Summary of Acidovorax sp. CF316, 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 29-Oct-2024 from the annotated genome of Acidovorax sp. CF316 CF316, as obtained from RefSeq (annotation date: 02-AUG-2023). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [1, 2] 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_AKJX01000207	120	120	0	0	118,161	RefSeq:NZ_AKJX01000207
NZ_AKJX01000099	110	110	0	0	114,966	RefSeq:NZ_AKJX01000099
NZ_AKJX01000097	100	99	1	0	106,061	RefSeq:NZ_AKJX01000097
NZ_AKJX01000164	90	89	1	0	105,105	RefSeq:NZ_AKJX01000164
NZ_AKJX01000162	97	97	0	0	93,137	RefSeq:NZ_AKJX01000162
NZ_AKJX01000089	87	87	0	0	90,099	RefSeq:NZ_AKJX01000089
NZ_AKJX01000122	91	87	4	0	89,544	RefSeq:NZ_AKJX01000122
NZ_AKJX01000178	69	69	0	0	84,603	RefSeq:NZ_AKJX01000178
NZ_AKJX01000026	83	83	0	0	82,160	RefSeq:NZ_AKJX01000026
NZ_AKJX01000117	60	60	0	0	79,741	RefSeq:NZ_AKJX01000117
NZ_AKJX01000094	71	67	0	4	78,278	RefSeq:NZ_AKJX01000094
NZ_AKJX01000093	68	67	1	0	74,479	RefSeq:NZ_AKJX01000093
NZ_AKJX01000020	66	66	0	0	73,110	RefSeq:NZ_AKJX01000020
NZ_AKJX01000124	71	71	0	0	73,061	RefSeq:NZ_AKJX01000124
NZ_AKJX01000013	84	82	0	2	70,689	RefSeq:NZ_AKJX01000013
NZ_AKJX01000119	65	64	0	1	70,065	RefSeq:NZ_AKJX01000119
NZ_AKJX01000111	51	51	0	0	65,554	RefSeq:NZ_AKJX01000111
NZ_AKJX01000261	59	58	0	1	65,302	RefSeq:NZ_AKJX01000261
NZ_AKJX01000112	59	58	0	1	65,291	RefSeq:NZ_AKJX01000112
NZ_AKJX01000098	74	72	0	2	63,414	RefSeq:NZ_AKJX01000098
NZ_AKJX01000155	60	59	1	0	63,301	RefSeq:NZ_AKJX01000155
NZ_AKJX01000198	69	67	1	1	62,253	RefSeq:NZ_AKJX01000198
NZ_AKJX01000165	62	59	3	0	61,284	RefSeq:NZ_AKJX01000165
NZ_AKJX01000019	59	58	1	0	59,707	RefSeq:NZ_AKJX01000019
NZ_AKJX01000221	58	57	1	0	58,646	RefSeq:NZ_AKJX01000221
NZ_AKJX01000101	60	60	0	0	58,471	RefSeq:NZ_AKJX01000101
NZ_AKJX01000088	52	51	0	1	58,128	RefSeq:NZ_AKJX01000088
NZ_AKJX01000163	55	54	0	1	55,593	RefSeq:NZ_AKJX01000163
NZ_AKJX01000005	44	44	0	0	54,059	RefSeq:NZ_AKJX01000005
NZ_AKJX01000095	44	44	0	0	52,534	RefSeq:NZ_AKJX01000095
NZ_AKJX01000188	57	55	2	0	52,334	RefSeq:NZ_AKJX01000188
NZ_AKJX01000284	53	53	0	0	52,267	RefSeq:NZ_AKJX01000284
NZ_AKJX01000025	51	51	0	0	51,963	RefSeq:NZ_AKJX01000025
NZ_AKJX01000006	49	48	0	1	51,560	RefSeq:NZ_AKJX01000006
NZ_AKJX01000104	39	38	0	1	50,714	RefSeq:NZ_AKJX01000104
