Summary of Acidovorax delafieldii 2AN, version 29.0

Tier 3 Uncurated Organism Database

Database Authors

Pallavi Subhraveti¹, Anamika Kothari¹, Peter Midford¹, Ron Caspi¹, Lisa Moore¹, Peter D Karp¹

Summary

This Pathway/Genome Database (PGDB) was generated on 30-Oct-2024 from the annotated genome of Acidovorax delafieldii 2AN, as obtained from RefSeq (annotation date: 17-FEB-2024). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [Karp11, Karp16] using MetaCyc version 28.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.

Genome

Contig	Total Genes	Protein Genes	RNA Genes	Pseudogenes	Size (bp)	NCBI Link
NZ_ACQT01000001	109	102	0	7	128,214	RefSeq:NZ_ACQT01000001
NZ_ACQT01000002	118	114	0	4	125,992	RefSeq:NZ_ACQT01000002
NZ_ACQT01000003	86	86	0	0	83,456	RefSeq:NZ_ACQT01000003
NZ_ACQT01000004	63	59	0	4	75,332	RefSeq:NZ_ACQT01000004
NZ_ACQT01000005	65	63	1	1	67,706	RefSeq:NZ_ACQT01000005
NZ_ACQT01000006	44	42	0	2	58,107	RefSeq:NZ_ACQT01000006
NZ_ACQT01000007	51	50	0	1	56,988	RefSeq:NZ_ACQT01000007
NZ_ACQT01000008	52	50	1	1	56,413	RefSeq:NZ_ACQT01000008
NZ_ACQT01000009	56	55	0	1	55,638	RefSeq:NZ_ACQT01000009
NZ_ACQT01000010	37	37	0	0	52,348	RefSeq:NZ_ACQT01000010
NZ_ACQT01000011	48	46	0	2	51,785	RefSeq:NZ_ACQT01000011
NZ_ACQT01000012	38	36	0	2	49,567	RefSeq:NZ_ACQT01000012
NZ_ACQT01000013	59	52	1	6	47,530	RefSeq:NZ_ACQT01000013
NZ_ACQT01000014	62	61	0	1	47,010	RefSeq:NZ_ACQT01000014
NZ_ACQT01000015	40	39	0	1	40,119	RefSeq:NZ_ACQT01000015
NZ_ACQT01000016	36	32	3	1	39,739	RefSeq:NZ_ACQT01000016
NZ_ACQT01000017	37	35	1	1	39,205	RefSeq:NZ_ACQT01000017
NZ_ACQT01000018	37	34	2	1	38,646	RefSeq:NZ_ACQT01000018
NZ_ACQT01000019	39	36	2	1	37,710	RefSeq:NZ_ACQT01000019
NZ_ACQT01000020	36	35	0	1	36,703	RefSeq:NZ_ACQT01000020
NZ_ACQT01000021	27	26	0	1	35,568	RefSeq:NZ_ACQT01000021
NZ_ACQT01000022	33	32	1	0	35,500	RefSeq:NZ_ACQT01000022
NZ_ACQT01000023	29	28	0	1	33,592	RefSeq:NZ_ACQT01000023
NZ_ACQT01000024	27	27	0	0	32,470	RefSeq:NZ_ACQT01000024
NZ_ACQT01000025	32	31	0	1	31,613	RefSeq:NZ_ACQT01000025
NZ_ACQT01000026	28	28	0	0	31,552	RefSeq:NZ_ACQT01000026
NZ_ACQT01000027	36	33	3	0	31,226	RefSeq:NZ_ACQT01000027
NZ_ACQT01000028	25	23	1	1	30,612	RefSeq:NZ_ACQT01000028
NZ_ACQT01000029	28	28	0	0	30,009	RefSeq:NZ_ACQT01000029
NZ_ACQT01000030	33	29	1	3	29,863	RefSeq:NZ_ACQT01000030
NZ_ACQT01000031	27	22	4	1	27,649	RefSeq:NZ_ACQT01000031
NZ_ACQT01000032	26	26	0	0	26,990	RefSeq:NZ_ACQT01000032
NZ_ACQT01000033	13	13	0	0	25,581	RefSeq:NZ_ACQT01000033
NZ_ACQT01000034	24	23	0	1	25,023	RefSeq:NZ_ACQT01000034
NZ_ACQT01000035	21	19	1	1	24,862	RefSeq:NZ_ACQT01000035
NZ_ACQT01000036	24	23	0	1	24,226	RefSeq:NZ_ACQT01000036
NZ_ACQT01000037	24	24	0	0	24,089	RefSeq:NZ_ACQT01000037
NZ_ACQT01000038	23	23	0	0	23,571	RefSeq:NZ_ACQT01000038
