Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 27-Feb-2018 from the annotated genome of Flavobacterium terrigena DSM 17934, 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 22.0) [Karp16, Karp11] using MetaCyc version 21.5 [Caspi18]. 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 Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_FNYA0100000171269697742,471RefSeq:NZ_FNYA01000001
NZ_FNYA0100000261260093727,238RefSeq:NZ_FNYA01000002
NZ_FNYA0100000322021811283,557RefSeq:NZ_FNYA01000003
NZ_FNYA0100000427126524275,559RefSeq:NZ_FNYA01000004
NZ_FNYA0100000523923261257,408RefSeq:NZ_FNYA01000005
NZ_FNYA0100000621921612214,956RefSeq:NZ_FNYA01000006
NZ_FNYA0100000720920351197,963RefSeq:NZ_FNYA01000007
NZ_FNYA0100000813513221150,061RefSeq:NZ_FNYA01000008
NZ_FNYA0100000973720181,186RefSeq:NZ_FNYA01000009
NZ_FNYA0100001074722076,873RefSeq:NZ_FNYA01000010
NZ_FNYA0100001135332041,503RefSeq:NZ_FNYA01000011
NZ_FNYA0100001221200140,528RefSeq:NZ_FNYA01000012
NZ_FNYA0100001324230137,528RefSeq:NZ_FNYA01000013
NZ_FNYA0100001416150115,140RefSeq:NZ_FNYA01000014
NZ_FNYA0100001514130115,109RefSeq:NZ_FNYA01000015
NZ_FNYA0100001621016,221RefSeq:NZ_FNYA01000016
NZ_FNYA0100001750505,914RefSeq:NZ_FNYA01000017
NZ_FNYA0100001832013,200RefSeq:NZ_FNYA01000018
Total:2,8842,81344273,172,415
Ortholog data available?Yes
Database Contents
Genes2,885
Pathways154
Enzymatic Reactions944
Transport Reactions32
Polypeptides2,815
Protein Complexes0
Enzymes577
Transporters163
Compounds791
Transcription Units1,868
tRNAs39
Protein Features3,151
GO Terms10,473
Database Version29.0
Synonyms DSM 17934
KCTC 12761
strain DS-20
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
FCB group
Bacteroidota/Chlorobiota group
Bacteroidota
Flavobacteriia
Flavobacteriales
Flavobacteriaceae
Flavobacterium
Flavobacterium terrigena
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05660918
NCBI BioProjectPRJNA224116
NCBI-Taxonomy402734
NCBI Genome Typerepresentative

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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