NZ_AKJX01000116	49	49	0	0	50,423	RefSeq:NZ_AKJX01000116
NZ_AKJX01000109	41	40	0	1	50,047	RefSeq:NZ_AKJX01000109
NZ_AKJX01000272	44	44	0	0	49,400	RefSeq:NZ_AKJX01000272
NZ_AKJX01000129	49	45	3	1	49,058	RefSeq:NZ_AKJX01000129
NZ_AKJX01000138	52	50	2	0	49,026	RefSeq:NZ_AKJX01000138
NZ_AKJX01000275	45	44	0	1	49,001	RefSeq:NZ_AKJX01000275
NZ_AKJX01000110	47	45	2	0	48,425	RefSeq:NZ_AKJX01000110
NZ_AKJX01000133	40	37	0	3	47,183	RefSeq:NZ_AKJX01000133
NZ_AKJX01000173	36	36	0	0	46,765	RefSeq:NZ_AKJX01000173
NZ_AKJX01000090	44	39	2	3	45,896	RefSeq:NZ_AKJX01000090
NZ_AKJX01000276	45	44	0	1	45,526	RefSeq:NZ_AKJX01000276
NZ_AKJX01000003	35	34	0	1	43,256	RefSeq:NZ_AKJX01000003
NZ_AKJX01000137	41	39	1	1	43,013	RefSeq:NZ_AKJX01000137
NZ_AKJX01000154	41	41	0	0	41,758	RefSeq:NZ_AKJX01000154
NZ_AKJX01000168	41	41	0	0	41,308	RefSeq:NZ_AKJX01000168
NZ_AKJX01000008	40	40	0	0	40,866	RefSeq:NZ_AKJX01000008
NZ_AKJX01000286	43	42	1	0	40,658	RefSeq:NZ_AKJX01000286
NZ_AKJX01000108	35	35	0	0	40,298	RefSeq:NZ_AKJX01000108
NZ_AKJX01000113	40	40	0	0	40,021	RefSeq:NZ_AKJX01000113
NZ_AKJX01000121	42	41	1	0	39,468	RefSeq:NZ_AKJX01000121
NZ_AKJX01000120	33	33	0	0	39,452	RefSeq:NZ_AKJX01000120
NZ_AKJX01000193	32	32	0	0	38,814	RefSeq:NZ_AKJX01000193
NZ_AKJX01000205	29	29	0	0	37,861	RefSeq:NZ_AKJX01000205
NZ_AKJX01000118	32	32	0	0	37,104	RefSeq:NZ_AKJX01000118
NZ_AKJX01000011	34	32	0	2	36,998	RefSeq:NZ_AKJX01000011
NZ_AKJX01000021	33	32	0	1	36,883	RefSeq:NZ_AKJX01000021
NZ_AKJX01000131	33	33	0	0	36,627	RefSeq:NZ_AKJX01000131
NZ_AKJX01000262	34	33	1	0	35,961	RefSeq:NZ_AKJX01000262
NZ_AKJX01000265	36	36	0	0	35,879	RefSeq:NZ_AKJX01000265
NZ_AKJX01000030	31	31	0	0	35,839	RefSeq:NZ_AKJX01000030
NZ_AKJX01000103	30	29	0	1	35,744	RefSeq:NZ_AKJX01000103
NZ_AKJX01000268	28	28	0	0	34,046	RefSeq:NZ_AKJX01000268
NZ_AKJX01000146	33	32	0	1	33,809	RefSeq:NZ_AKJX01000146
NZ_AKJX01000134	35	35	0	0	33,192	RefSeq:NZ_AKJX01000134
NZ_AKJX01000157	39	38	0	1	33,037	RefSeq:NZ_AKJX01000157
NZ_AKJX01000197	33	33	0	0	32,650	RefSeq:NZ_AKJX01000197
NZ_AKJX01000196	31	31	0	0	32,630	RefSeq:NZ_AKJX01000196
NZ_AKJX01000125	33	32	0	1	32,618	RefSeq:NZ_AKJX01000125
NZ_AKJX01000169	21	20	0	1	32,355	RefSeq:NZ_AKJX01000169
NZ_AKJX01000291	30	30	0	0	32,316	RefSeq:NZ_AKJX01000291
NZ_AKJX01000204	29	29	0	0	32,012	RefSeq:NZ_AKJX01000204
