Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 25-Oct-2020 from the annotated genome of Acidiplasma aeolicum VT, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_LKBG0100000166624051,578RefSeq:NZ_LKBG01000001
NZ_LKBG0100011144431044,244RefSeq:NZ_LKBG01000111
NZ_LKBG0100022045450041,442RefSeq:NZ_LKBG01000220
NZ_LKBG0100023141400140,359RefSeq:NZ_LKBG01000231
NZ_LKBG0100024249471137,571RefSeq:NZ_LKBG01000242
NZ_LKBG0100025342420036,082RefSeq:NZ_LKBG01000253
NZ_LKBG0100026436350132,390RefSeq:NZ_LKBG01000264
NZ_LKBG0100027534331029,169RefSeq:NZ_LKBG01000275
NZ_LKBG0100028630300027,759RefSeq:NZ_LKBG01000286
NZ_LKBG0100000219180123,196RefSeq:NZ_LKBG01000002
NZ_LKBG0100001223221022,835RefSeq:NZ_LKBG01000012
NZ_LKBG0100002319190021,606RefSeq:NZ_LKBG01000023
NZ_LKBG0100003418180021,294RefSeq:NZ_LKBG01000034
NZ_LKBG0100004518170120,605RefSeq:NZ_LKBG01000045
NZ_LKBG0100005621210020,098RefSeq:NZ_LKBG01000056
NZ_LKBG0100006718161118,697RefSeq:NZ_LKBG01000067
NZ_LKBG0100007822192117,364RefSeq:NZ_LKBG01000078
NZ_LKBG0100008916151016,753RefSeq:NZ_LKBG01000089
NZ_LKBG0100010018171016,506RefSeq:NZ_LKBG01000100
NZ_LKBG0100011217142115,681RefSeq:NZ_LKBG01000112
NZ_LKBG0100012313130015,599RefSeq:NZ_LKBG01000123
NZ_LKBG0100013414122015,172RefSeq:NZ_LKBG01000134
NZ_LKBG0100014513130015,087RefSeq:NZ_LKBG01000145
NZ_LKBG0100015618180014,837RefSeq:NZ_LKBG01000156
NZ_LKBG0100016715150014,379RefSeq:NZ_LKBG01000167
NZ_LKBG0100017818170113,993RefSeq:NZ_LKBG01000178
NZ_LKBG0100018917150213,856RefSeq:NZ_LKBG01000189
NZ_LKBG0100020015150013,778RefSeq:NZ_LKBG01000200
NZ_LKBG0100021114140013,746RefSeq:NZ_LKBG01000211
NZ_LKBG0100022121210013,674RefSeq:NZ_LKBG01000221
NZ_LKBG0100022212110113,650RefSeq:NZ_LKBG01000222
NZ_LKBG0100022318180013,567RefSeq:NZ_LKBG01000223
NZ_LKBG0100022411110013,396RefSeq:NZ_LKBG01000224
NZ_LKBG0100022714140013,046RefSeq:NZ_LKBG01000227
NZ_LKBG0100022815150013,032RefSeq:NZ_LKBG01000228
NZ_LKBG0100022913120113,007RefSeq:NZ_LKBG01000229
NZ_LKBG0100023014140012,916RefSeq:NZ_LKBG01000230
NZ_LKBG0100023216160012,839RefSeq:NZ_LKBG01000232
NZ_LKBG0100023315113112,449RefSeq:NZ_LKBG01000233
NZ_LKBG0100023515131112,214RefSeq:NZ_LKBG01000235
NZ_LKBG0100023912110111,466RefSeq:NZ_LKBG01000239
NZ_LKBG0100024013121011,393RefSeq:NZ_LKBG01000240
NZ_LKBG0100024116141111,281RefSeq:NZ_LKBG01000241
NZ_LKBG0100024414121111,132RefSeq:NZ_LKBG01000244
NZ_LKBG0100024516123111,090RefSeq:NZ_LKBG01000245
NZ_LKBG0100025015131110,803RefSeq:NZ_LKBG01000250
NZ_LKBG0100025112120010,199RefSeq:NZ_LKBG01000251
NZ_LKBG010002591210028,879RefSeq:NZ_LKBG01000259
248 Undisplayed Contigs/Replicons7016782386863,192
Total:1,7941,635511081,778,901
Ortholog data available?Yes
Database Contents
Genes1,794
Pathways83
Enzymatic Reactions582
Transport Reactions17
Polypeptides1,759
Protein Complexes13
Enzymes361
Transporters179
Compounds554
Transcription Units1,301
tRNAs46
Protein Features1,741
GO Terms6,073
Database Version29.0
Sequence SourceGCF_001402945.1
Taxonomic Lineage cellular organisms
Archaea
Candidatus Thermoplasmatota
Thermoplasmata
Thermoplasmatales
Ferroplasmaceae
Acidiplasma
Acidiplasma aeolicum
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04087216
NCBI BioProjectPRJNA224116
NCBI-Taxonomy507754
Environmenthydrothermal pool (sand/gravel)
Geographic LocationItaly
Collection Date2009
Annotation ProviderNCBI RefSeq
Annotation Date2020-02-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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