Summary of Acidocella aminolytica 101 = DSM 11237, 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 Acidocella aminolytica 101 = DSM 11237, 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_BANC01000020	171	168	2	1	172,366	RefSeq:NZ_BANC01000020
NZ_BANC01000034	140	133	1	6	151,520	RefSeq:NZ_BANC01000034
NZ_BANC01000059	114	106	6	2	129,627	RefSeq:NZ_BANC01000059
NZ_BANC01000087	117	113	2	2	119,259	RefSeq:NZ_BANC01000087
NZ_BANC01000054	117	112	3	2	114,648	RefSeq:NZ_BANC01000054
NZ_BANC01000021	98	98	0	0	110,571	RefSeq:NZ_BANC01000021
NZ_BANC01000017	83	82	1	0	87,358	RefSeq:NZ_BANC01000017
NZ_BANC01000025	83	82	0	1	84,317	RefSeq:NZ_BANC01000025
NZ_BANC01000007	80	78	0	2	83,746	RefSeq:NZ_BANC01000007
NZ_BANC01000005	89	84	3	2	82,829	RefSeq:NZ_BANC01000005
NZ_BANC01000046	81	78	1	2	80,003	RefSeq:NZ_BANC01000046
NZ_BANC01000011	78	75	2	1	79,488	RefSeq:NZ_BANC01000011
NZ_BANC01000035	82	82	0	0	73,074	RefSeq:NZ_BANC01000035
NZ_BANC01000010	59	58	0	1	67,796	RefSeq:NZ_BANC01000010
NZ_BANC01000016	66	56	0	10	59,750	RefSeq:NZ_BANC01000016
NZ_BANC01000039	52	51	0	1	56,522	RefSeq:NZ_BANC01000039
NZ_BANC01000023	46	46	0	0	55,582	RefSeq:NZ_BANC01000023
NZ_BANC01000124	52	50	1	1	52,525	RefSeq:NZ_BANC01000124
NZ_BANC01000041	62	57	2	3	52,080	RefSeq:NZ_BANC01000041
NZ_BANC01000040	63	63	0	0	51,257	RefSeq:NZ_BANC01000040
NZ_BANC01000064	51	51	0	0	51,001	RefSeq:NZ_BANC01000064
NZ_BANC01000045	61	60	0	1	50,438	RefSeq:NZ_BANC01000045
NZ_BANC01000090	49	46	1	2	46,920	RefSeq:NZ_BANC01000090
NZ_BANC01000026	44	41	3	0	45,425	RefSeq:NZ_BANC01000026
NZ_BANC01000095	34	34	0	0	44,400	RefSeq:NZ_BANC01000095
NZ_BANC01000030	62	62	0	0	44,154	RefSeq:NZ_BANC01000030
NZ_BANC01000125	37	36	1	0	42,691	RefSeq:NZ_BANC01000125
NZ_BANC01000018	45	44	0	1	42,485	RefSeq:NZ_BANC01000018
NZ_BANC01000053	42	40	0	2	40,714	RefSeq:NZ_BANC01000053
NZ_BANC01000104	30	30	0	0	40,651	RefSeq:NZ_BANC01000104
NZ_BANC01000048	38	37	0	1	38,512	RefSeq:NZ_BANC01000048
NZ_BANC01000036	34	33	0	1	38,384	RefSeq:NZ_BANC01000036
NZ_BANC01000022	36	30	0	6	37,133	RefSeq:NZ_BANC01000022
NZ_BANC01000089	37	36	1	0	36,819	RefSeq:NZ_BANC01000089
NZ_BANC01000117	35	33	1	1	35,729	RefSeq:NZ_BANC01000117
NZ_BANC01000076	41	40	0	1	35,023	RefSeq:NZ_BANC01000076
NZ_BANC01000070	28	28	0	0	34,547	RefSeq:NZ_BANC01000070
NZ_BANC01000044	32	29	0	3	34,155	RefSeq:NZ_BANC01000044
NZ_BANC01000112	33	29	2	2	33,274	RefSeq:NZ_BANC01000112
NZ_BANC01000071	32	28	2	2	33,145	RefSeq:NZ_BANC01000071
NZ_BANC01000094	33	31	0	2	32,361	RefSeq:NZ_BANC01000094
NZ_BANC01000012	29	27	0	2	32,350	RefSeq:NZ_BANC01000012
NZ_BANC01000110	34	31	1	2	32,159	RefSeq:NZ_BANC01000110
NZ_BANC01000050	26	24	1	1	30,448	RefSeq:NZ_BANC01000050
NZ_BANC01000312	29	29	0	0	30,437	RefSeq:NZ_BANC01000312
NZ_BANC01000015	40	37	1	2	30,363	RefSeq:NZ_BANC01000015
NZ_BANC01000068	35	33	0	2	29,678	RefSeq:NZ_BANC01000068
NZ_BANC01000121	24	24	0	0	27,448	RefSeq:NZ_BANC01000121
NZ_BANC01000009	23	21	0	2	25,675	RefSeq:NZ_BANC01000009
