Summary of Achromobacter sp. DMS1, 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 Achromobacter sp. DMS1 DMS1, 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_LHSJ01000010	77	50	0	27	72,245	RefSeq:NZ_LHSJ01000010
NZ_LHSJ01000001	69	65	0	4	67,502	RefSeq:NZ_LHSJ01000001
NZ_LHSJ01000002	67	62	1	4	62,571	RefSeq:NZ_LHSJ01000002
NZ_LHSJ01000019	58	35	9	14	62,038	RefSeq:NZ_LHSJ01000019
NZ_LHSJ01000022	53	41	0	12	58,965	RefSeq:NZ_LHSJ01000022
NZ_LHSJ01000003	51	49	1	1	55,963	RefSeq:NZ_LHSJ01000003
NZ_LHSJ01000030	52	41	0	11	53,382	RefSeq:NZ_LHSJ01000030
NZ_LHSJ01000004	47	42	0	5	50,677	RefSeq:NZ_LHSJ01000004
NZ_LHSJ01000005	54	33	0	21	48,271	RefSeq:NZ_LHSJ01000005
NZ_LHSJ01000070	42	27	0	15	46,978	RefSeq:NZ_LHSJ01000070
NZ_LHSJ01000032	43	29	0	14	45,299	RefSeq:NZ_LHSJ01000032
NZ_LHSJ01000015	45	42	2	1	44,157	RefSeq:NZ_LHSJ01000015
NZ_LHSJ01000086	40	27	0	13	44,101	RefSeq:NZ_LHSJ01000086
NZ_LHSJ01000020	57	48	0	9	43,957	RefSeq:NZ_LHSJ01000020
NZ_LHSJ01000013	34	26	1	7	42,205	RefSeq:NZ_LHSJ01000013
NZ_LHSJ01000009	43	34	1	8	40,031	RefSeq:NZ_LHSJ01000009
NZ_LHSJ01000006	45	38	1	6	39,824	RefSeq:NZ_LHSJ01000006
NZ_LHSJ01000012	46	39	0	7	37,061	RefSeq:NZ_LHSJ01000012
NZ_LHSJ01000088	31	27	0	4	36,574	RefSeq:NZ_LHSJ01000088
NZ_LHSJ01000007	36	31	0	5	36,269	RefSeq:NZ_LHSJ01000007
NZ_LHSJ01000111	35	26	0	9	35,035	RefSeq:NZ_LHSJ01000111
NZ_LHSJ01000008	26	22	0	4	34,578	RefSeq:NZ_LHSJ01000008
NZ_LHSJ01000065	41	32	1	8	33,685	RefSeq:NZ_LHSJ01000065
NZ_LHSJ01000081	30	18	0	12	32,191	RefSeq:NZ_LHSJ01000081
NZ_LHSJ01000011	21	19	1	1	32,116	RefSeq:NZ_LHSJ01000011
NZ_LHSJ01000026	23	20	0	3	31,847	RefSeq:NZ_LHSJ01000026
NZ_LHSJ01000105	29	20	0	9	31,811	RefSeq:NZ_LHSJ01000105
NZ_LHSJ01000029	27	13	0	14	30,926	RefSeq:NZ_LHSJ01000029
NZ_LHSJ01000014	26	21	1	4	30,701	RefSeq:NZ_LHSJ01000014
NZ_LHSJ01000027	30	24	0	6	30,610	RefSeq:NZ_LHSJ01000027
NZ_LHSJ01000066	42	37	2	3	30,326	RefSeq:NZ_LHSJ01000066
NZ_LHSJ01000016	26	19	0	7	30,227	RefSeq:NZ_LHSJ01000016
NZ_LHSJ01000017	33	31	1	1	29,819	RefSeq:NZ_LHSJ01000017
NZ_LHSJ01000049	24	13	0	11	29,342	RefSeq:NZ_LHSJ01000049
NZ_LHSJ01000018	28	27	0	1	29,292	RefSeq:NZ_LHSJ01000018
NZ_LHSJ01000074	31	17	6	8	29,203	RefSeq:NZ_LHSJ01000074
NZ_LHSJ01000021	22	19	0	3	28,953	RefSeq:NZ_LHSJ01000021
NZ_LHSJ01000100	34	21	1	12	28,913	RefSeq:NZ_LHSJ01000100
NZ_LHSJ01000050	27	18	0	9	28,843	RefSeq:NZ_LHSJ01000050
NZ_LHSJ01000073	22	17	0	5	27,576	RefSeq:NZ_LHSJ01000073
NZ_LHSJ01000091	23	16	0	7	27,384	RefSeq:NZ_LHSJ01000091
NZ_LHSJ01000023	24	22	0	2	27,181	RefSeq:NZ_LHSJ01000023
