Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Marinilactibacillus psychrotolerans DSM 19582, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_FMZD0100000121521410229,026RefSeq:NZ_FMZD01000001
NZ_FMZD0100000216716502188,868RefSeq:NZ_FMZD01000002
NZ_FMZD0100000318418031181,649RefSeq:NZ_FMZD01000003
NZ_FMZD0100000414314210145,792RefSeq:NZ_FMZD01000004
NZ_FMZD0100000514313931137,238RefSeq:NZ_FMZD01000005
NZ_FMZD0100000612512401134,520RefSeq:NZ_FMZD01000006
NZ_FMZD0100000714714610132,788RefSeq:NZ_FMZD01000007
NZ_FMZD0100000811511311117,953RefSeq:NZ_FMZD01000008
NZ_FMZD0100000910410211101,974RefSeq:NZ_FMZD01000009
NZ_FMZD01000010909000100,084RefSeq:NZ_FMZD01000010
NZ_FMZD0100001179780187,782RefSeq:NZ_FMZD01000011
NZ_FMZD0100001275740186,203RefSeq:NZ_FMZD01000012
NZ_FMZD0100001361600169,361RefSeq:NZ_FMZD01000013
NZ_FMZD0100001456530363,120RefSeq:NZ_FMZD01000014
NZ_FMZD0100001547470060,433RefSeq:NZ_FMZD01000015
NZ_FMZD0100001661610060,116RefSeq:NZ_FMZD01000016
NZ_FMZD0100001746460057,878RefSeq:NZ_FMZD01000017
NZ_FMZD0100001851501056,252RefSeq:NZ_FMZD01000018
NZ_FMZD0100001943403042,152RefSeq:NZ_FMZD01000019
NZ_FMZD0100002041410040,952RefSeq:NZ_FMZD01000020
NZ_FMZD0100002139390039,924RefSeq:NZ_FMZD01000021
NZ_FMZD0100002246388036,734RefSeq:NZ_FMZD01000022
NZ_FMZD0100002337360136,066RefSeq:NZ_FMZD01000023
NZ_FMZD0100002425250035,849RefSeq:NZ_FMZD01000024
NZ_FMZD0100002533301235,122RefSeq:NZ_FMZD01000025
NZ_FMZD0100002633321032,823RefSeq:NZ_FMZD01000026
NZ_FMZD0100002725240127,511RefSeq:NZ_FMZD01000027
NZ_FMZD0100002825250023,690RefSeq:NZ_FMZD01000028
NZ_FMZD0100002919190022,826RefSeq:NZ_FMZD01000029
NZ_FMZD0100003017170022,565RefSeq:NZ_FMZD01000030
NZ_FMZD0100003113130016,481RefSeq:NZ_FMZD01000031
NZ_FMZD0100003211110014,280RefSeq:NZ_FMZD01000032
NZ_FMZD0100003313112012,232RefSeq:NZ_FMZD01000033
NZ_FMZD0100003512111010,300RefSeq:NZ_FMZD01000035
NZ_FMZD010000421221001,925RefSeq:NZ_FMZD01000042
NZ_FMZD010000451401401,743RefSeq:NZ_FMZD01000045
11 Undisplayed Contigs/Replicons31293444,372
Total:2,4032,32755212,508,584
Ortholog data available?Yes
Database Contents
Genes2,398
Pathways183
Enzymatic Reactions874
Transport Reactions75
Polypeptides2,360
Protein Complexes95
Enzymes519
Transporters235
Compounds693
Transcription Units1,574
tRNAs43
Protein Features3,050
GO Terms224
Database Version29.0
Sequence SourceGCF_900101525.1
Synonyms Marinolactobacillus psychrotolerans
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Lactobacillales
Carnobacteriaceae
Marinilactibacillus
Marinilactibacillus psychrotolerans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04488013
NCBI BioProjectPRJNA224116
NCBI-Taxonomy191770
Annotation ProviderNCBI RefSeq
Annotation Date2021-07-14
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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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