Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 27-Feb-2018 from the annotated genome of Acidovorax konjaci DSM 7481, 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 22.0) [Karp16, Karp11] using MetaCyc version 21.5 [Caspi18]. 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 Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_FOMQ01000001529509119612,984RefSeq:NZ_FOMQ01000001
NZ_FOMQ0100000238137137456,131RefSeq:NZ_FOMQ01000002
NZ_FOMQ0100000338937577452,506RefSeq:NZ_FOMQ01000003
NZ_FOMQ01000004405388314446,024RefSeq:NZ_FOMQ01000004
NZ_FOMQ0100000536335805397,158RefSeq:NZ_FOMQ01000005
NZ_FOMQ0100000634133119369,808RefSeq:NZ_FOMQ01000006
NZ_FOMQ0100000724924351286,729RefSeq:NZ_FOMQ01000007
NZ_FOMQ0100000818117704208,315RefSeq:NZ_FOMQ01000008
NZ_FOMQ0100000914614402189,148RefSeq:NZ_FOMQ01000009
NZ_FOMQ0100001018016569188,532RefSeq:NZ_FOMQ01000010
NZ_FOMQ0100001116215471184,748RefSeq:NZ_FOMQ01000011
NZ_FOMQ0100001214514311163,492RefSeq:NZ_FOMQ01000012
NZ_FOMQ0100001311011000137,695RefSeq:NZ_FOMQ01000013
NZ_FOMQ0100001413913432125,224RefSeq:NZ_FOMQ01000014
NZ_FOMQ0100001510510302123,680RefSeq:NZ_FOMQ01000015
NZ_FOMQ01000016979322109,732RefSeq:NZ_FOMQ01000016
NZ_FOMQ0100001757540376,120RefSeq:NZ_FOMQ01000017
NZ_FOMQ0100001869671175,863RefSeq:NZ_FOMQ01000018
NZ_FOMQ0100001971710069,927RefSeq:NZ_FOMQ01000019
NZ_FOMQ0100002061563262,018RefSeq:NZ_FOMQ01000020
NZ_FOMQ0100002152481355,621RefSeq:NZ_FOMQ01000021
NZ_FOMQ0100002241391149,193RefSeq:NZ_FOMQ01000022
NZ_FOMQ0100002334310341,776RefSeq:NZ_FOMQ01000023
NZ_FOMQ0100002443410236,431RefSeq:NZ_FOMQ01000024
NZ_FOMQ0100002529262132,784RefSeq:NZ_FOMQ01000025
NZ_FOMQ0100002627241227,246RefSeq:NZ_FOMQ01000026
NZ_FOMQ0100002722200226,725RefSeq:NZ_FOMQ01000027
NZ_FOMQ0100002821210024,551RefSeq:NZ_FOMQ01000028
NZ_FOMQ0100002911110015,669RefSeq:NZ_FOMQ01000029
7 Undisplayed Contigs/Replicons17136631,698
Total:4,4854,320541115,077,528
Ortholog data available?Yes
Database Contents
Genes4,483
Pathways242
Enzymatic Reactions1,447
Transport Reactions86
Polypeptides4,327
Protein Complexes33
Enzymes960
Transporters511
Compounds1,203
Transcription Units3,165
tRNAs44
Protein Features5,546
GO Terms17,991
Database Version29.0
Synonyms ATCC 33996
Acidivorax konjaci
Acidovorax konjaci (Goto 1983) Willems et al. 1992
CCUG 17394
CFBP 4460
CIP 106439
DSM 7481
ICMP 7733
JCM 2397
LMG 5691
NCPPB 3698
PDDCC 7733
Pseudomonas avenae subsp. konjaci
Pseudomonas avenae subsp. konjaci (Goto 1983) Hu et al. 1991
Pseudomonas pseudoalcaligenes subsp. konjaci
Pseudomonas pseudoalcaligenes subsp. konjaci Goto 1983
strain K2
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Acidovorax
Acidovorax konjaci
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04489710
NCBI BioProjectPRJNA224116
NCBI-Taxonomy32040
NCBI Genome Typerepresentative

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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