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 Methanomassiliicoccus luminyensis B10, 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_CAJE01000012763745186765,266RefSeq:NZ_CAJE01000012
NZ_CAJE01000013334322127299,984RefSeq:NZ_CAJE01000013
NZ_CAJE0100001518017732177,149RefSeq:NZ_CAJE01000015
NZ_CAJE0100000414814445167,531RefSeq:NZ_CAJE01000004
NZ_CAJE0100002414714702152,908RefSeq:NZ_CAJE01000024
NZ_CAJE0100002112212021126,785RefSeq:NZ_CAJE01000021
NZ_CAJE01000003929201101,706RefSeq:NZ_CAJE01000003
NZ_CAJE0100002398962599,984RefSeq:NZ_CAJE01000023
NZ_CAJE0100001786860298,672RefSeq:NZ_CAJE01000017
NZ_CAJE0100002086833190,121RefSeq:NZ_CAJE01000020
NZ_CAJE0100001486851185,479RefSeq:NZ_CAJE01000014
NZ_CAJE0100001161610165,531RefSeq:NZ_CAJE01000011
NZ_CAJE0100000562602163,410RefSeq:NZ_CAJE01000005
NZ_CAJE0100001977752162,406RefSeq:NZ_CAJE01000019
NZ_CAJE0100000650500150,647RefSeq:NZ_CAJE01000006
NZ_CAJE0100000139381034,612RefSeq:NZ_CAJE01000001
NZ_CAJE0100002225241034,288RefSeq:NZ_CAJE01000022
NZ_CAJE0100002634331031,549RefSeq:NZ_CAJE01000026
NZ_CAJE0100000725250229,165RefSeq:NZ_CAJE01000007
NZ_CAJE0100001830300127,211RefSeq:NZ_CAJE01000018
NZ_CAJE0100000922211126,514RefSeq:NZ_CAJE01000009
NZ_CAJE01000010990111,815RefSeq:NZ_CAJE01000010
NZ_CAJE0100001644018,413RefSeq:NZ_CAJE01000016
NZ_CAJE0100000822003,723RefSeq:NZ_CAJE01000008
NZ_CAJE0100002522003,111RefSeq:NZ_CAJE01000025
NZ_CAJE0100000233002,253RefSeq:NZ_CAJE01000002
Total:2,6302,53453432,620,233
Ortholog data available?Yes
Database Contents
Genes2,587
Pathways91
Enzymatic Reactions632
Transport Reactions34
Polypeptides2,546
Protein Complexes26
Enzymes390
Transporters197
Compounds578
Transcription Units1,822
tRNAs47
Protein Features2,748
Database Version29.6
Sequence SourceGCF_000308215.1
Synonyms Methanomassiliicoccus luminyensis str. B10
Methanomassiliicoccus luminyensis strain B10
Methanomassiliicoccus luminyensis B10
Taxonomic Lineage cellular organisms
Archaea
Methanobacteriati
Thermoplasmatota
Thermoplasmata
Methanomassiliicoccales
Methanomassiliicoccaceae
Methanomassiliicoccus
Methanomassiliicoccus luminyensis
Methanomassiliicoccus luminyensis B10
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA3138426
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1175296
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-7
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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