Database Authors
Pallavi Subhraveti1, Peter Midford, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2019 from the annotated genome of Haloferax gibbonsii ATCC 33959, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.0 [Caspi18]. 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 Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AOLJ01000011891864207846,450RefSeq:NZ_AOLJ01000011
NZ_AOLJ0100002828628213318,423RefSeq:NZ_AOLJ01000028
NZ_AOLJ0100001828527609311,056RefSeq:NZ_AOLJ01000018
NZ_AOLJ0100002228727935286,445RefSeq:NZ_AOLJ01000022
NZ_AOLJ0100002426025523244,321RefSeq:NZ_AOLJ01000024
NZ_AOLJ0100001523523050232,176RefSeq:NZ_AOLJ01000015
NZ_AOLJ0100001924022992230,556RefSeq:NZ_AOLJ01000019
NZ_AOLJ0100001425825152228,641RefSeq:NZ_AOLJ01000014
NZ_AOLJ0100000518617907217,981RefSeq:NZ_AOLJ01000005
NZ_AOLJ0100000313012802157,070RefSeq:NZ_AOLJ01000003
NZ_AOLJ0100002516115542150,267RefSeq:NZ_AOLJ01000025
NZ_AOLJ01000027130113017143,919RefSeq:NZ_AOLJ01000027
NZ_AOLJ01000001117105012134,315RefSeq:NZ_AOLJ01000001
NZ_AOLJ0100001313212660126,143RefSeq:NZ_AOLJ01000013
NZ_AOLJ01000012939030101,479RefSeq:NZ_AOLJ01000012
NZ_AOLJ0100001771681273,175RefSeq:NZ_AOLJ01000017
NZ_AOLJ0100000778711669,291RefSeq:NZ_AOLJ01000007
NZ_AOLJ0100002641400144,699RefSeq:NZ_AOLJ01000026
NZ_AOLJ0100000429270238,728RefSeq:NZ_AOLJ01000004
NZ_AOLJ0100000632290337,616RefSeq:NZ_AOLJ01000006
NZ_AOLJ0100002015132014,708RefSeq:NZ_AOLJ01000020
9 Undisplayed Contigs/Replicons32320849,863
Total:3,9973,84262934,057,322
Ortholog data available?Yes
Database Contents
Genes3,997
Pathways118
Enzymatic Reactions1,034
Transport Reactions9
Polypeptides3,848
Protein Complexes16
Enzymes625
Transporters410
Compounds913
Transcription Units3,084
tRNAs57
Database Version29.0
Taxonomic Lineage cellular organisms
Archaea
Euryarchaeota
Stenosarchaea group
Halobacteria
Halobacteriales
Haloferacaceae
Haloferax
Haloferax gibbonsii
Haloferax gibbonsii ATCC 33959
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471685
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1227459
Annotation ProviderNCBI
Annotation Date2017-04-8
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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