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 Achromobacter arsenitoxydans SY8, 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_AGUF0100005535133795342,688RefSeq:NZ_AGUF01000055
NZ_AGUF0100005220820404266,142RefSeq:NZ_AGUF01000052
NZ_AGUF0100004221020901231,634RefSeq:NZ_AGUF01000042
NZ_AGUF0100001320820341225,462RefSeq:NZ_AGUF01000013
NZ_AGUF0100007418618222195,428RefSeq:NZ_AGUF01000074
NZ_AGUF0100005717317210191,193RefSeq:NZ_AGUF01000057
NZ_AGUF0100008716516230190,985RefSeq:NZ_AGUF01000087
NZ_AGUF0100004016916711185,892RefSeq:NZ_AGUF01000040
NZ_AGUF0100002113313201154,482RefSeq:NZ_AGUF01000021
NZ_AGUF0100000114414130152,423RefSeq:NZ_AGUF01000001
NZ_AGUF0100006413112902150,759RefSeq:NZ_AGUF01000064
NZ_AGUF0100007312812611149,497RefSeq:NZ_AGUF01000073
NZ_AGUF0100004713413031137,037RefSeq:NZ_AGUF01000047
NZ_AGUF0100007512712700126,243RefSeq:NZ_AGUF01000075
NZ_AGUF0100004614314030124,992RefSeq:NZ_AGUF01000046
NZ_AGUF0100001010610501116,870RefSeq:NZ_AGUF01000010
NZ_AGUF0100000710710232112,638RefSeq:NZ_AGUF01000007
NZ_AGUF01000058949301106,744RefSeq:NZ_AGUF01000058
NZ_AGUF01000039928930101,112RefSeq:NZ_AGUF01000039
NZ_AGUF0100004393930097,452RefSeq:NZ_AGUF01000043
NZ_AGUF0100003188870195,590RefSeq:NZ_AGUF01000031
NZ_AGUF0100008285802392,301RefSeq:NZ_AGUF01000082
NZ_AGUF0100002977734092,071RefSeq:NZ_AGUF01000029
NZ_AGUF0100005683821091,393RefSeq:NZ_AGUF01000056
NZ_AGUF0100006772710189,008RefSeq:NZ_AGUF01000067
NZ_AGUF0100007173730082,966RefSeq:NZ_AGUF01000071
NZ_AGUF0100010485850080,698RefSeq:NZ_AGUF01000104
NZ_AGUF0100002880782080,010RefSeq:NZ_AGUF01000028
NZ_AGUF0100003382820079,168RefSeq:NZ_AGUF01000033
NZ_AGUF0100006868680079,120RefSeq:NZ_AGUF01000068
NZ_AGUF0100003566650174,438RefSeq:NZ_AGUF01000035
NZ_AGUF0100005179751370,965RefSeq:NZ_AGUF01000051
NZ_AGUF0100003462610170,141RefSeq:NZ_AGUF01000034
NZ_AGUF0100006565631166,265RefSeq:NZ_AGUF01000065
NZ_AGUF0100003263612065,393RefSeq:NZ_AGUF01000032
NZ_AGUF0100008556550164,574RefSeq:NZ_AGUF01000085
NZ_AGUF0100005458570164,424RefSeq:NZ_AGUF01000054
NZ_AGUF0100008949470262,674RefSeq:NZ_AGUF01000089
NZ_AGUF0100009047450261,738RefSeq:NZ_AGUF01000090
NZ_AGUF0100007959563060,495RefSeq:NZ_AGUF01000079
NZ_AGUF0100005952490360,326RefSeq:NZ_AGUF01000059
NZ_AGUF0100003756560054,684RefSeq:NZ_AGUF01000037
NZ_AGUF0100010251510054,431RefSeq:NZ_AGUF01000102
NZ_AGUF0100008152510151,306RefSeq:NZ_AGUF01000081
NZ_AGUF0100001746450150,542RefSeq:NZ_AGUF01000017
NZ_AGUF0100002648470149,836RefSeq:NZ_AGUF01000026
NZ_AGUF0100000839380147,560RefSeq:NZ_AGUF01000008
NZ_AGUF0100006054520247,398RefSeq:NZ_AGUF01000060
NZ_AGUF0100004845441045,710RefSeq:NZ_AGUF01000048
NZ_AGUF0100003835340142,681RefSeq:NZ_AGUF01000038
NZ_AGUF0100000935340141,048RefSeq:NZ_AGUF01000009
NZ_AGUF0100002343411139,775RefSeq:NZ_AGUF01000023
NZ_AGUF0100006335340138,514RefSeq:NZ_AGUF01000063
NZ_AGUF0100007639390035,580RefSeq:NZ_AGUF01000076
NZ_AGUF0100001429290034,522RefSeq:NZ_AGUF01000014
NZ_AGUF0100008631290234,390RefSeq:NZ_AGUF01000086
NZ_AGUF0100001623210231,609RefSeq:NZ_AGUF01000016
NZ_AGUF0100002524240029,176RefSeq:NZ_AGUF01000025
NZ_AGUF0100002232311026,861RefSeq:NZ_AGUF01000022
NZ_AGUF0100004525250026,029RefSeq:NZ_AGUF01000045
NZ_AGUF0100005325230225,656RefSeq:NZ_AGUF01000053
NZ_AGUF0100000527251124,953RefSeq:NZ_AGUF01000005
NZ_AGUF0100000318171023,427RefSeq:NZ_AGUF01000003
NZ_AGUF0100007820200022,774RefSeq:NZ_AGUF01000078
NZ_AGUF0100003022210122,602RefSeq:NZ_AGUF01000030
NZ_AGUF0100001920190122,354RefSeq:NZ_AGUF01000019
NZ_AGUF0100001221190221,785RefSeq:NZ_AGUF01000012
NZ_AGUF0100009418180021,457RefSeq:NZ_AGUF01000094
NZ_AGUF0100006217170020,355RefSeq:NZ_AGUF01000062
NZ_AGUF0100008415150020,254RefSeq:NZ_AGUF01000084
NZ_AGUF0100003618180020,056RefSeq:NZ_AGUF01000036
NZ_AGUF0100004418170119,359RefSeq:NZ_AGUF01000044
NZ_AGUF0100002713130019,119RefSeq:NZ_AGUF01000027
NZ_AGUF0100009615150019,068RefSeq:NZ_AGUF01000096
NZ_AGUF0100005019190018,408RefSeq:NZ_AGUF01000050
NZ_AGUF0100008311110016,952RefSeq:NZ_AGUF01000083
NZ_AGUF0100008018160216,488RefSeq:NZ_AGUF01000080
28 Undisplayed Contigs/Replicons464331176,514
Total:5,6655,52760786,156,664
Ortholog data available?Yes
Database Contents
Genes5,665
Pathways310
Enzymatic Reactions1,611
Transport Reactions98
Polypeptides5,615
Protein Complexes205
Enzymes975
Transporters731
Compounds1,158
Transcription Units3,610
tRNAs52
Protein Features7,272
GO Terms798
Database Version29.0
Sequence SourceGCF_000236785.1
Synonyms Achromobacter arsenitoxydans strain SY8
Achromobacter arsenitoxydans str. SY8
Achromobacter sp. SY8
arsenite-oxidizing bacterium SY8
Achromobacter arsenitoxydans SY8
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter arsenitoxydans
Achromobacter arsenitoxydans SY8
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02469904
NCBI BioProjectPRJNA224116
NCBI-Taxonomy477184
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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