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 Pseudosphingobacterium domesticum DSM 18733, 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_FOAF010000012,1332,09310302,465,563RefSeq:NZ_FOAF01000001
NZ_FOAF0100000274873873946,904RefSeq:NZ_FOAF01000002
NZ_FOAF0100000341641132554,627RefSeq:NZ_FOAF01000003
NZ_FOAF0100000429528906412,460RefSeq:NZ_FOAF01000004
NZ_FOAF0100000521120623289,099RefSeq:NZ_FOAF01000005
NZ_FOAF0100000623523212278,319RefSeq:NZ_FOAF01000006
NZ_FOAF0100000724223921276,675RefSeq:NZ_FOAF01000007
NZ_FOAF0100000819819143242,713RefSeq:NZ_FOAF01000008
NZ_FOAF0100000920920126231,149RefSeq:NZ_FOAF01000009
NZ_FOAF0100001018618411203,889RefSeq:NZ_FOAF01000010
NZ_FOAF0100001113112803202,226RefSeq:NZ_FOAF01000011
NZ_FOAF0100001211211020135,512RefSeq:NZ_FOAF01000012
NZ_FOAF010000131049761121,015RefSeq:NZ_FOAF01000013
NZ_FOAF01000014838102112,001RefSeq:NZ_FOAF01000014
NZ_FOAF01000015827822106,745RefSeq:NZ_FOAF01000015
NZ_FOAF0100001657570066,595RefSeq:NZ_FOAF01000016
NZ_FOAF0100001739362140,981RefSeq:NZ_FOAF01000017
NZ_FOAF0100001831310037,444RefSeq:NZ_FOAF01000018
NZ_FOAF0100001930281134,080RefSeq:NZ_FOAF01000019
NZ_FOAF0100002013112011,792RefSeq:NZ_FOAF01000020
NZ_FOAF0100002187018,187RefSeq:NZ_FOAF01000021
NZ_FOAF0100002211001,341RefSeq:NZ_FOAF01000022
NZ_FOAF0100002320021,178RefSeq:NZ_FOAF01000023
Total:5,5665,44947706,780,495
Ortholog data available?Yes
Database Contents
Genes5,565
Pathways188
Enzymatic Reactions1,184
Transport Reactions60
Polypeptides5,456
Protein Complexes5
Enzymes839
Transporters458
Compounds1,004
Transcription Units4,018
tRNAs41
Protein Features6,815
GO Terms18,928
Database Version29.0
Synonyms CCUG 54353
DSM 18733
LMG 23837
strain DC-186
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
FCB group
Bacteroidota/Chlorobiota group
Bacteroidota
Sphingobacteriia
Sphingobacteriales
Sphingobacteriaceae
Pseudosphingobacterium
Pseudosphingobacterium domesticum
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05661044
NCBI BioProjectPRJNA224116
NCBI-Taxonomy407022
Latitude/Longitude41.15 N 8.62 W
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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