NZ_AKJX01000213	27	27	0	0	31,805	RefSeq:NZ_AKJX01000213
NZ_AKJX01000015	32	31	0	1	31,734	RefSeq:NZ_AKJX01000015
NZ_AKJX01000242	25	25	0	0	31,488	RefSeq:NZ_AKJX01000242
NZ_AKJX01000279	29	28	0	1	30,830	RefSeq:NZ_AKJX01000279
NZ_AKJX01000036	28	27	0	1	30,782	RefSeq:NZ_AKJX01000036
NZ_AKJX01000046	27	26	0	1	30,782	RefSeq:NZ_AKJX01000046
NZ_AKJX01000128	23	22	0	1	30,424	RefSeq:NZ_AKJX01000128
NZ_AKJX01000135	28	28	0	0	30,132	RefSeq:NZ_AKJX01000135
NZ_AKJX01000126	28	26	0	2	29,978	RefSeq:NZ_AKJX01000126
NZ_AKJX01000192	28	28	0	0	29,957	RefSeq:NZ_AKJX01000192
NZ_AKJX01000038	28	27	0	1	29,482	RefSeq:NZ_AKJX01000038
NZ_AKJX01000167	26	26	0	0	29,395	RefSeq:NZ_AKJX01000167
NZ_AKJX01000287	29	29	0	0	29,037	RefSeq:NZ_AKJX01000287
NZ_AKJX01000017	30	30	0	0	28,637	RefSeq:NZ_AKJX01000017
NZ_AKJX01000259	19	19	0	0	28,490	RefSeq:NZ_AKJX01000259
NZ_AKJX01000004	38	38	0	0	28,357	RefSeq:NZ_AKJX01000004
NZ_AKJX01000054	27	27	0	0	28,228	RefSeq:NZ_AKJX01000054
NZ_AKJX01000027	29	22	6	1	27,955	RefSeq:NZ_AKJX01000027
NZ_AKJX01000231	24	24	0	0	27,901	RefSeq:NZ_AKJX01000231
NZ_AKJX01000280	21	21	0	0	27,822	RefSeq:NZ_AKJX01000280
NZ_AKJX01000158	32	31	0	1	27,814	RefSeq:NZ_AKJX01000158
NZ_AKJX01000115	29	28	0	1	27,775	RefSeq:NZ_AKJX01000115
NZ_AKJX01000156	28	28	0	0	27,763	RefSeq:NZ_AKJX01000156
NZ_AKJX01000215	34	34	0	0	27,651	RefSeq:NZ_AKJX01000215
NZ_AKJX01000114	16	16	0	0	27,382	RefSeq:NZ_AKJX01000114
NZ_AKJX01000277	23	22	0	1	27,096	RefSeq:NZ_AKJX01000277
NZ_AKJX01000047	19	19	0	0	26,639	RefSeq:NZ_AKJX01000047
NZ_AKJX01000140	25	24	0	1	26,567	RefSeq:NZ_AKJX01000140
NZ_AKJX01000161	28	28	0	0	26,127	RefSeq:NZ_AKJX01000161
NZ_AKJX01000209	20	20	0	0	25,719	RefSeq:NZ_AKJX01000209
NZ_AKJX01000230	28	28	0	0	25,665	RefSeq:NZ_AKJX01000230
NZ_AKJX01000200	20	20	0	0	25,451	RefSeq:NZ_AKJX01000200
NZ_AKJX01000289	23	23	0	0	24,522	RefSeq:NZ_AKJX01000289
NZ_AKJX01000160	24	24	0	0	24,195	RefSeq:NZ_AKJX01000160
NZ_AKJX01000283	19	18	0	1	23,819	RefSeq:NZ_AKJX01000283
NZ_AKJX01000153	17	16	0	1	23,656	RefSeq:NZ_AKJX01000153
NZ_AKJX01000096	18	18	0	0	23,629	RefSeq:NZ_AKJX01000096
NZ_AKJX01000264	22	22	0	0	23,488	RefSeq:NZ_AKJX01000264
NZ_AKJX01000212	15	14	0	1	23,461	RefSeq:NZ_AKJX01000212
NZ_AKJX01000023	20	18	0	2	23,364	RefSeq:NZ_AKJX01000023
NZ_AKJX01000127	22	21	0	1	23,079	RefSeq:NZ_AKJX01000127