NZ_LHSJ01000033	19	17	0	2	27,048	RefSeq:NZ_LHSJ01000033
NZ_LHSJ01000035	25	16	0	9	26,574	RefSeq:NZ_LHSJ01000035
NZ_LHSJ01000024	24	22	0	2	26,088	RefSeq:NZ_LHSJ01000024
NZ_LHSJ01000041	21	16	0	5	25,958	RefSeq:NZ_LHSJ01000041
NZ_LHSJ01000053	26	20	1	5	25,842	RefSeq:NZ_LHSJ01000053
NZ_LHSJ01000025	22	21	0	1	25,789	RefSeq:NZ_LHSJ01000025
NZ_LHSJ01000028	29	17	0	12	25,332	RefSeq:NZ_LHSJ01000028
NZ_LHSJ01000097	24	20	0	4	25,191	RefSeq:NZ_LHSJ01000097
NZ_LHSJ01000072	26	11	0	15	25,006	RefSeq:NZ_LHSJ01000072
NZ_LHSJ01000135	23	10	0	13	24,207	RefSeq:NZ_LHSJ01000135
NZ_LHSJ01000031	27	24	0	3	23,809	RefSeq:NZ_LHSJ01000031
NZ_LHSJ01000082	21	15	1	5	23,612	RefSeq:NZ_LHSJ01000082
NZ_LHSJ01000044	18	16	0	2	23,311	RefSeq:NZ_LHSJ01000044
NZ_LHSJ01000067	19	13	0	6	23,059	RefSeq:NZ_LHSJ01000067
NZ_LHSJ01000051	20	17	0	3	22,907	RefSeq:NZ_LHSJ01000051
NZ_LHSJ01000075	22	10	0	12	22,885	RefSeq:NZ_LHSJ01000075
NZ_LHSJ01000057	25	14	0	11	22,715	RefSeq:NZ_LHSJ01000057
NZ_LHSJ01000034	21	15	0	6	22,592	RefSeq:NZ_LHSJ01000034
NZ_LHSJ01000055	23	13	0	10	22,571	RefSeq:NZ_LHSJ01000055
NZ_LHSJ01000158	20	17	0	3	22,247	RefSeq:NZ_LHSJ01000158
NZ_LHSJ01000068	16	13	0	3	21,999	RefSeq:NZ_LHSJ01000068
NZ_LHSJ01000036	27	17	0	10	21,955	RefSeq:NZ_LHSJ01000036
NZ_LHSJ01000077	27	16	2	9	21,791	RefSeq:NZ_LHSJ01000077
NZ_LHSJ01000037	22	18	0	4	21,753	RefSeq:NZ_LHSJ01000037
NZ_LHSJ01000061	23	13	0	10	21,744	RefSeq:NZ_LHSJ01000061
NZ_LHSJ01000150	19	14	0	5	21,044	RefSeq:NZ_LHSJ01000150
NZ_LHSJ01000076	19	14	1	4	21,032	RefSeq:NZ_LHSJ01000076
NZ_LHSJ01000038	20	18	0	2	20,948	RefSeq:NZ_LHSJ01000038
NZ_LHSJ01000039	21	14	0	7	20,458	RefSeq:NZ_LHSJ01000039
NZ_LHSJ01000185	13	10	0	3	20,457	RefSeq:NZ_LHSJ01000185
NZ_LHSJ01000040	17	9	0	8	20,394	RefSeq:NZ_LHSJ01000040
NZ_LHSJ01000084	15	13	0	2	20,199	RefSeq:NZ_LHSJ01000084
NZ_LHSJ01000071	21	18	0	3	20,113	RefSeq:NZ_LHSJ01000071
NZ_LHSJ01000042	17	16	0	1	20,085	RefSeq:NZ_LHSJ01000042
NZ_LHSJ01000043	16	9	0	7	19,987	RefSeq:NZ_LHSJ01000043
NZ_LHSJ01000095	19	15	0	4	19,900	RefSeq:NZ_LHSJ01000095
NZ_LHSJ01000045	19	18	0	1	19,870	RefSeq:NZ_LHSJ01000045
NZ_LHSJ01000093	13	9	0	4	19,866	RefSeq:NZ_LHSJ01000093
NZ_LHSJ01000046	23	17	2	4	19,778	RefSeq:NZ_LHSJ01000046
NZ_LHSJ01000085	20	11	4	5	19,460	RefSeq:NZ_LHSJ01000085
NZ_LHSJ01000047	15	10	0	5	19,139	RefSeq:NZ_LHSJ01000047
NZ_LHSJ01000048	17	14	0	3	18,988	RefSeq:NZ_LHSJ01000048
NZ_LHSJ01000114	16	11	0	5	18,758	RefSeq:NZ_LHSJ01000114
NZ_LHSJ01000099	19	16	0	3	18,602	RefSeq:NZ_LHSJ01000099
NZ_LHSJ01000128	16	11	0	5	18,535	RefSeq:NZ_LHSJ01000128