NZ_BANC01000074	24	23	0	1	25,193	RefSeq:NZ_BANC01000074
NZ_BANC01000043	31	30	0	1	25,111	RefSeq:NZ_BANC01000043
NZ_BANC01000101	21	21	0	0	25,095	RefSeq:NZ_BANC01000101
NZ_BANC01000006	25	25	0	0	23,973	RefSeq:NZ_BANC01000006
NZ_BANC01000060	24	23	0	1	23,699	RefSeq:NZ_BANC01000060
NZ_BANC01000146	22	21	0	1	23,361	RefSeq:NZ_BANC01000146
NZ_BANC01000088	20	20	0	0	22,981	RefSeq:NZ_BANC01000088
NZ_BANC01000116	25	23	1	1	22,702	RefSeq:NZ_BANC01000116
NZ_BANC01000106	21	21	0	0	21,466	RefSeq:NZ_BANC01000106
NZ_BANC01000001	20	19	1	0	21,139	RefSeq:NZ_BANC01000001
NZ_BANC01000061	21	19	0	2	20,540	RefSeq:NZ_BANC01000061
NZ_BANC01000057	14	14	0	0	19,805	RefSeq:NZ_BANC01000057
NZ_BANC01000156	13	13	0	0	19,005	RefSeq:NZ_BANC01000156
NZ_BANC01000108	15	14	0	1	18,518	RefSeq:NZ_BANC01000108
NZ_BANC01000170	15	11	0	4	18,068	RefSeq:NZ_BANC01000170
NZ_BANC01000142	19	19	0	0	17,663	RefSeq:NZ_BANC01000142
NZ_BANC01000028	17	16	0	1	17,553	RefSeq:NZ_BANC01000028
NZ_BANC01000019	18	16	0	2	17,417	RefSeq:NZ_BANC01000019
NZ_BANC01000055	16	14	1	1	17,042	RefSeq:NZ_BANC01000055
NZ_BANC01000024	15	12	0	3	16,513	RefSeq:NZ_BANC01000024
NZ_BANC01000115	12	12	0	0	16,456	RefSeq:NZ_BANC01000115
NZ_BANC01000167	18	18	0	0	16,175	RefSeq:NZ_BANC01000167
NZ_BANC01000096	17	12	0	5	15,613	RefSeq:NZ_BANC01000096
NZ_BANC01000029	14	14	0	0	15,360	RefSeq:NZ_BANC01000029
NZ_BANC01000052	14	13	0	1	14,740	RefSeq:NZ_BANC01000052
NZ_BANC01000091	12	9	0	3	14,277	RefSeq:NZ_BANC01000091
NZ_BANC01000031	14	13	0	1	14,186	RefSeq:NZ_BANC01000031
NZ_BANC01000150	14	13	0	1	13,833	RefSeq:NZ_BANC01000150
NZ_BANC01000107	15	13	0	2	13,661	RefSeq:NZ_BANC01000107
NZ_BANC01000118	14	14	0	0	13,141	RefSeq:NZ_BANC01000118
NZ_BANC01000003	13	13	0	0	13,108	RefSeq:NZ_BANC01000003
NZ_BANC01000097	11	10	0	1	12,996	RefSeq:NZ_BANC01000097
NZ_BANC01000062	12	11	0	1	12,053	RefSeq:NZ_BANC01000062
NZ_BANC01000127	13	12	1	0	12,008	RefSeq:NZ_BANC01000127
NZ_BANC01000169	12	11	0	1	11,986	RefSeq:NZ_BANC01000169
411 Undisplayed Contigs/Replicons	344	337	7	119	517,458

Total:	3,871	3,595	49	227	3,984,732

Ortholog data available?	No

Database Contents

Genes	3,871
Pathways	292
Enzymatic Reactions	1,356
Transport Reactions	57
Polypeptides	3,697
Protein Complexes	60
Enzymes	823
Transporters	335
Compounds	1,029
Transcription Units	2,409
tRNAs	42
Protein Features	4,500
GO Terms	12,907

Database Version

29.0

Sequence Source	GCF_000964385.1
Synonyms	Acidocella aminolytica 101 Acidocella aminolytica DSM 11237 Acidocella aminolytica DSM 11237 = 101 Acidocella aminolytica 101 = DSM 11237
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Alphaproteobacteria Rhodospirillales Acetobacteraceae Acidocella Acidocella aminolytica Acidocella aminolytica 101 = DSM 11237
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMD00036638
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1120923
Environment	G_DNA_Vaginal introitus
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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