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 Acidibacillus ferrooxidans SLC66, 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_LSUQ0100000113713403136,991RefSeq:NZ_LSUQ01000001
NZ_LSUQ0100000211911801135,524RefSeq:NZ_LSUQ01000002
NZ_LSUQ0100000312312300130,485RefSeq:NZ_LSUQ01000003
NZ_LSUQ0100000410710601119,803RefSeq:NZ_LSUQ01000004
NZ_LSUQ0100000512712070118,532RefSeq:NZ_LSUQ01000005
NZ_LSUQ0100000611911810101,975RefSeq:NZ_LSUQ01000006
NZ_LSUQ0100000710710520100,190RefSeq:NZ_LSUQ01000007
NZ_LSUQ0100000895900597,699RefSeq:NZ_LSUQ01000008
NZ_LSUQ0100000983810289,041RefSeq:NZ_LSUQ01000009
NZ_LSUQ0100001094886086,669RefSeq:NZ_LSUQ01000010
NZ_LSUQ0100001168670168,246RefSeq:NZ_LSUQ01000011
NZ_LSUQ0100001267660158,168RefSeq:NZ_LSUQ01000012
NZ_LSUQ0100001353530055,329RefSeq:NZ_LSUQ01000013
NZ_LSUQ0100001451510054,354RefSeq:NZ_LSUQ01000014
NZ_LSUQ0100001544391454,191RefSeq:NZ_LSUQ01000015
NZ_LSUQ0100001654485152,641RefSeq:NZ_LSUQ01000016
NZ_LSUQ0100001755495151,304RefSeq:NZ_LSUQ01000017
NZ_LSUQ0100001854530149,097RefSeq:NZ_LSUQ01000018
NZ_LSUQ0100001952490348,120RefSeq:NZ_LSUQ01000019
NZ_LSUQ0100002042420045,068RefSeq:NZ_LSUQ01000020
NZ_LSUQ0100002136341143,427RefSeq:NZ_LSUQ01000021
NZ_LSUQ0100002240360441,736RefSeq:NZ_LSUQ01000022
NZ_LSUQ0100002337370038,641RefSeq:NZ_LSUQ01000023
NZ_LSUQ0100002433330038,565RefSeq:NZ_LSUQ01000024
NZ_LSUQ0100002531280336,379RefSeq:NZ_LSUQ01000025
NZ_LSUQ0100002640372135,464RefSeq:NZ_LSUQ01000026
NZ_LSUQ0100002734340035,252RefSeq:NZ_LSUQ01000027
NZ_LSUQ0100002844420234,431RefSeq:NZ_LSUQ01000028
NZ_LSUQ0100002929253134,104RefSeq:NZ_LSUQ01000029
NZ_LSUQ0100003034340033,766RefSeq:NZ_LSUQ01000030
NZ_LSUQ0100003124222032,855RefSeq:NZ_LSUQ01000031
NZ_LSUQ0100003225250028,958RefSeq:NZ_LSUQ01000032
NZ_LSUQ0100003322220026,415RefSeq:NZ_LSUQ01000033
NZ_LSUQ0100003428252126,092RefSeq:NZ_LSUQ01000034
NZ_LSUQ0100003518180025,960RefSeq:NZ_LSUQ01000035
NZ_LSUQ0100003625250025,739RefSeq:NZ_LSUQ01000036
NZ_LSUQ0100003728280025,296RefSeq:NZ_LSUQ01000037
NZ_LSUQ0100003819190024,063RefSeq:NZ_LSUQ01000038
NZ_LSUQ0100003923220123,645RefSeq:NZ_LSUQ01000039
NZ_LSUQ0100004021190223,179RefSeq:NZ_LSUQ01000040
NZ_LSUQ0100004123230022,418RefSeq:NZ_LSUQ01000041
NZ_LSUQ0100004222220022,160RefSeq:NZ_LSUQ01000042
NZ_LSUQ0100004321200121,898RefSeq:NZ_LSUQ01000043
NZ_LSUQ0100004425240120,723RefSeq:NZ_LSUQ01000044
NZ_LSUQ0100004521190220,348RefSeq:NZ_LSUQ01000045
NZ_LSUQ0100004620190120,038RefSeq:NZ_LSUQ01000046
NZ_LSUQ0100004724200419,240RefSeq:NZ_LSUQ01000047
NZ_LSUQ0100004819170219,025RefSeq:NZ_LSUQ01000048
NZ_LSUQ0100004918180018,992RefSeq:NZ_LSUQ01000049
NZ_LSUQ0100005018161118,951RefSeq:NZ_LSUQ01000050
NZ_LSUQ0100005117160118,090RefSeq:NZ_LSUQ01000051
NZ_LSUQ0100005218135018,061RefSeq:NZ_LSUQ01000052
NZ_LSUQ0100005316150117,798RefSeq:NZ_LSUQ01000053
NZ_LSUQ0100005522192117,659RefSeq:NZ_LSUQ01000055
NZ_LSUQ0100005613130017,404RefSeq:NZ_LSUQ01000056
NZ_LSUQ0100005717170017,191RefSeq:NZ_LSUQ01000057
NZ_LSUQ0100005817150217,043RefSeq:NZ_LSUQ01000058
NZ_LSUQ0100005918170116,295RefSeq:NZ_LSUQ01000059
NZ_LSUQ0100006016150115,832RefSeq:NZ_LSUQ01000060
NZ_LSUQ0100006120140615,527RefSeq:NZ_LSUQ01000061
NZ_LSUQ0100006214140015,366RefSeq:NZ_LSUQ01000062
NZ_LSUQ0100006313120114,576RefSeq:NZ_LSUQ01000063
NZ_LSUQ0100006411110014,073RefSeq:NZ_LSUQ01000064
NZ_LSUQ0100006513130013,991RefSeq:NZ_LSUQ01000065
NZ_LSUQ0100006612120013,243RefSeq:NZ_LSUQ01000066
NZ_LSUQ0100006913120111,369RefSeq:NZ_LSUQ01000069
NZ_LSUQ0100007110100011,191RefSeq:NZ_LSUQ01000071
NZ_LSUQ0100007313130010,990RefSeq:NZ_LSUQ01000073
NZ_LSUQ0100007412120010,973RefSeq:NZ_LSUQ01000074
NZ_LSUQ010000761817019,787RefSeq:NZ_LSUQ01000076
NZ_LSUQ010000791111009,457RefSeq:NZ_LSUQ01000079
NZ_LSUQ010000941651106,544RefSeq:NZ_LSUQ01000094
26 Undisplayed Contigs/Replicons165162311230,782
Total:2,9592,82159793,034,429
Ortholog data available?Yes
Database Contents
Genes2,959
Pathways216
Enzymatic Reactions1,101
Transport Reactions34
Polypeptides2,909
Protein Complexes76
Enzymes616
Transporters242
Compounds792
Transcription Units1,904
tRNAs54
Protein Features3,485
GO Terms199
Database Version29.0
Sequence SourceGCF_001642725.1
Synonyms Alicyclobacillaceae bacterium ITV01
Alicyclobacillaceae bacterium SLC40
bacterium GS1
Firmicutes bacterium BSH1
Firmicutes bacterium MCF99
Gram-positive iron-oxidizing acidophile G1
Gram-positive iron-oxidizing acidophile SLC66
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Bacillales
Bacillales incertae sedis
Acidibacillus
Acidibacillus ferrooxidans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04505005
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1765683
EnvironmentMine waste
Geographic LocationUSA
Collection Date1994
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-14
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17A.