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 Acidithrix ferrooxidans Py-F3, 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_JXYS0100000112812701188,300RefSeq:NZ_JXYS01000001
NZ_JXYS0100001811711322143,436RefSeq:NZ_JXYS01000018
NZ_JXYS010000261029741114,129RefSeq:NZ_JXYS01000026
NZ_JXYS01000025908703105,714RefSeq:NZ_JXYS01000025
NZ_JXYS01000029797504101,058RefSeq:NZ_JXYS01000029
NZ_JXYS0100002776723193,794RefSeq:NZ_JXYS01000027
NZ_JXYS0100001293874281,363RefSeq:NZ_JXYS01000012
NZ_JXYS0100003162590377,497RefSeq:NZ_JXYS01000031
NZ_JXYS0100002361581276,987RefSeq:NZ_JXYS01000023
NZ_JXYS0100007860581172,506RefSeq:NZ_JXYS01000078
NZ_JXYS0100000755521270,535RefSeq:NZ_JXYS01000007
NZ_JXYS0100000460542468,663RefSeq:NZ_JXYS01000004
NZ_JXYS0100006153510265,621RefSeq:NZ_JXYS01000061
NZ_JXYS0100000350432564,243RefSeq:NZ_JXYS01000003
NZ_JXYS0100007542420063,086RefSeq:NZ_JXYS01000075
NZ_JXYS0100003446440259,002RefSeq:NZ_JXYS01000034
NZ_JXYS0100007046460057,433RefSeq:NZ_JXYS01000070
NZ_JXYS0100008147461054,697RefSeq:NZ_JXYS01000081
NZ_JXYS0100008052501154,440RefSeq:NZ_JXYS01000080
NZ_JXYS0100007339390049,113RefSeq:NZ_JXYS01000073
NZ_JXYS0100007241380348,172RefSeq:NZ_JXYS01000072
NZ_JXYS0100006639381046,883RefSeq:NZ_JXYS01000066
NZ_JXYS0100007939370243,682RefSeq:NZ_JXYS01000079
NZ_JXYS0100003531290243,319RefSeq:NZ_JXYS01000035
NZ_JXYS0100008331310042,826RefSeq:NZ_JXYS01000083
NZ_JXYS0100002227261041,611RefSeq:NZ_JXYS01000022
NZ_JXYS0100007435330240,925RefSeq:NZ_JXYS01000074
NZ_JXYS0100006535321240,592RefSeq:NZ_JXYS01000065
NZ_JXYS0100006827260139,355RefSeq:NZ_JXYS01000068
NZ_JXYS0100006240372138,554RefSeq:NZ_JXYS01000062
NZ_JXYS0100006729290037,795RefSeq:NZ_JXYS01000067
NZ_JXYS0100006935301436,518RefSeq:NZ_JXYS01000069
NZ_JXYS0100003629262135,478RefSeq:NZ_JXYS01000036
NZ_JXYS0100009128260235,139RefSeq:NZ_JXYS01000091
NZ_JXYS0100001733293134,687RefSeq:NZ_JXYS01000017
NZ_JXYS0100008726240233,391RefSeq:NZ_JXYS01000087
NZ_JXYS0100010130290133,321RefSeq:NZ_JXYS01000101
NZ_JXYS0100000522210132,778RefSeq:NZ_JXYS01000005
NZ_JXYS0100003220180232,555RefSeq:NZ_JXYS01000032
NZ_JXYS0100008927251132,431RefSeq:NZ_JXYS01000089
NZ_JXYS0100008830262231,717RefSeq:NZ_JXYS01000088
NZ_JXYS0100009220180231,037RefSeq:NZ_JXYS01000092
NZ_JXYS0100007126242030,828RefSeq:NZ_JXYS01000071
NZ_JXYS0100010427261029,212RefSeq:NZ_JXYS01000104
NZ_JXYS0100013329280129,142RefSeq:NZ_JXYS01000133
NZ_JXYS0100010221200128,388RefSeq:NZ_JXYS01000102
NZ_JXYS0100011127243028,210RefSeq:NZ_JXYS01000111
NZ_JXYS0100004229270228,083RefSeq:NZ_JXYS01000042
NZ_JXYS0100003024221127,821RefSeq:NZ_JXYS01000030
NZ_JXYS0100001029290027,518RefSeq:NZ_JXYS01000010
NZ_JXYS0100008422210127,418RefSeq:NZ_JXYS01000084
NZ_JXYS0100006021210027,173RefSeq:NZ_JXYS01000060
NZ_JXYS0100002816151026,599RefSeq:NZ_JXYS01000028
NZ_JXYS0100007720190126,310RefSeq:NZ_JXYS01000077
NZ_JXYS0100001121210026,101RefSeq:NZ_JXYS01000011
NZ_JXYS0100001920171225,919RefSeq:NZ_JXYS01000019
