefSeq:NZ_BAWO01000032
NZ_BAWO0100003368650359,504RefSeq:NZ_BAWO01000033
NZ_BAWO0100003455530257,221RefSeq:NZ_BAWO01000034
NZ_BAWO0100004372720056,689RefSeq:NZ_BAWO01000043
NZ_BAWO0100004464523954,360RefSeq:NZ_BAWO01000044
NZ_BAWO0100004552480453,238RefSeq:NZ_BAWO01000045
NZ_BAWO01000046645311053,156RefSeq:NZ_BAWO01000046
NZ_BAWO0100004755510452,598RefSeq:NZ_BAWO01000047
NZ_BAWO0100004851442549,201RefSeq:NZ_BAWO01000048
NZ_BAWO0100004945420349,114RefSeq:NZ_BAWO01000049
NZ_BAWO01000012644716148,696RefSeq:NZ_BAWO01000012
NZ_BAWO0100005046430348,602RefSeq:NZ_BAWO01000050
NZ_BAWO0100005148480047,596RefSeq:NZ_BAWO01000051
NZ_BAWO0100005245430246,622RefSeq:NZ_BAWO01000052
NZ_BAWO0100005344430145,317RefSeq:NZ_BAWO01000053
NZ_BAWO01000054714622345,240RefSeq:NZ_BAWO01000054
NZ_BAWO0100005550490143,920RefSeq:NZ_BAWO01000055
NZ_BAWO0100002047470042,259RefSeq:NZ_BAWO01000020
NZ_BAWO0100005643410242,113RefSeq:NZ_BAWO01000056
NZ_BAWO0100001833330041,845RefSeq:NZ_BAWO01000018
NZ_BAWO0100002647450238,858RefSeq:NZ_BAWO01000026
NZ_BAWO0100000738380038,436RefSeq:NZ_BAWO01000007
NZ_BAWO0100005750500038,251RefSeq:NZ_BAWO01000057
NZ_BAWO0100005831271337,235RefSeq:NZ_BAWO01000058
NZ_BAWO0100005941370436,900RefSeq:NZ_BAWO01000059
NZ_BAWO0100006034330136,390RefSeq:NZ_BAWO01000060
NZ_BAWO0100002542420036,093RefSeq:NZ_BAWO01000025
NZ_BAWO0100006129290033,233RefSeq:NZ_BAWO01000061
NZ_BAWO0100006224230132,914RefSeq:NZ_BAWO01000062
NZ_BAWO0100006325240130,425RefSeq:NZ_BAWO01000063
NZ_BAWO0100006430290129,379RefSeq:NZ_BAWO01000064
NZ_BAWO0100006524240027,779RefSeq:NZ_BAWO01000065
NZ_BAWO0100006824230127,211RefSeq:NZ_BAWO01000068
NZ_BAWO0100006928261127,153RefSeq:NZ_BAWO01000069
NZ_BAWO0100006623220126,219RefSeq:NZ_BAWO01000066
NZ_BAWO0100007028200825,889RefSeq:NZ_BAWO01000070
NZ_BAWO0100007122220024,479RefSeq:NZ_BAWO01000071
NZ_BAWO0100007221210022,236RefSeq:NZ_BAWO01000072
NZ_BAWO0100002722220021,205RefSeq:NZ_BAWO01000027
NZ_BAWO0100001417160120,988RefSeq:NZ_BAWO01000014
NZ_BAWO0100007321180320,563RefSeq:NZ_BAWO01000073
NZ_BAWO0100007414140017,747RefSeq:NZ_BAWO01000074
NZ_BAWO0100007514130117,099RefSeq:NZ_BAWO01000075
NZ_BAWO0100007613130016,976RefSeq:NZ_BAWO01000076
NZ_BAWO0100007714100416,232RefSeq:NZ_BAWO01000077
NZ_BAWO0100001918180015,798RefSeq:NZ_BAWO01000019
NZ_BAWO0100007816150115,199RefSeq:NZ_BAWO01000078
NZ_BAWO0100007917152014,972RefSeq:NZ_BAWO01000079
NZ_BAWO010000801583414,581RefSeq:NZ_BAWO01000080
NZ_BAWO0100003717160114,396RefSeq:NZ_BAWO01000037
NZ_BAWO0100001517150212,728RefSeq:NZ_BAWO01000015
NZ_BAWO0100008316140212,429RefSeq:NZ_BAWO01000083
NZ_BAWO0100004111110011,264RefSeq:NZ_BAWO01000041
NZ_BAWO0100008512100210,534RefSeq:NZ_BAWO01000085
NZ_BAWO0100008813100310,202RefSeq:NZ_BAWO01000088
NZ_BAWO010000391211019,977RefSeq:NZ_BAWO01000039
NZ_BAWO010000901111009,802RefSeq:NZ_BAWO01000090
NZ_BAWO010000951211108,893RefSeq:NZ_BAWO01000095
56 Undisplayed Contigs/Replicons167163451234,764
Total:3,8553,565911993,798,752
Ortholog data available?Yes
Database Contents
Genes3,855
Pathways302
Enzymatic Reactions1,344
Transport Reactions107
Polypeptides3,608
Protein Complexes66
Enzymes818
Transporters438
Compounds995
Transcription Units2,490
tRNAs82
Protein Features4,620
GO Terms9
Database Version29.0
Sequence SourceGCF_000632715.1
Synonyms Geobacillus caldoxylosilyticus NBRC 107762
Parageobacillus caldoxylosilyticus NBRC 107762
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Bacillales
Bacillaceae
Parageobacillus
Parageobacillus caldoxylosilyticus
Parageobacillus caldoxylosilyticus NBRC 107762
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00000342
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1220594
Annotation ProviderNCBI RefSeq
Annotation Date2020-06-28
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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