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 Acidithiobacillus thiooxidans ATCC 19377, 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_AFOH0100012211910946116,035RefSeq:NZ_AFOH01000122
NZ_AFOH0100011710710610101,737RefSeq:NZ_AFOH01000117
NZ_AFOH01000056928921100,183RefSeq:NZ_AFOH01000056
NZ_AFOH010000401061041199,400RefSeq:NZ_AFOH01000040
NZ_AFOH0100004675730275,279RefSeq:NZ_AFOH01000046
NZ_AFOH0100008267641271,791RefSeq:NZ_AFOH01000082
NZ_AFOH0100010680772171,261RefSeq:NZ_AFOH01000106
NZ_AFOH0100004768650366,987RefSeq:NZ_AFOH01000047
NZ_AFOH0100001374740066,127RefSeq:NZ_AFOH01000013
NZ_AFOH0100000656532163,894RefSeq:NZ_AFOH01000006
NZ_AFOH0100005055550059,542RefSeq:NZ_AFOH01000050
NZ_AFOH0100013059551357,615RefSeq:NZ_AFOH01000130
NZ_AFOH0100008158550356,736RefSeq:NZ_AFOH01000081
NZ_AFOH0100014064610356,386RefSeq:NZ_AFOH01000140
NZ_AFOH0100013248471055,629RefSeq:NZ_AFOH01000132
NZ_AFOH0100004134340051,906RefSeq:NZ_AFOH01000041
NZ_AFOH0100003950443351,476RefSeq:NZ_AFOH01000039
NZ_AFOH0100012052455250,232RefSeq:NZ_AFOH01000120
NZ_AFOH0100003741392047,649RefSeq:NZ_AFOH01000037
NZ_AFOH0100005142420046,573RefSeq:NZ_AFOH01000051
NZ_AFOH0100003641410044,626RefSeq:NZ_AFOH01000036
NZ_AFOH0100004438371043,737RefSeq:NZ_AFOH01000044
NZ_AFOH0100002548460243,225RefSeq:NZ_AFOH01000025
NZ_AFOH0100011033330042,790RefSeq:NZ_AFOH01000110
NZ_AFOH0100010837370041,410RefSeq:NZ_AFOH01000108
NZ_AFOH0100010741390239,609RefSeq:NZ_AFOH01000107
NZ_AFOH0100012137360139,167RefSeq:NZ_AFOH01000121
NZ_AFOH0100004543410237,358RefSeq:NZ_AFOH01000045
NZ_AFOH0100013734330136,457RefSeq:NZ_AFOH01000137
NZ_AFOH0100002835330235,921RefSeq:NZ_AFOH01000028
NZ_AFOH0100002932310135,806RefSeq:NZ_AFOH01000029
NZ_AFOH0100012336340235,081RefSeq:NZ_AFOH01000123
NZ_AFOH0100004235330233,490RefSeq:NZ_AFOH01000042
NZ_AFOH0100013842400233,365RefSeq:NZ_AFOH01000138
NZ_AFOH0100013132292133,049RefSeq:NZ_AFOH01000131
NZ_AFOH0100013935320332,674RefSeq:NZ_AFOH01000139
NZ_AFOH0100000320191030,121RefSeq:NZ_AFOH01000003
NZ_AFOH0100004327261030,043RefSeq:NZ_AFOH01000043
NZ_AFOH0100001128270128,970RefSeq:NZ_AFOH01000011
NZ_AFOH0100013319190028,887RefSeq:NZ_AFOH01000133
NZ_AFOH0100001234330127,251RefSeq:NZ_AFOH01000012
NZ_AFOH0100000726260026,409RefSeq:NZ_AFOH01000007
NZ_AFOH0100001030281126,015RefSeq:NZ_AFOH01000010
NZ_AFOH0100011128280025,528RefSeq:NZ_AFOH01000111
NZ_AFOH0100013630260425,062RefSeq:NZ_AFOH01000136
NZ_AFOH0100013524240024,662RefSeq:NZ_AFOH01000135
NZ_AFOH0100003033312023,739RefSeq:NZ_AFOH01000030
NZ_AFOH0100003826240223,675RefSeq:NZ_AFOH01000038
NZ_AFOH0100005216160023,450RefSeq:NZ_AFOH01000052
NZ_AFOH0100009821191122,480RefSeq:NZ_AFOH01000098
NZ_AFOH0100010527270022,342RefSeq:NZ_AFOH01000105
NZ_AFOH0100011925240120,452RefSeq:NZ_AFOH01000119
NZ_AFOH0100008319161219,468RefSeq:NZ_AFOH01000083
NZ_AFOH0100001419190017,872RefSeq:NZ_AFOH01000014
NZ_AFOH0100000413101216,790RefSeq:NZ_AFOH01000004
NZ_AFOH0100014116151016,681RefSeq:NZ_AFOH01000141
NZ_AFOH0100006934303116,663RefSeq:NZ_AFOH01000069
NZ_AFOH0100007825230216,582RefSeq:NZ_AFOH01000078
NZ_AFOH0100011814111215,840RefSeq:NZ_AFOH01000118
NZ_AFOH0100007115150015,163RefSeq:NZ_AFOH01000071
NZ_AFOH0100012416151014,616RefSeq:NZ_AFOH01000124
NZ_AFOH0100009617150214,419RefSeq:NZ_AFOH01000096
NZ_AFOH0100000214121113,681RefSeq:NZ_AFOH01000002
NZ_AFOH0100000112120013,323RefSeq:NZ_AFOH01000001
NZ_AFOH0100010117160113,003RefSeq:NZ_AFOH01000101
NZ_AFOH0100012612110112,600RefSeq:NZ_AFOH01000126
NZ_AFOH0100015013130012,441RefSeq:NZ_AFOH01000150
NZ_AFOH010000321191111,530RefSeq:NZ_AFOH01000032
NZ_AFOH0100005713130011,377RefSeq:NZ_AFOH01000057
NZ_AFOH0100000512120011,184RefSeq:NZ_AFOH01000005
NZ_AFOH0100015812120010,925RefSeq:NZ_AFOH01000158
NZ_AFOH0100011211100110,137RefSeq:NZ_AFOH01000112
NZ_AFOH0100008713121010,042RefSeq:NZ_AFOH01000087
NZ_AFOH010001131614029,016RefSeq:NZ_AFOH01000113
NZ_AFOH010000671210025,366RefSeq:NZ_AFOH01000067
89 Undisplayed Contigs/Replicons274267730327,860
Total:3,0202,855521133,019,868
Ortholog data available?Yes
Database Contents
Genes3,019
Pathways199
Enzymatic Reactions1,075
Transport Reactions29
Polypeptides2,960
Protein Complexes54
Enzymes687
Transporters223
Compounds755
Transcription Units1,650
tRNAs43
Protein Features3,357
GO Terms160
Database Version29.0
Sequence SourceGCF_000227215.1
Synonyms Acidithiobacillus thiooxidans strain ATCC 19377
Acidithiobacillus thiooxidans str. ATCC 19377
Acidithiobacillus thiooxidans ATCC 19377
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Acidithiobacillia
Acidithiobacillales
Acidithiobacillaceae
Acidithiobacillus
Acidithiobacillus thiooxidans
Acidithiobacillus thiooxidans ATCC 19377
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02469801
NCBI BioProjectPRJNA224116
NCBI-Taxonomy637390
Annotation ProviderNCBI RefSeq
Annotation Date2022-02-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.0
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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