NZ_ACQT01000039	18	17	0	1	23,015	RefSeq:NZ_ACQT01000039
NZ_ACQT01000040	25	25	0	0	22,352	RefSeq:NZ_ACQT01000040
NZ_ACQT01000041	13	12	0	1	22,231	RefSeq:NZ_ACQT01000041
NZ_ACQT01000042	25	25	0	0	22,129	RefSeq:NZ_ACQT01000042
NZ_ACQT01000043	20	19	1	0	22,036	RefSeq:NZ_ACQT01000043
NZ_ACQT01000044	22	21	0	1	21,994	RefSeq:NZ_ACQT01000044
NZ_ACQT01000045	17	16	1	0	21,974	RefSeq:NZ_ACQT01000045
NZ_ACQT01000046	20	18	1	1	21,816	RefSeq:NZ_ACQT01000046
NZ_ACQT01000047	19	18	0	1	21,656	RefSeq:NZ_ACQT01000047
NZ_ACQT01000048	15	15	0	0	21,383	RefSeq:NZ_ACQT01000048
NZ_ACQT01000049	17	16	0	1	21,273	RefSeq:NZ_ACQT01000049
NZ_ACQT01000050	21	18	1	2	21,085	RefSeq:NZ_ACQT01000050
NZ_ACQT01000051	21	19	0	2	21,028	RefSeq:NZ_ACQT01000051
NZ_ACQT01000052	19	18	0	1	20,911	RefSeq:NZ_ACQT01000052
NZ_ACQT01000053	20	19	0	1	20,835	RefSeq:NZ_ACQT01000053
NZ_ACQT01000054	19	17	0	2	20,746	RefSeq:NZ_ACQT01000054
NZ_ACQT01000055	37	28	7	2	20,352	RefSeq:NZ_ACQT01000055
NZ_ACQT01000056	18	15	0	3	19,889	RefSeq:NZ_ACQT01000056
NZ_ACQT01000057	15	15	0	0	19,449	RefSeq:NZ_ACQT01000057
NZ_ACQT01000058	19	19	0	0	19,441	RefSeq:NZ_ACQT01000058
NZ_ACQT01000059	15	15	0	0	19,383	RefSeq:NZ_ACQT01000059
NZ_ACQT01000060	16	16	0	0	19,247	RefSeq:NZ_ACQT01000060
NZ_ACQT01000061	23	21	2	0	19,145	RefSeq:NZ_ACQT01000061
NZ_ACQT01000062	15	14	0	1	19,041	RefSeq:NZ_ACQT01000062
NZ_ACQT01000063	20	18	0	2	18,280	RefSeq:NZ_ACQT01000063
NZ_ACQT01000064	16	15	0	1	17,864	RefSeq:NZ_ACQT01000064
NZ_ACQT01000065	16	15	0	1	17,283	RefSeq:NZ_ACQT01000065
NZ_ACQT01000066	17	17	0	0	17,205	RefSeq:NZ_ACQT01000066
NZ_ACQT01000067	14	13	0	1	16,770	RefSeq:NZ_ACQT01000067
NZ_ACQT01000068	15	13	0	2	16,749	RefSeq:NZ_ACQT01000068
NZ_ACQT01000069	14	14	0	0	16,390	RefSeq:NZ_ACQT01000069
NZ_ACQT01000070	17	15	1	1	16,323	RefSeq:NZ_ACQT01000070
NZ_ACQT01000071	15	15	0	0	16,322	RefSeq:NZ_ACQT01000071
NZ_ACQT01000072	12	12	0	0	16,304	RefSeq:NZ_ACQT01000072
NZ_ACQT01000073	16	16	0	0	16,229	RefSeq:NZ_ACQT01000073
NZ_ACQT01000074	23	19	4	0	16,147	RefSeq:NZ_ACQT01000074
NZ_ACQT01000075	12	10	0	2	16,083	RefSeq:NZ_ACQT01000075
NZ_ACQT01000076	13	13	0	0	16,051	RefSeq:NZ_ACQT01000076
NZ_ACQT01000077	13	12	0	1	15,953	RefSeq:NZ_ACQT01000077
NZ_ACQT01000078	12	11	0	1	15,891	RefSeq:NZ_ACQT01000078
NZ_ACQT01000079	15	15	0	0	15,766	RefSeq:NZ_ACQT01000079
NZ_ACQT01000080	14	13	0	1	15,753	RefSeq:NZ_ACQT01000080
NZ_ACQT01000081	17	15	1	1	15,556	RefSeq:NZ_ACQT01000081
NZ_ACQT01000082	23	22	0	1	15,500	RefSeq:NZ_ACQT01000082
NZ_ACQT01000083	17	16	0	1	15,470	RefSeq:NZ_ACQT01000083
NZ_ACQT01000084	15	15	0	0	15,000	RefSeq:NZ_ACQT01000084
NZ_ACQT01000085	13	13	0	0	14,873	RefSeq:NZ_ACQT01000085
NZ_ACQT01000086	16	14	0	2	14,751	RefSeq:NZ_ACQT01000086
NZ_ACQT01000087	15	15	0	0	14,741	RefSeq:NZ_ACQT01000087