NZ_AKJX01000141	22	22	0	0	22,916	RefSeq:NZ_AKJX01000141
NZ_AKJX01000263	24	21	1	2	22,901	RefSeq:NZ_AKJX01000263
NZ_AKJX01000224	26	25	0	1	22,733	RefSeq:NZ_AKJX01000224
NZ_AKJX01000100	24	24	0	0	22,710	RefSeq:NZ_AKJX01000100
NZ_AKJX01000171	19	19	0	0	22,688	RefSeq:NZ_AKJX01000171
NZ_AKJX01000092	23	22	0	1	22,678	RefSeq:NZ_AKJX01000092
NZ_AKJX01000218	17	17	0	0	22,536	RefSeq:NZ_AKJX01000218
NZ_AKJX01000273	21	21	0	0	22,478	RefSeq:NZ_AKJX01000273
NZ_AKJX01000220	25	21	4	0	22,255	RefSeq:NZ_AKJX01000220
NZ_AKJX01000010	21	20	0	1	21,713	RefSeq:NZ_AKJX01000010
NZ_AKJX01000166	18	15	0	3	21,576	RefSeq:NZ_AKJX01000166
NZ_AKJX01000040	16	16	0	0	21,433	RefSeq:NZ_AKJX01000040
NZ_AKJX01000041	17	17	0	0	21,389	RefSeq:NZ_AKJX01000041
NZ_AKJX01000016	19	18	0	1	21,172	RefSeq:NZ_AKJX01000016
NZ_AKJX01000210	22	22	0	0	20,656	RefSeq:NZ_AKJX01000210
NZ_AKJX01000139	16	16	0	0	20,583	RefSeq:NZ_AKJX01000139
NZ_AKJX01000037	16	16	0	0	20,337	RefSeq:NZ_AKJX01000037
NZ_AKJX01000145	16	16	0	0	19,921	RefSeq:NZ_AKJX01000145
NZ_AKJX01000208	19	19	0	0	19,911	RefSeq:NZ_AKJX01000208
NZ_AKJX01000132	24	24	0	0	19,661	RefSeq:NZ_AKJX01000132
NZ_AKJX01000203	23	23	0	0	19,452	RefSeq:NZ_AKJX01000203
NZ_AKJX01000060	18	17	0	1	19,359	RefSeq:NZ_AKJX01000060
NZ_AKJX01000150	20	19	0	1	19,283	RefSeq:NZ_AKJX01000150
NZ_AKJX01000042	12	12	0	0	18,830	RefSeq:NZ_AKJX01000042
NZ_AKJX01000148	17	17	0	0	18,820	RefSeq:NZ_AKJX01000148
NZ_AKJX01000214	19	19	0	0	18,797	RefSeq:NZ_AKJX01000214
NZ_AKJX01000227	17	17	0	0	18,534	RefSeq:NZ_AKJX01000227
NZ_AKJX01000297	19	19	0	0	18,263	RefSeq:NZ_AKJX01000297
NZ_AKJX01000106	19	19	0	0	18,094	RefSeq:NZ_AKJX01000106
NZ_AKJX01000028	15	14	0	1	18,025	RefSeq:NZ_AKJX01000028
NZ_AKJX01000177	17	16	0	1	17,953	RefSeq:NZ_AKJX01000177
NZ_AKJX01000091	12	12	0	0	17,718	RefSeq:NZ_AKJX01000091
NZ_AKJX01000143	11	11	0	0	17,253	RefSeq:NZ_AKJX01000143
NZ_AKJX01000012	10	10	0	0	16,781	RefSeq:NZ_AKJX01000012
NZ_AKJX01000267	12	12	0	0	16,464	RefSeq:NZ_AKJX01000267
NZ_AKJX01000159	13	13	0	0	16,353	RefSeq:NZ_AKJX01000159
NZ_AKJX01000258	19	19	0	0	16,284	RefSeq:NZ_AKJX01000258
NZ_AKJX01000181	14	14	0	0	16,194	RefSeq:NZ_AKJX01000181
NZ_AKJX01000235	17	17	0	0	16,020	RefSeq:NZ_AKJX01000235
NZ_AKJX01000102	12	12	0	0	15,931	RefSeq:NZ_AKJX01000102
