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 Clostridium oryzae DSM 28571, 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_MZGV0100000127627602337,290RefSeq:NZ_MZGV01000001
NZ_MZGV0100000215015002149,673RefSeq:NZ_MZGV01000002
NZ_MZGV0100000312612162133,826RefSeq:NZ_MZGV01000003
NZ_MZGV0100000411611605127,952RefSeq:NZ_MZGV01000004
NZ_MZGV01000005131113183126,998RefSeq:NZ_MZGV01000005
NZ_MZGV0100000610910903123,328RefSeq:NZ_MZGV01000006
NZ_MZGV0100000712712521123,026RefSeq:NZ_MZGV01000007
NZ_MZGV0100000810110101120,389RefSeq:NZ_MZGV01000008
NZ_MZGV0100000911310760119,247RefSeq:NZ_MZGV01000009
NZ_MZGV0100001011611600109,457RefSeq:NZ_MZGV01000010
NZ_MZGV01000011969610108,424RefSeq:NZ_MZGV01000011
NZ_MZGV01000012909002106,977RefSeq:NZ_MZGV01000012
NZ_MZGV01000013929200104,356RefSeq:NZ_MZGV01000013
NZ_MZGV01000014848405102,574RefSeq:NZ_MZGV01000014
NZ_MZGV0100001591910097,914RefSeq:NZ_MZGV01000015
NZ_MZGV0100001683767186,253RefSeq:NZ_MZGV01000016
NZ_MZGV0100001772720184,193RefSeq:NZ_MZGV01000017
NZ_MZGV0100001859590383,427RefSeq:NZ_MZGV01000018
NZ_MZGV0100001980800078,931RefSeq:NZ_MZGV01000019
NZ_MZGV0100002053530177,347RefSeq:NZ_MZGV01000020
NZ_MZGV0100002159590176,364RefSeq:NZ_MZGV01000021
NZ_MZGV0100002263630075,803RefSeq:NZ_MZGV01000022
NZ_MZGV0100002354540272,452RefSeq:NZ_MZGV01000023
NZ_MZGV0100002461610172,188RefSeq:NZ_MZGV01000024
NZ_MZGV0100002558535064,915RefSeq:NZ_MZGV01000025
NZ_MZGV0100002649482064,308RefSeq:NZ_MZGV01000026
NZ_MZGV0100002758580063,335RefSeq:NZ_MZGV01000027
NZ_MZGV0100002851511260,316RefSeq:NZ_MZGV01000028
NZ_MZGV0100002977752058,379RefSeq:NZ_MZGV01000029
NZ_MZGV0100003052520150,368RefSeq:NZ_MZGV01000030
NZ_MZGV0100003140400049,201RefSeq:NZ_MZGV01000031
NZ_MZGV0100003250455048,987RefSeq:NZ_MZGV01000032
NZ_MZGV0100003341410048,563RefSeq:NZ_MZGV01000033
NZ_MZGV0100003432320047,104RefSeq:NZ_MZGV01000034
NZ_MZGV0100003543412043,410RefSeq:NZ_MZGV01000035
NZ_MZGV0100003632320242,700RefSeq:NZ_MZGV01000036
NZ_MZGV0100003745450442,669RefSeq:NZ_MZGV01000037
NZ_MZGV0100003836360041,818RefSeq:NZ_MZGV01000038
NZ_MZGV0100003936360039,222RefSeq:NZ_MZGV01000039
NZ_MZGV0100004034340038,633RefSeq:NZ_MZGV01000040
NZ_MZGV0100004128280036,697RefSeq:NZ_MZGV01000041
NZ_MZGV0100004237361036,163RefSeq:NZ_MZGV01000042
NZ_MZGV0100004328280135,566RefSeq:NZ_MZGV01000043
NZ_MZGV0100004433321131,182RefSeq:NZ_MZGV01000044
NZ_MZGV0100004527261130,244RefSeq:NZ_MZGV01000045
NZ_MZGV0100004624240029,517RefSeq:NZ_MZGV01000046
NZ_MZGV0100004721210029,395RefSeq:NZ_MZGV01000047
NZ_MZGV0100004820200028,180RefSeq:NZ_MZGV01000048
NZ_MZGV0100004920200027,944RefSeq:NZ_MZGV01000049
NZ_MZGV0100005026251027,810RefSeq:NZ_MZGV01000050
NZ_MZGV0100005130255027,188RefSeq:NZ_MZGV01000051
NZ_MZGV0100005222221027,062RefSeq:NZ_MZGV01000052
NZ_MZGV0100005332320026,931RefSeq:NZ_MZGV01000053
NZ_MZGV0100005421210026,818RefSeq:NZ_MZGV01000054
