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 Fusicatenibacter saccharivorans 2789STDY5608849, 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_CYYV01000001304288313323,356RefSeq:NZ_CYYV01000001
NZ_CYYV01000002253241102291,015RefSeq:NZ_CYYV01000002
NZ_CYYV0100000324223174279,141RefSeq:NZ_CYYV01000003
NZ_CYYV0100000424824053263,599RefSeq:NZ_CYYV01000004
NZ_CYYV01000005245229133260,688RefSeq:NZ_CYYV01000005
NZ_CYYV0100000621220723244,910RefSeq:NZ_CYYV01000006
NZ_CYYV0100000719018424223,559RefSeq:NZ_CYYV01000007
NZ_CYYV0100000819218903214,253RefSeq:NZ_CYYV01000008
NZ_CYYV0100000919418833209,563RefSeq:NZ_CYYV01000009
NZ_CYYV0100001020319526204,662RefSeq:NZ_CYYV01000010
NZ_CYYV0100001114013604145,413RefSeq:NZ_CYYV01000011
NZ_CYYV0100001212211624139,588RefSeq:NZ_CYYV01000012
NZ_CYYV0100001312211525129,234RefSeq:NZ_CYYV01000013
NZ_CYYV0100001477703481,994RefSeq:NZ_CYYV01000014
NZ_CYYV0100001587780981,687RefSeq:NZ_CYYV01000015
NZ_CYYV0100001682741780,413RefSeq:NZ_CYYV01000016
NZ_CYYV0100001767661080,034RefSeq:NZ_CYYV01000017
NZ_CYYV0100001855541074,252RefSeq:NZ_CYYV01000018
NZ_CYYV0100001960546070,299RefSeq:NZ_CYYV01000019
NZ_CYYV0100002052480454,637RefSeq:NZ_CYYV01000020
NZ_CYYV0100002134322042,063RefSeq:NZ_CYYV01000021
NZ_CYYV0100002230240627,936RefSeq:NZ_CYYV01000022
NZ_CYYV0100002318160221,061RefSeq:NZ_CYYV01000023
NZ_CYYV0100002417160119,141RefSeq:NZ_CYYV01000024
NZ_CYYV0100002514140019,111RefSeq:NZ_CYYV01000025
NZ_CYYV0100002619154018,269RefSeq:NZ_CYYV01000026
NZ_CYYV010000271180315,507RefSeq:NZ_CYYV01000027
NZ_CYYV0100002810100011,552RefSeq:NZ_CYYV01000028
12 Undisplayed Contigs/Replicons26234726,949
Total:3,3343,161731003,653,886
Ortholog data available?Yes
Database Contents
Genes3,329
Pathways173
Enzymatic Reactions946
Transport Reactions31
Polypeptides3,210
Protein Complexes99
Enzymes598
Transporters253
Compounds718
Transcription Units2,117
tRNAs60
Protein Features4,118
GO Terms232
Database Version29.0
Sequence SourceGCF_001405555.1
Synonyms Clostridium sp. HT03-11
Clostridium sp. HT03-14
Clostridium sp. HT03-186
Clostridium sp. HT03-22
Clostridium sp. KO-38
Clostridium sp. TT-111
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Lachnospirales
Lachnospiraceae
Fusicatenibacter
Fusicatenibacter saccharivorans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA3545257
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1150298
Environmentfeces
Geographic LocationUnited Kingdom
Collection Date2013
Annotation ProviderNCBI RefSeq
Annotation Date2022-03-31
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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