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 25-Oct-2020 from the annotated genome of Acidobacteriaceae bacterium URHE0068 URHE0068, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_KK21117332631538399,486RefSeq:NZ_KK211173
NZ_JIAQ0100000328728511372,521RefSeq:NZ_JIAQ01000003
NZ_KK21117430029064365,668RefSeq:NZ_KK211174
NZ_JIAQ0100000623923612352,427RefSeq:NZ_JIAQ01000006
NZ_JIAQ0100000730730025351,169RefSeq:NZ_JIAQ01000007
NZ_JIAQ0100000824524005341,900RefSeq:NZ_JIAQ01000008
NZ_JIAQ0100000926125812324,280RefSeq:NZ_JIAQ01000009
NZ_JIAQ0100001020920243261,103RefSeq:NZ_JIAQ01000010
NZ_JIAQ0100001119419013214,870RefSeq:NZ_JIAQ01000011
NZ_JIAQ0100001216416310203,032RefSeq:NZ_JIAQ01000012
NZ_JIAQ0100001315714863201,201RefSeq:NZ_JIAQ01000013
NZ_JIAQ0100001417116722189,812RefSeq:NZ_JIAQ01000014
NZ_JIAQ0100001515614925184,063RefSeq:NZ_JIAQ01000015
NZ_JIAQ0100001614013442163,235RefSeq:NZ_JIAQ01000016
NZ_JIAQ0100001714313625163,101RefSeq:NZ_JIAQ01000017
NZ_KK21117511110722157,678RefSeq:NZ_KK211175
NZ_JIAQ0100002010910900152,186RefSeq:NZ_JIAQ01000020
NZ_JIAQ0100002111410914139,923RefSeq:NZ_JIAQ01000021
NZ_JIAQ01000022878610115,051RefSeq:NZ_JIAQ01000022
NZ_JIAQ0100002310610402109,602RefSeq:NZ_JIAQ01000023
NZ_KK211176888305107,124RefSeq:NZ_KK211176
NZ_JIAQ01000026898621104,770RefSeq:NZ_JIAQ01000026
NZ_JIAQ01000027787602104,668RefSeq:NZ_JIAQ01000027
NZ_JIAQ01000028616001100,889RefSeq:NZ_JIAQ01000028
NZ_JIAQ01000029767222100,245RefSeq:NZ_JIAQ01000029
NZ_JIAQ0100003061600194,165RefSeq:NZ_JIAQ01000030
NZ_JIAQ0100003168680088,506RefSeq:NZ_JIAQ01000031
NZ_JIAQ0100003271682184,114RefSeq:NZ_JIAQ01000032
NZ_JIAQ0100003368660280,607RefSeq:NZ_JIAQ01000033
NZ_JIAQ0100003453530070,987RefSeq:NZ_JIAQ01000034
NZ_JIAQ0100003561600170,808RefSeq:NZ_JIAQ01000035
NZ_JIAQ0100003662620070,719RefSeq:NZ_JIAQ01000036
NZ_JIAQ0100003745421262,490RefSeq:NZ_JIAQ01000037
NZ_JIAQ0100003850490159,381RefSeq:NZ_JIAQ01000038
NZ_JIAQ0100003931280354,527RefSeq:NZ_JIAQ01000039
NZ_JIAQ0100004047460154,462RefSeq:NZ_JIAQ01000040
NZ_KK21117741370448,296RefSeq:NZ_KK211177
NZ_JIAQ0100004131301047,652RefSeq:NZ_JIAQ01000041
NZ_JIAQ0100004435320340,042RefSeq:NZ_JIAQ01000044
NZ_JIAQ0100004531291132,962RefSeq:NZ_JIAQ01000045
NZ_JIAQ0100004615140129,380RefSeq:NZ_JIAQ01000046
NZ_JIAQ0100004728271027,911RefSeq:NZ_JIAQ01000047
NZ_JIAQ0100004821201024,778RefSeq:NZ_JIAQ01000048
NZ_JIAQ0100004923200323,161RefSeq:NZ_JIAQ01000049
NZ_JIAQ0100005020180220,715RefSeq:NZ_JIAQ01000050
NZ_JIAQ0100005114140019,920RefSeq:NZ_JIAQ01000051
NZ_JIAQ0100005216160018,266RefSeq:NZ_JIAQ01000052
NZ_JIAQ0100005313130018,246RefSeq:NZ_JIAQ01000053
NZ_JIAQ0100005412120017,311RefSeq:NZ_JIAQ01000054
NZ_JIAQ0100005613121015,782RefSeq:NZ_JIAQ01000056
NZ_JIAQ0100005713130015,733RefSeq:NZ_JIAQ01000057
NZ_JIAQ0100005813120115,571RefSeq:NZ_JIAQ01000058
NZ_JIAQ0100006021180314,647RefSeq:NZ_JIAQ01000060
NZ_JIAQ0100005913111114,623RefSeq:NZ_JIAQ01000059
NZ_JIAQ0100006113110213,239RefSeq:NZ_JIAQ01000061
NZ_JIAQ0100006311110012,531RefSeq:NZ_JIAQ01000063
NZ_JIAQ0100006514110311,524RefSeq:NZ_JIAQ01000065
26 Undisplayed Contigs/Replicons909005126,125
Total:5,3415,178531106,679,185
Ortholog data available?No
Database Contents
Genes5,341
Pathways224
Enzymatic Reactions1,260
Transport Reactions52
Polypeptides5,230
Protein Complexes30
Enzymes792
Transporters341
Compounds922
Transcription Units4,161
tRNAs47
Protein Features6,245
Database Version29.0
Sequence SourceGCF_000620725.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Acidobacteriota
Acidobacteriia
Acidobacteriales
Acidobacteriaceae
unclassified Acidobacteriaceae
Acidobacteriaceae bacterium URHE0068
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02743954
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1380348
EnvironmentSoil
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-9
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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