Summary of Acidovorax caeni R-24608, version 29.0

Tier 3 Uncurated Organism Database

Database Authors

Pallavi Subhraveti¹, Peter Midford¹, Ingrid Keseler¹, Anamika Kothari¹, Ron Caspi¹, Peter D Karp¹

Summary

This Pathway/Genome Database (PGDB) was generated on 25-Oct-2020 from the annotated genome of Acidovorax caeni R-24608, 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

Contig	Total Genes	Protein Genes	RNA Genes	Pseudogenes	Size (bp)	NCBI Link
NZ_CYIG01000007	256	250	3	3	265,271	RefSeq:NZ_CYIG01000007
NZ_CYIG01000005	191	185	5	1	224,301	RefSeq:NZ_CYIG01000005
NZ_CYIG01000001	182	177	3	2	186,448	RefSeq:NZ_CYIG01000001
NZ_CYIG01000002	150	147	2	1	159,864	RefSeq:NZ_CYIG01000002
NZ_CYIG01000003	102	98	2	2	123,770	RefSeq:NZ_CYIG01000003
NZ_CYIG01000012	102	99	0	3	123,221	RefSeq:NZ_CYIG01000012
NZ_CYIG01000004	108	105	3	0	114,831	RefSeq:NZ_CYIG01000004
NZ_CYIG01000030	97	92	2	3	111,404	RefSeq:NZ_CYIG01000030
NZ_CYIG01000006	93	91	1	1	110,286	RefSeq:NZ_CYIG01000006
NZ_CYIG01000008	97	90	6	1	105,062	RefSeq:NZ_CYIG01000008
NZ_CYIG01000009	100	98	0	2	101,621	RefSeq:NZ_CYIG01000009
NZ_CYIG01000031	89	88	0	1	90,068	RefSeq:NZ_CYIG01000031
NZ_CYIG01000010	84	82	1	1	90,062	RefSeq:NZ_CYIG01000010
NZ_CYIG01000011	72	70	0	2	88,144	RefSeq:NZ_CYIG01000011
NZ_CYIG01000013	85	78	4	3	85,430	RefSeq:NZ_CYIG01000013
NZ_CYIG01000014	60	58	0	2	79,295	RefSeq:NZ_CYIG01000014
NZ_CYIG01000015	73	72	1	0	78,994	RefSeq:NZ_CYIG01000015
NZ_CYIG01000020	67	65	1	1	74,516	RefSeq:NZ_CYIG01000020
NZ_CYIG01000016	72	71	0	1	70,911	RefSeq:NZ_CYIG01000016
NZ_CYIG01000017	57	56	0	1	69,382	RefSeq:NZ_CYIG01000017
NZ_CYIG01000018	80	77	0	3	67,184	RefSeq:NZ_CYIG01000018
NZ_CYIG01000019	61	60	0	1	67,181	RefSeq:NZ_CYIG01000019
NZ_CYIG01000033	66	51	0	15	60,348	RefSeq:NZ_CYIG01000033
NZ_CYIG01000021	48	46	0	2	58,218	RefSeq:NZ_CYIG01000021
NZ_CYIG01000023	45	44	0	1	55,880	RefSeq:NZ_CYIG01000023
NZ_CYIG01000022	74	73	0	1	55,687	RefSeq:NZ_CYIG01000022
NZ_CYIG01000024	43	42	1	0	52,338	RefSeq:NZ_CYIG01000024
NZ_CYIG01000046	40	38	0	2	52,133	RefSeq:NZ_CYIG01000046
NZ_CYIG01000039	48	47	0	1	50,433	RefSeq:NZ_CYIG01000039
NZ_CYIG01000025	43	41	0	2	50,118	RefSeq:NZ_CYIG01000025
NZ_CYIG01000026	43	42	0	1	49,535	RefSeq:NZ_CYIG01000026
NZ_CYIG01000027	40	38	0	2	47,731	RefSeq:NZ_CYIG01000027
NZ_CYIG01000028	42	35	3	4	47,116	RefSeq:NZ_CYIG01000028
NZ_CYIG01000029	39	38	0	1	46,894	RefSeq:NZ_CYIG01000029
NZ_CYIG01000032	38	36	0	2	42,734	RefSeq:NZ_CYIG01000032
NZ_CYIG01000036	39	35	1	3	41,050	RefSeq:NZ_CYIG01000036
NZ_CYIG01000034	33	30	3	0	40,236	RefSeq:NZ_CYIG01000034
NZ_CYIG01000037	34	24	4	6	39,618	RefSeq:NZ_CYIG01000037
NZ_CYIG01000035	36	36	0	0	39,596	RefSeq:NZ_CYIG01000035