NZ_LHSJ01000101	18	13	0	5	18,338	RefSeq:NZ_LHSJ01000101
NZ_LHSJ01000052	18	12	0	6	18,253	RefSeq:NZ_LHSJ01000052
NZ_LHSJ01000054	16	14	0	2	18,232	RefSeq:NZ_LHSJ01000054
NZ_LHSJ01000056	21	20	1	0	17,981	RefSeq:NZ_LHSJ01000056
NZ_LHSJ01000058	13	12	0	1	17,538	RefSeq:NZ_LHSJ01000058
NZ_LHSJ01000059	15	12	0	3	17,460	RefSeq:NZ_LHSJ01000059
NZ_LHSJ01000060	17	11	1	5	17,206	RefSeq:NZ_LHSJ01000060
NZ_LHSJ01000126	15	12	1	2	17,146	RefSeq:NZ_LHSJ01000126
NZ_LHSJ01000136	19	16	0	3	17,119	RefSeq:NZ_LHSJ01000136
NZ_LHSJ01000062	13	12	0	1	17,090	RefSeq:NZ_LHSJ01000062
NZ_LHSJ01000063	17	6	1	10	16,915	RefSeq:NZ_LHSJ01000063
NZ_LHSJ01000147	13	7	0	6	16,631	RefSeq:NZ_LHSJ01000147
NZ_LHSJ01000155	17	8	0	9	16,604	RefSeq:NZ_LHSJ01000155
NZ_LHSJ01000064	14	13	0	1	16,271	RefSeq:NZ_LHSJ01000064
NZ_LHSJ01000069	18	16	0	2	15,959	RefSeq:NZ_LHSJ01000069
NZ_LHSJ01000138	19	15	0	4	15,915	RefSeq:NZ_LHSJ01000138
NZ_LHSJ01000137	18	11	0	7	15,443	RefSeq:NZ_LHSJ01000137
NZ_LHSJ01000197	12	9	0	3	15,373	RefSeq:NZ_LHSJ01000197
NZ_LHSJ01000161	16	10	1	5	15,221	RefSeq:NZ_LHSJ01000161
NZ_LHSJ01000170	21	16	0	5	15,095	RefSeq:NZ_LHSJ01000170
NZ_LHSJ01000168	14	12	0	2	14,994	RefSeq:NZ_LHSJ01000168
NZ_LHSJ01000183	17	5	0	12	14,977	RefSeq:NZ_LHSJ01000183
NZ_LHSJ01000078	16	14	0	2	14,968	RefSeq:NZ_LHSJ01000078
NZ_LHSJ01000079	15	10	0	5	14,961	RefSeq:NZ_LHSJ01000079
NZ_LHSJ01000080	12	6	1	5	14,928	RefSeq:NZ_LHSJ01000080
NZ_LHSJ01000083	15	9	0	6	14,720	RefSeq:NZ_LHSJ01000083
NZ_LHSJ01000153	14	5	0	9	14,691	RefSeq:NZ_LHSJ01000153
NZ_LHSJ01000087	14	13	0	1	14,482	RefSeq:NZ_LHSJ01000087
NZ_LHSJ01000089	12	7	0	5	14,373	RefSeq:NZ_LHSJ01000089
NZ_LHSJ01000169	15	12	0	3	14,289	RefSeq:NZ_LHSJ01000169
NZ_LHSJ01000157	13	9	0	4	14,176	RefSeq:NZ_LHSJ01000157
NZ_LHSJ01000090	14	10	1	3	14,106	RefSeq:NZ_LHSJ01000090
NZ_LHSJ01000092	17	12	0	5	14,087	RefSeq:NZ_LHSJ01000092
NZ_LHSJ01000094	15	14	0	1	14,043	RefSeq:NZ_LHSJ01000094
NZ_LHSJ01000162	17	11	0	6	13,955	RefSeq:NZ_LHSJ01000162
NZ_LHSJ01000096	14	10	0	4	13,896	RefSeq:NZ_LHSJ01000096
NZ_LHSJ01000098	14	13	0	1	13,684	RefSeq:NZ_LHSJ01000098
NZ_LHSJ01000159	14	7	1	6	13,573	RefSeq:NZ_LHSJ01000159
NZ_LHSJ01000207	13	11	0	2	13,480	RefSeq:NZ_LHSJ01000207
NZ_LHSJ01000190	14	4	0	10	13,478	RefSeq:NZ_LHSJ01000190
NZ_LHSJ01000171	15	7	0	8	13,461	RefSeq:NZ_LHSJ01000171
NZ_LHSJ01000102	11	10	0	1	13,239	RefSeq:NZ_LHSJ01000102
NZ_LHSJ01000103	12	7	0	5	13,216	RefSeq:NZ_LHSJ01000103
NZ_LHSJ01000104	18	13	0	5	13,188	RefSeq:NZ_LHSJ01000104
NZ_LHSJ01000233	14	12	0	2	13,118	RefSeq:NZ_LHSJ01000233