NZ_JXYS0100009919180125,863RefSeq:NZ_JXYS01000099
NZ_JXYS0100009631290225,773RefSeq:NZ_JXYS01000096
NZ_JXYS0100000917130424,790RefSeq:NZ_JXYS01000009
NZ_JXYS0100011723220124,484RefSeq:NZ_JXYS01000117
NZ_JXYS0100000222200224,238RefSeq:NZ_JXYS01000002
NZ_JXYS0100002118170123,572RefSeq:NZ_JXYS01000021
NZ_JXYS0100009518180023,333RefSeq:NZ_JXYS01000095
NZ_JXYS0100000819180122,681RefSeq:NZ_JXYS01000008
NZ_JXYS0100001528270122,397RefSeq:NZ_JXYS01000015
NZ_JXYS0100003819170221,100RefSeq:NZ_JXYS01000038
NZ_JXYS0100009316150120,477RefSeq:NZ_JXYS01000093
NZ_JXYS0100011019190020,427RefSeq:NZ_JXYS01000110
NZ_JXYS0100008214140020,128RefSeq:NZ_JXYS01000082
NZ_JXYS0100009816160018,671RefSeq:NZ_JXYS01000098
NZ_JXYS0100010918170118,567RefSeq:NZ_JXYS01000109
NZ_JXYS0100004311110018,541RefSeq:NZ_JXYS01000043
NZ_JXYS0100007619160318,035RefSeq:NZ_JXYS01000076
NZ_JXYS0100003315140117,865RefSeq:NZ_JXYS01000033
NZ_JXYS0100013519190017,585RefSeq:NZ_JXYS01000135
NZ_JXYS0100003721124517,166RefSeq:NZ_JXYS01000037
NZ_JXYS0100009413130016,986RefSeq:NZ_JXYS01000094
NZ_JXYS0100001422200216,518RefSeq:NZ_JXYS01000014
NZ_JXYS0100011418150316,282RefSeq:NZ_JXYS01000114
NZ_JXYS0100001616160016,250RefSeq:NZ_JXYS01000016
NZ_JXYS0100008612100215,732RefSeq:NZ_JXYS01000086
NZ_JXYS0100015515120315,681RefSeq:NZ_JXYS01000155
NZ_JXYS010000531290315,586RefSeq:NZ_JXYS01000053
NZ_JXYS0100004116150115,140RefSeq:NZ_JXYS01000041
NZ_JXYS0100013413100314,697RefSeq:NZ_JXYS01000134
NZ_JXYS0100010012100214,540RefSeq:NZ_JXYS01000100
NZ_JXYS0100010314130113,491RefSeq:NZ_JXYS01000103
NZ_JXYS0100001312110113,324RefSeq:NZ_JXYS01000013
NZ_JXYS0100004413112013,113RefSeq:NZ_JXYS01000044
NZ_JXYS0100011511110012,057RefSeq:NZ_JXYS01000115
NZ_JXYS0100004614140011,921RefSeq:NZ_JXYS01000046
NZ_JXYS0100014312100211,455RefSeq:NZ_JXYS01000143
NZ_JXYS010001481392210,941RefSeq:NZ_JXYS01000148
NZ_JXYS0100000611100110,825RefSeq:NZ_JXYS01000006
NZ_JXYS0100015612110110,487RefSeq:NZ_JXYS01000156
NZ_JXYS010001391311029,334RefSeq:NZ_JXYS01000139
NZ_JXYS01000131117048,559RefSeq:NZ_JXYS01000131
NZ_JXYS010001191210028,529RefSeq:NZ_JXYS01000119
85 Undisplayed Contigs/Replicons295290685419,621
Total:3,4243,142592234,019,867
Ortholog data available?No
Database Contents
Genes3,420
Pathways177
Enzymatic Reactions974
Transport Reactions29
Polypeptides3,261
Protein Complexes31
Enzymes662
Transporters179
Compounds804
Transcription Units2,720
tRNAs48
Protein Features3,421
GO Terms10,302
Database Version29.0
Sequence SourceGCF_000949295.1
Synonyms acid streamer bacterium Py-F3
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Acidimicrobiia
Acidimicrobiales
Acidimicrobiaceae
Acidithrix
Acidithrix ferrooxidans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03301760
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1280514
Environmentmine water
Geographic LocationUnited Kingdom
Annotation ProviderNCBI RefSeq
Annotation Date2020-02-10
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.