NZ_AKJX01000057	17	16	0	1	15,857	RefSeq:NZ_AKJX01000057
NZ_AKJX01000199	15	15	0	0	15,420	RefSeq:NZ_AKJX01000199
NZ_AKJX01000024	15	15	0	0	14,967	RefSeq:NZ_AKJX01000024
NZ_AKJX01000105	12	12	0	0	14,951	RefSeq:NZ_AKJX01000105
NZ_AKJX01000087	14	12	0	2	14,648	RefSeq:NZ_AKJX01000087
NZ_AKJX01000039	11	11	0	0	13,959	RefSeq:NZ_AKJX01000039
NZ_AKJX01000107	13	12	0	1	13,694	RefSeq:NZ_AKJX01000107
NZ_AKJX01000298	14	13	1	0	13,594	RefSeq:NZ_AKJX01000298
NZ_AKJX01000058	12	12	0	0	13,324	RefSeq:NZ_AKJX01000058
NZ_AKJX01000123	14	13	1	0	13,081	RefSeq:NZ_AKJX01000123
NZ_AKJX01000301	11	11	0	0	12,742	RefSeq:NZ_AKJX01000301
NZ_AKJX01000018	11	10	1	0	12,556	RefSeq:NZ_AKJX01000018
NZ_AKJX01000052	12	12	0	0	11,843	RefSeq:NZ_AKJX01000052
NZ_AKJX01000211	15	15	0	0	11,736	RefSeq:NZ_AKJX01000211
NZ_AKJX01000274	12	11	0	1	11,673	RefSeq:NZ_AKJX01000274
NZ_AKJX01000229	12	12	0	0	11,532	RefSeq:NZ_AKJX01000229
NZ_AKJX01000294	12	11	0	1	11,415	RefSeq:NZ_AKJX01000294
NZ_AKJX01000216	13	13	0	0	11,148	RefSeq:NZ_AKJX01000216
NZ_AKJX01000223	12	11	0	1	10,857	RefSeq:NZ_AKJX01000223
NZ_AKJX01000048	12	12	0	0	10,787	RefSeq:NZ_AKJX01000048
NZ_AKJX01000302	11	10	1	0	10,106	RefSeq:NZ_AKJX01000302
137 Undisplayed Contigs/Replicons	573	561	15	37	758,747

Total:	6,538	6,367	59	112	7,086,227

Ortholog data available?	No

Database Contents

Genes	6,535
Pathways	340
Enzymatic Reactions	1,908
Transport Reactions	74
Polypeptides	6,628
Protein Complexes	182
Enzymes	1,189
Transporters	748
Compounds	1,658
Transcription Units	4,804
tRNAs	49
Protein Features	8,106
GO Terms	7,802

Database Version

29.0

Sequence Source	GCF_000276605.1
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Betaproteobacteria Burkholderiales Comamonadaceae Acidovorax unclassified Acidovorax Acidovorax sp. CF316
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN00839625
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1144317
Environment	root
Geographic Location	USA
Collection Date	2010-09
Host	Populus deltoides
Annotation Provider	NCBI RefSeq
Annotation Date	2023-08-2
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	6.5
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

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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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