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 Oxalobacteraceae bacterium IMCC9480 IMCC9480, 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 [Caspi19]. 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_AEPR0100002946440238,513RefSeq:NZ_AEPR01000029
NZ_AEPR0100005439381035,566RefSeq:NZ_AEPR01000054
NZ_AEPR0100017621210028,535RefSeq:NZ_AEPR01000176
NZ_AEPR0100018722210127,218RefSeq:NZ_AEPR01000187
NZ_AEPR0100007125250027,167RefSeq:NZ_AEPR01000071
NZ_AEPR0100011525230227,089RefSeq:NZ_AEPR01000115
NZ_AEPR0100000829270226,848RefSeq:NZ_AEPR01000008
NZ_AEPR0100026725240125,363RefSeq:NZ_AEPR01000267
NZ_AEPR0100000419170224,864RefSeq:NZ_AEPR01000004
NZ_AEPR0100016626241123,463RefSeq:NZ_AEPR01000166
NZ_AEPR0100037119180123,432RefSeq:NZ_AEPR01000371
NZ_AEPR0100008018180021,251RefSeq:NZ_AEPR01000080
NZ_AEPR0100021319190020,551RefSeq:NZ_AEPR01000213
NZ_AEPR0100006623212020,017RefSeq:NZ_AEPR01000066
NZ_AEPR0100003723230019,957RefSeq:NZ_AEPR01000037
NZ_AEPR0100007915120319,289RefSeq:NZ_AEPR01000079
NZ_AEPR0100012215150019,125RefSeq:NZ_AEPR01000122
NZ_AEPR0100035519171119,111RefSeq:NZ_AEPR01000355
NZ_AEPR0100024819171119,069RefSeq:NZ_AEPR01000248
NZ_AEPR0100009816160019,052RefSeq:NZ_AEPR01000098
NZ_AEPR0100028614140018,572RefSeq:NZ_AEPR01000286
NZ_AEPR0100042216150117,658RefSeq:NZ_AEPR01000422
NZ_AEPR0100013613120117,311RefSeq:NZ_AEPR01000136
NZ_AEPR0100009715150017,245RefSeq:NZ_AEPR01000097
NZ_AEPR0100057114140016,845RefSeq:NZ_AEPR01000571
NZ_AEPR0100026017170016,770RefSeq:NZ_AEPR01000260
NZ_AEPR0100002514120216,400RefSeq:NZ_AEPR01000025
NZ_AEPR0100009413130016,313RefSeq:NZ_AEPR01000094
NZ_AEPR0100025816160016,060RefSeq:NZ_AEPR01000258
NZ_AEPR0100008219180115,836RefSeq:NZ_AEPR01000082
NZ_AEPR0100009912100215,834RefSeq:NZ_AEPR01000099
NZ_AEPR0100006517160115,626RefSeq:NZ_AEPR01000065
NZ_AEPR0100010113120115,595RefSeq:NZ_AEPR01000101
NZ_AEPR0100000516151015,574RefSeq:NZ_AEPR01000005
NZ_AEPR0100025313130015,542RefSeq:NZ_AEPR01000253
NZ_AEPR0100004314140015,365RefSeq:NZ_AEPR01000043
NZ_AEPR0100013014130115,048RefSeq:NZ_AEPR01000130
NZ_AEPR010001321191114,719RefSeq:NZ_AEPR01000132
NZ_AEPR0100022915150014,681RefSeq:NZ_AEPR01000229
NZ_AEPR0100001315140114,324RefSeq:NZ_AEPR01000013
NZ_AEPR0100000212110114,119RefSeq:NZ_AEPR01000002
NZ_AEPR0100051213120114,081RefSeq:NZ_AEPR01000512
NZ_AEPR0100007212120013,955RefSeq:NZ_AEPR01000072
NZ_AEPR0100005511110013,640RefSeq:NZ_AEPR01000055
NZ_AEPR0100018415130213,621RefSeq:NZ_AEPR01000184
NZ_AEPR0100029815130213,594RefSeq:NZ_AEPR01000298
NZ_AEPR0100030812100213,586RefSeq:NZ_AEPR01000308
NZ_AEPR0100036015150013,130RefSeq:NZ_AEPR01000360
NZ_AEPR0100011914140013,100RefSeq:NZ_AEPR01000119
NZ_AEPR0100026812111012,997RefSeq:NZ_AEPR01000268
NZ_AEPR0100000917140312,911RefSeq:NZ_AEPR01000009
NZ_AEPR0100006313130012,610RefSeq:NZ_AEPR01000063
NZ_AEPR0100047512110112,517RefSeq:NZ_AEPR01000475
NZ_AEPR0100060011100112,421RefSeq:NZ_AEPR01000600
NZ_AEPR0100051512120012,325RefSeq:NZ_AEPR01000515
NZ_AEPR0100010312111012,307RefSeq:NZ_AEPR01000103
NZ_AEPR0100045313120111,628RefSeq:NZ_AEPR01000453
NZ_AEPR0100000111110011,431RefSeq:NZ_AEPR01000001
NZ_AEPR0100036512101111,371RefSeq:NZ_AEPR01000365
NZ_AEPR0100010812110111,155RefSeq:NZ_AEPR01000108
NZ_AEPR0100015311110010,945RefSeq:NZ_AEPR01000153
NZ_AEPR0100040111110010,646RefSeq:NZ_AEPR01000401
NZ_AEPR010006491211019,936RefSeq:NZ_AEPR01000649
NZ_AEPR010006721211019,745RefSeq:NZ_AEPR01000672
NZ_AEPR01000233128229,709RefSeq:NZ_AEPR01000233
NZ_AEPR010004371212009,512RefSeq:NZ_AEPR01000437
NZ_AEPR010004491211018,692RefSeq:NZ_AEPR01000449
NZ_AEPR010000101312018,385RefSeq:NZ_AEPR01000010
NZ_AEPR01000224119024,891RefSeq:NZ_AEPR01000224
1,008 Undisplayed Contigs/Replicons2,3972,378324333,355,741
Total:3,9593,428454864,501,499
Ortholog data available?No
Database Contents
Genes3,946
Pathways265
Enzymatic Reactions1,333
Transport Reactions78
Polypeptides3,987
Protein Complexes60
Enzymes813
Transporters424
Compounds985
Transcription Units2,952
tRNAs27
Protein Features4,379
GO Terms12,129
Database Version29.0
Sequence SourceGCF_000195205.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Oxalobacteraceae
unclassified Oxalobacteraceae
Oxalobacteraceae bacterium IMCC9480
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02469921
NCBI BioProjectPRJNA224116
NCBI-Taxonomy937450
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-29
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi19: 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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