Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Actibacterium mucosum KCTC 23349, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_JFKE0100000166365553679,914RefSeq:NZ_JFKE01000001
NZ_JFKE0100000263562771629,651RefSeq:NZ_JFKE01000002
NZ_JFKE01000003552535116548,243RefSeq:NZ_JFKE01000003
NZ_JFKE0100000452952153536,952RefSeq:NZ_JFKE01000004
NZ_JFKE0100000541240831409,937RefSeq:NZ_JFKE01000005
NZ_JFKE0100000623623222222,387RefSeq:NZ_JFKE01000006
NZ_JFKE0100000717616862184,958RefSeq:NZ_JFKE01000007
NZ_JFKE0100000810610321110,630RefSeq:NZ_JFKE01000008
NZ_JFKE0100000997941298,131RefSeq:NZ_JFKE01000009
NZ_JFKE010000101011001097,999RefSeq:NZ_JFKE01000010
NZ_JFKE0100001193910287,656RefSeq:NZ_JFKE01000011
NZ_JFKE0100001239370228,861RefSeq:NZ_JFKE01000012
NZ_JFKE0100001327261027,639RefSeq:NZ_JFKE01000013
NZ_JFKE0100001419190023,659RefSeq:NZ_JFKE01000014
8 Undisplayed Contigs/Replicons24213128,720
Total:3,7103,63747263,715,337
Ortholog data available?Yes
Database Contents
Genes3,710
Pathways295
Enzymatic Reactions1,494
Transport Reactions61
Polypeptides3,647
Protein Complexes58
Enzymes809
Transporters436
Compounds1,051
Transcription Units2,207
tRNAs41
Protein Features4,649
Database Version29.0
Sequence SourceGCF_000647975.1
Synonyms Actibacterium mucosum CECT 7668
alpha proteobacterium CECT 7668
Actibacterium mucosum KCTC 23349
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodobacterales
Paracoccaceae
Actibacterium
Actibacterium mucosum
Actibacterium mucosum KCTC 23349
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02671722
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1454373
Environmentseawater
Geographic LocationSpain
Collection Date2008
Annotation ProviderNCBI RefSeq
Annotation Date2019-10-29
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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