NZ_ACQT01000088	10	9	0	1	14,521	RefSeq:NZ_ACQT01000088
NZ_ACQT01000089	13	13	0	0	14,360	RefSeq:NZ_ACQT01000089
NZ_ACQT01000090	14	12	0	2	14,212	RefSeq:NZ_ACQT01000090
NZ_ACQT01000091	11	11	0	0	14,103	RefSeq:NZ_ACQT01000091
NZ_ACQT01000093	12	10	0	2	13,835	RefSeq:NZ_ACQT01000093
NZ_ACQT01000094	14	11	0	3	13,817	RefSeq:NZ_ACQT01000094
NZ_ACQT01000096	12	11	0	1	13,679	RefSeq:NZ_ACQT01000096
NZ_ACQT01000097	15	13	1	1	13,672	RefSeq:NZ_ACQT01000097
NZ_ACQT01000099	11	9	0	2	13,330	RefSeq:NZ_ACQT01000099
NZ_ACQT01000101	12	12	0	0	13,220	RefSeq:NZ_ACQT01000101
NZ_ACQT01000102	11	10	0	1	13,200	RefSeq:NZ_ACQT01000102
NZ_ACQT01000104	15	14	0	1	12,666	RefSeq:NZ_ACQT01000104
NZ_ACQT01000105	11	10	0	1	12,636	RefSeq:NZ_ACQT01000105
NZ_ACQT01000107	11	10	0	1	12,418	RefSeq:NZ_ACQT01000107
NZ_ACQT01000110	12	11	0	1	12,231	RefSeq:NZ_ACQT01000110
NZ_ACQT01000111	11	10	0	1	12,213	RefSeq:NZ_ACQT01000111
NZ_ACQT01000114	14	14	0	0	11,977	RefSeq:NZ_ACQT01000114
NZ_ACQT01000115	12	11	0	1	11,913	RefSeq:NZ_ACQT01000115
NZ_ACQT01000116	11	11	0	0	11,844	RefSeq:NZ_ACQT01000116
NZ_ACQT01000117	12	10	0	2	11,822	RefSeq:NZ_ACQT01000117
NZ_ACQT01000118	13	11	0	2	11,631	RefSeq:NZ_ACQT01000118
NZ_ACQT01000120	18	17	0	1	11,107	RefSeq:NZ_ACQT01000120
NZ_ACQT01000122	11	9	1	1	11,046	RefSeq:NZ_ACQT01000122
NZ_ACQT01000123	11	11	0	0	11,019	RefSeq:NZ_ACQT01000123
NZ_ACQT01000125	12	11	0	1	10,914	RefSeq:NZ_ACQT01000125
NZ_ACQT01000134	11	9	0	2	9,925	RefSeq:NZ_ACQT01000134
NZ_ACQT01000139	14	13	0	1	9,517	RefSeq:NZ_ACQT01000139
NZ_ACQT01000154	12	10	0	2	8,943	RefSeq:NZ_ACQT01000154
NZ_ACQT01000167	11	11	0	0	8,530	RefSeq:NZ_ACQT01000167
NZ_ACQT01000166	13	9	0	4	8,530	RefSeq:NZ_ACQT01000166
521 Undisplayed Contigs/Replicons	1,227	1,213	14	187	1,861,394

Total:	4,236	3,870	57	309	4,842,094

Ortholog data available?	No

Database Contents

Genes	4,236
Pathways	311
Enzymatic Reactions	1,770
Transport Reactions	83
Polypeptides	4,466
Protein Complexes	113
Enzymes	926
Transporters	485
Compounds	1,550
Transcription Units	3,553
tRNAs	50
Protein Features	5,036
GO Terms	5,398

Database Version

29.0

Sequence Source	GCF_000175235.1
Synonyms	Acidovorax delafieldii str. 2AN Acidovorax delafieldii strain 2AN Acidovorax delafieldii 2AN
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Betaproteobacteria Burkholderiales Comamonadaceae Acidovorax Acidovorax delafieldii Acidovorax delafieldii 2AN
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN02441799
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	573060
Annotation Provider	NCBI RefSeq
Annotation Date	2024-02-17
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	6.6
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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