NZ_LHSJ01000106	12	8	0	4	13,026	RefSeq:NZ_LHSJ01000106
NZ_LHSJ01000109	13	7	0	6	12,922	RefSeq:NZ_LHSJ01000109
NZ_LHSJ01000110	14	11	0	3	12,850	RefSeq:NZ_LHSJ01000110
NZ_LHSJ01000212	14	9	0	5	12,741	RefSeq:NZ_LHSJ01000212
NZ_LHSJ01000240	12	6	0	6	12,530	RefSeq:NZ_LHSJ01000240
NZ_LHSJ01000230	12	6	0	6	12,306	RefSeq:NZ_LHSJ01000230
NZ_LHSJ01000115	11	11	0	0	12,272	RefSeq:NZ_LHSJ01000115
NZ_LHSJ01000116	16	7	0	9	12,223	RefSeq:NZ_LHSJ01000116
NZ_LHSJ01000117	11	6	0	5	12,154	RefSeq:NZ_LHSJ01000117
NZ_LHSJ01000118	12	9	0	3	12,132	RefSeq:NZ_LHSJ01000118
NZ_LHSJ01000119	11	10	0	1	12,101	RefSeq:NZ_LHSJ01000119
NZ_LHSJ01000121	13	12	0	1	12,081	RefSeq:NZ_LHSJ01000121
NZ_LHSJ01000122	14	12	0	2	12,068	RefSeq:NZ_LHSJ01000122
NZ_LHSJ01000123	16	8	4	4	12,038	RefSeq:NZ_LHSJ01000123
NZ_LHSJ01000232	13	9	0	4	11,799	RefSeq:NZ_LHSJ01000232
NZ_LHSJ01000255	12	6	0	6	11,795	RefSeq:NZ_LHSJ01000255
NZ_LHSJ01000127	12	8	1	3	11,744	RefSeq:NZ_LHSJ01000127
NZ_LHSJ01000239	12	9	0	3	11,403	RefSeq:NZ_LHSJ01000239
NZ_LHSJ01000130	13	8	0	5	11,222	RefSeq:NZ_LHSJ01000130
NZ_LHSJ01000238	12	3	0	9	10,737	RefSeq:NZ_LHSJ01000238
NZ_LHSJ01000152	14	12	0	2	9,969	RefSeq:NZ_LHSJ01000152
NZ_LHSJ01000163	12	9	2	1	9,502	RefSeq:NZ_LHSJ01000163
NZ_LHSJ01000172	11	10	0	1	9,052	RefSeq:NZ_LHSJ01000172
NZ_LHSJ01000173	11	10	0	1	8,997	RefSeq:NZ_LHSJ01000173
NZ_LHSJ01000177	12	6	0	6	8,696	RefSeq:NZ_LHSJ01000177
NZ_LHSJ01000189	13	12	0	1	8,233	RefSeq:NZ_LHSJ01000189
NZ_LHSJ01000205	11	10	0	1	7,622	RefSeq:NZ_LHSJ01000205
197 Undisplayed Contigs/Replicons	808	795	14	373	1,296,921

Total:	4,749	3,443	69	1,237	4,941,236

Ortholog data available?	No

Database Contents

Genes	4,747
Pathways	197
Enzymatic Reactions	1,088
Transport Reactions	78
Polypeptides	3,713
Protein Complexes	58
Enzymes	696
Transporters	600
Compounds	842
Transcription Units	3,327
tRNAs	56
Protein Features	4,368
GO Terms	13,692

Database Version

29.0

Sequence Source	GCF_001270295.1
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Betaproteobacteria Burkholderiales Alcaligenaceae Achromobacter unclassified Achromobacter Achromobacter sp. DMS1
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN03891578
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1688405
Environment	industrial effluent contaminated site
Geographic Location	India
Collection Date	2014-12-16
Annotation Provider	NCBI RefSeq
Annotation Date	2020-01-24
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, BIOCYC17.

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