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 Halorubrum lipolyticum DSM 21995, 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_AOJG0100003030529618303,345RefSeq:NZ_AOJG01000030
NZ_AOJG0100004130528997274,445RefSeq:NZ_AOJG01000041
NZ_AOJG01000028204194010242,385RefSeq:NZ_AOJG01000028
NZ_AOJG0100001217016721178,866RefSeq:NZ_AOJG01000012
NZ_AOJG0100000915314814167,056RefSeq:NZ_AOJG01000009
NZ_AOJG0100001716415644164,598RefSeq:NZ_AOJG01000017
NZ_AOJG0100000115715133154,174RefSeq:NZ_AOJG01000001
NZ_AOJG0100003813813620149,188RefSeq:NZ_AOJG01000038
NZ_AOJG0100002512711935148,576RefSeq:NZ_AOJG01000025
NZ_AOJG0100001811411103137,502RefSeq:NZ_AOJG01000018
NZ_AOJG0100000711911522130,902RefSeq:NZ_AOJG01000007
NZ_AOJG0100000612011415116,945RefSeq:NZ_AOJG01000006
NZ_AOJG0100001011110641105,871RefSeq:NZ_AOJG01000010
NZ_AOJG0100004011811314105,243RefSeq:NZ_AOJG01000040
NZ_AOJG0100001591861492,121RefSeq:NZ_AOJG01000015
NZ_AOJG0100000874680676,044RefSeq:NZ_AOJG01000008
NZ_AOJG0100003954512171,174RefSeq:NZ_AOJG01000039
NZ_AOJG0100000375712271,042RefSeq:NZ_AOJG01000003
NZ_AOJG0100001366651069,584RefSeq:NZ_AOJG01000013
NZ_AOJG0100003461600166,483RefSeq:NZ_AOJG01000034
NZ_AOJG0100000259553160,996RefSeq:NZ_AOJG01000002
NZ_AOJG0100002053457158,663RefSeq:NZ_AOJG01000020
NZ_AOJG0100001956513257,357RefSeq:NZ_AOJG01000019
NZ_AOJG0100003746430355,730RefSeq:NZ_AOJG01000037
NZ_AOJG0100000447440355,667RefSeq:NZ_AOJG01000004
NZ_AOJG0100001154540052,765RefSeq:NZ_AOJG01000011
NZ_AOJG0100003342401143,146RefSeq:NZ_AOJG01000033
NZ_AOJG0100003126260032,772RefSeq:NZ_AOJG01000031
NZ_AOJG0100003229290032,758RefSeq:NZ_AOJG01000032
NZ_AOJG0100003528260230,868RefSeq:NZ_AOJG01000035
NZ_AOJG0100002724220228,487RefSeq:NZ_AOJG01000027
NZ_AOJG0100002327260126,774RefSeq:NZ_AOJG01000023
NZ_AOJG0100001424240024,678RefSeq:NZ_AOJG01000014
NZ_AOJG0100002415150012,583RefSeq:NZ_AOJG01000024
7 Undisplayed Contigs/Replicons16160426,254
Total:3,2763,13253913,425,042
Ortholog data available?Yes
Database Contents
Genes3,276
Pathways116
Enzymatic Reactions766
Transport Reactions46
Polypeptides3,138
Protein Complexes29
Enzymes505
Transporters249
Compounds671
Transcription Units2,541
tRNAs47
Protein Features3,310
Database Version29.0
Sequence SourceGCF_000337375.1
Taxonomic Lineage cellular organisms
Archaea
Euryarchaeota
Stenosarchaea group
Halobacteria
Halobacteriales
Haloferacaceae
Halorubrum
Halorubrum lipolyticum
Halorubrum lipolyticum DSM 21995
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471632
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1227482
Annotation ProviderNCBI
Annotation Date2017-03-29
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+
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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