NZ_CYIG01000038	30	27	2	1	38,454	RefSeq:NZ_CYIG01000038
NZ_CYIG01000062	31	29	0	2	34,301	RefSeq:NZ_CYIG01000062
NZ_CYIG01000040	27	27	0	0	30,623	RefSeq:NZ_CYIG01000040
NZ_CYIG01000041	29	26	0	3	30,142	RefSeq:NZ_CYIG01000041
NZ_CYIG01000042	24	22	0	2	29,946	RefSeq:NZ_CYIG01000042
NZ_CYIG01000044	29	29	0	0	28,672	RefSeq:NZ_CYIG01000044
NZ_CYIG01000043	31	30	0	1	27,934	RefSeq:NZ_CYIG01000043
NZ_CYIG01000045	21	19	2	0	25,841	RefSeq:NZ_CYIG01000045
NZ_CYIG01000047	25	23	1	1	25,384	RefSeq:NZ_CYIG01000047
NZ_CYIG01000058	16	16	0	0	22,065	RefSeq:NZ_CYIG01000058
NZ_CYIG01000055	23	20	0	3	21,145	RefSeq:NZ_CYIG01000055
NZ_CYIG01000048	22	20	1	1	20,719	RefSeq:NZ_CYIG01000048
NZ_CYIG01000049	28	26	1	1	20,445	RefSeq:NZ_CYIG01000049
NZ_CYIG01000053	29	21	0	8	20,368	RefSeq:NZ_CYIG01000053
NZ_CYIG01000052	13	11	0	2	20,012	RefSeq:NZ_CYIG01000052
NZ_CYIG01000051	15	14	0	1	19,684	RefSeq:NZ_CYIG01000051
NZ_CYIG01000054	21	18	1	2	17,523	RefSeq:NZ_CYIG01000054
NZ_CYIG01000056	18	18	0	0	16,971	RefSeq:NZ_CYIG01000056
NZ_CYIG01000057	14	12	0	2	16,936	RefSeq:NZ_CYIG01000057
NZ_CYIG01000059	14	13	0	1	16,357	RefSeq:NZ_CYIG01000059
NZ_CYIG01000060	12	12	0	0	16,013	RefSeq:NZ_CYIG01000060
NZ_CYIG01000061	22	21	0	1	15,563	RefSeq:NZ_CYIG01000061
NZ_CYIG01000063	22	21	0	1	14,484	RefSeq:NZ_CYIG01000063
NZ_CYIG01000065	12	11	0	1	13,010	RefSeq:NZ_CYIG01000065
NZ_CYIG01000064	12	11	1	0	12,253	RefSeq:NZ_CYIG01000064
NZ_CYIG01000068	14	13	0	1	12,249	RefSeq:NZ_CYIG01000068
NZ_CYIG01000067	18	17	0	1	11,515	RefSeq:NZ_CYIG01000067
NZ_CYIG01000074	12	10	0	2	9,884	RefSeq:NZ_CYIG01000074
NZ_CYIG01000075	12	11	1	0	9,628	RefSeq:NZ_CYIG01000075
NZ_CYIG01000076	17	16	0	1	9,479	RefSeq:NZ_CYIG01000076
83 Undisplayed Contigs/Replicons	180	177	3	72	266,417

Total:	3,894	3,646	59	189	4,190,928

Ortholog data available?	No

Database Contents

Genes	3,892
Pathways	262
Enzymatic Reactions	1,331
Transport Reactions	73
Polypeptides	3,711
Protein Complexes	46
Enzymes	816
Transporters	363
Compounds	948
Transcription Units	2,440
tRNAs	49
Protein Features	4,702
GO Terms	14,678

Database Version

29.0

Sequence Source	GCF_001298675.1
Synonyms	Acidovorax sp. R-24607 Acidovorax sp. R-24608 Acidovorax sp. R-24613 Acidovorax sp. R-24614
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Betaproteobacteria Burkholderiales Comamonadaceae Acidovorax Acidovorax caeni
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMEA3520081
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	343013
Annotation Provider	NCBI RefSeq
Annotation Date	2020-01-7
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	4.10
Annotation Comment	Best-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, BIOCYC18A.

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