NZ_MZGV0100005521210026,449RefSeq:NZ_MZGV01000055
NZ_MZGV0100005634340026,212RefSeq:NZ_MZGV01000056
NZ_MZGV0100005725233025,980RefSeq:NZ_MZGV01000057
NZ_MZGV0100005822220025,374RefSeq:NZ_MZGV01000058
NZ_MZGV0100005922220025,141RefSeq:NZ_MZGV01000059
NZ_MZGV0100006019190024,975RefSeq:NZ_MZGV01000060
NZ_MZGV0100006128280023,945RefSeq:NZ_MZGV01000061
NZ_MZGV0100006218180022,322RefSeq:NZ_MZGV01000062
NZ_MZGV0100006315150022,257RefSeq:NZ_MZGV01000063
NZ_MZGV0100006419190122,043RefSeq:NZ_MZGV01000064
NZ_MZGV0100006522220021,896RefSeq:NZ_MZGV01000065
NZ_MZGV0100006614140121,208RefSeq:NZ_MZGV01000066
NZ_MZGV0100006718180021,130RefSeq:NZ_MZGV01000067
NZ_MZGV0100006817170020,976RefSeq:NZ_MZGV01000068
NZ_MZGV0100006916160120,559RefSeq:NZ_MZGV01000069
NZ_MZGV0100007018180020,138RefSeq:NZ_MZGV01000070
NZ_MZGV0100007117170020,067RefSeq:NZ_MZGV01000071
NZ_MZGV0100007219181020,029RefSeq:NZ_MZGV01000072
NZ_MZGV0100007317171019,673RefSeq:NZ_MZGV01000073
NZ_MZGV0100007417170018,846RefSeq:NZ_MZGV01000074
NZ_MZGV0100007512120018,688RefSeq:NZ_MZGV01000075
NZ_MZGV0100007618180218,552RefSeq:NZ_MZGV01000076
NZ_MZGV0100007718180018,404RefSeq:NZ_MZGV01000077
NZ_MZGV0100007814141018,215RefSeq:NZ_MZGV01000078
NZ_MZGV0100007916151018,058RefSeq:NZ_MZGV01000079
NZ_MZGV0100008114140017,988RefSeq:NZ_MZGV01000081
NZ_MZGV0100008211110017,660RefSeq:NZ_MZGV01000082
NZ_MZGV0100008312102017,652RefSeq:NZ_MZGV01000083
NZ_MZGV0100008416160117,651RefSeq:NZ_MZGV01000084
NZ_MZGV0100008514140017,243RefSeq:NZ_MZGV01000085
NZ_MZGV0100008616160017,113RefSeq:NZ_MZGV01000086
NZ_MZGV0100008713130116,309RefSeq:NZ_MZGV01000087
NZ_MZGV0100008823230215,912RefSeq:NZ_MZGV01000088
NZ_MZGV0100008916160015,909RefSeq:NZ_MZGV01000089
NZ_MZGV0100009114105014,247RefSeq:NZ_MZGV01000091
NZ_MZGV0100009215142014,232RefSeq:NZ_MZGV01000092
NZ_MZGV0100009320200113,900RefSeq:NZ_MZGV01000093
NZ_MZGV0100009614140112,845RefSeq:NZ_MZGV01000096
NZ_MZGV0100009912111111,532RefSeq:NZ_MZGV01000099
NZ_MZGV010001071212009,012RefSeq:NZ_MZGV01000107
82 Undisplayed Contigs/Replicons3002892013381,446
Total:4,5764,418104735,074,802
Ortholog data available?Yes
Database Contents
Genes4,503
Pathways206
Enzymatic Reactions1,093
Transport Reactions68
Polypeptides4,451
Protein Complexes158
Enzymes724
Transporters411
Compounds854
Transcription Units3,092
tRNAs69
Protein Features5,680
GO Annotations403
Database Version29.6
Sequence SourceGCF_002029235.1
Synonyms Clostridium sp. KC3
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Bacillati
Bacillota
Clostridia
Eubacteriales
Clostridiaceae
Clostridium
Clostridium oryzae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06461355
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1450648
Environmentrice field soil
Geographic LocationJapan
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-1
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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