Summary of Acetonema longum DSM 6540, version 29.0

Tier 3 Uncurated Organism Database

Database Authors

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

Summary

This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acetonema longum DSM 6540, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_AFGF01000017	226	220	4	2	223,575	RefSeq:NZ_AFGF01000017
NZ_AFGF01000126	139	139	0	0	133,767	RefSeq:NZ_AFGF01000126
NZ_AFGF01000050	117	115	0	2	128,928	RefSeq:NZ_AFGF01000050
NZ_AFGF01000049	102	96	5	1	127,366	RefSeq:NZ_AFGF01000049
NZ_AFGF01000234	99	95	0	4	115,823	RefSeq:NZ_AFGF01000234
NZ_AFGF01000056	104	102	1	1	105,611	RefSeq:NZ_AFGF01000056
NZ_AFGF01000107	123	120	2	1	100,070	RefSeq:NZ_AFGF01000107
NZ_AFGF01000040	101	100	1	0	97,835	RefSeq:NZ_AFGF01000040
NZ_AFGF01000240	88	87	0	1	92,808	RefSeq:NZ_AFGF01000240
NZ_AFGF01000269	84	82	0	2	89,007	RefSeq:NZ_AFGF01000269
NZ_AFGF01000053	85	85	0	0	88,740	RefSeq:NZ_AFGF01000053
NZ_AFGF01000085	70	69	0	1	84,717	RefSeq:NZ_AFGF01000085
NZ_AFGF01000081	74	68	6	0	80,672	RefSeq:NZ_AFGF01000081
NZ_AFGF01000015	66	66	0	0	72,761	RefSeq:NZ_AFGF01000015
NZ_AFGF01000016	68	64	2	2	72,004	RefSeq:NZ_AFGF01000016
NZ_AFGF01000280	71	68	1	2	71,996	RefSeq:NZ_AFGF01000280
NZ_AFGF01000144	58	56	0	2	68,977	RefSeq:NZ_AFGF01000144
NZ_AFGF01000007	59	56	0	3	67,247	RefSeq:NZ_AFGF01000007
NZ_AFGF01000241	67	64	0	3	66,976	RefSeq:NZ_AFGF01000241
NZ_AFGF01000157	58	56	0	2	63,182	RefSeq:NZ_AFGF01000157
NZ_AFGF01000012	23	22	0	1	61,407	RefSeq:NZ_AFGF01000012
NZ_AFGF01000119	54	52	0	2	60,880	RefSeq:NZ_AFGF01000119
NZ_AFGF01000221	54	53	1	0	60,581	RefSeq:NZ_AFGF01000221
NZ_AFGF01000054	48	47	0	1	59,655	RefSeq:NZ_AFGF01000054
NZ_AFGF01000121	58	50	5	3	59,457	RefSeq:NZ_AFGF01000121
NZ_AFGF01000005	48	48	0	0	54,626	RefSeq:NZ_AFGF01000005
NZ_AFGF01000019	65	64	0	1	53,616	RefSeq:NZ_AFGF01000019
NZ_AFGF01000079	54	53	0	1	50,140	RefSeq:NZ_AFGF01000079
NZ_AFGF01000102	60	60	0	0	48,790	RefSeq:NZ_AFGF01000102
NZ_AFGF01000066	46	44	1	1	47,695	RefSeq:NZ_AFGF01000066
NZ_AFGF01000024	37	37	0	0	44,577	RefSeq:NZ_AFGF01000024
NZ_AFGF01000076	37	37	0	0	42,585	RefSeq:NZ_AFGF01000076
NZ_AFGF01000074	43	42	0	1	42,539	RefSeq:NZ_AFGF01000074
NZ_AFGF01000294	36	36	0	0	41,863	RefSeq:NZ_AFGF01000294
NZ_AFGF01000098	34	33	0	1	41,513	RefSeq:NZ_AFGF01000098
NZ_AFGF01000025	30	30	0	0	39,325	RefSeq:NZ_AFGF01000025
NZ_AFGF01000013	41	31	10	0	38,224	RefSeq:NZ_AFGF01000013
NZ_AFGF01000163	31	30	0	1	38,024	RefSeq:NZ_AFGF01000163
NZ_AFGF01000078	35	31	0	4	37,898	RefSeq:NZ_AFGF01000078
NZ_AFGF01000205	35	32	3	0	36,815	RefSeq:NZ_AFGF01000205
NZ_AFGF01000087	30	29	0	1	34,725	RefSeq:NZ_AFGF01000087
NZ_AFGF01000166	32	32	0	0	33,848	RefSeq:NZ_AFGF01000166
NZ_AFGF01000065	25	25	0	0	31,813	RefSeq:NZ_AFGF01000065
NZ_AFGF01000006	29	28	0	1	31,507	RefSeq:NZ_AFGF01000006
NZ_AFGF01000135	26	26	0	0	31,335	RefSeq:NZ_AFGF01000135
NZ_AFGF01000115	39	30	7	2	30,489	RefSeq:NZ_AFGF01000115
NZ_AFGF01000173	27	26	0	1	30,242	RefSeq:NZ_AFGF01000173
NZ_AFGF01000162	27	26	0	1	29,827	RefSeq:NZ_AFGF01000162
NZ_AFGF01000083	29	28	0	1	29,752	RefSeq:NZ_AFGF01000083
NZ_AFGF01000026	23	23	0	0	27,907	RefSeq:NZ_AFGF01000026
NZ_AFGF01000038	22	21	0	1	27,754	RefSeq:NZ_AFGF01000038
NZ_AFGF01000030	33	32	1	0	27,661	RefSeq:NZ_AFGF01000030
NZ_AFGF01000211	28	28	0	0	27,076	RefSeq:NZ_AFGF01000211
NZ_AFGF01000060	24	24	0	0	26,813	RefSeq:NZ_AFGF01000060
NZ_AFGF01000032	28	28	0	0	25,186	RefSeq:NZ_AFGF01000032
NZ_AFGF01000101	23	23	0	0	24,174	RefSeq:NZ_AFGF01000101
NZ_AFGF01000014	27	25	2	0	22,600	RefSeq:NZ_AFGF01000014
NZ_AFGF01000191	20	17	0	3	22,445	RefSeq:NZ_AFGF01000191
NZ_AFGF01000084	20	20	0	0	22,174	RefSeq:NZ_AFGF01000084
NZ_AFGF01000118	13	13	0	0	21,289	RefSeq:NZ_AFGF01000118
NZ_AFGF01000010	19	19	0	0	21,176	RefSeq:NZ_AFGF01000010
NZ_AFGF01000197	26	26	0	0	20,847	RefSeq:NZ_AFGF01000197
NZ_AFGF01000193	21	20	0	1	20,462	RefSeq:NZ_AFGF01000193
NZ_AFGF01000290	14	14	0	0	20,456	RefSeq:NZ_AFGF01000290
NZ_AFGF01000270	20	19	0	1	19,807	RefSeq:NZ_AFGF01000270
NZ_AFGF01000037	21	21	0	0	19,528	RefSeq:NZ_AFGF01000037
NZ_AFGF01000041	17	16	1	0	18,779	RefSeq:NZ_AFGF01000041
NZ_AFGF01000042	19	18	0	1	17,922	RefSeq:NZ_AFGF01000042
NZ_AFGF01000181	13	13	0	0	17,320	RefSeq:NZ_AFGF01000181
NZ_AFGF01000143	18	18	0	0	16,212	RefSeq:NZ_AFGF01000143
NZ_AFGF01000071	14	13	1	0	16,082	RefSeq:NZ_AFGF01000071
NZ_AFGF01000051	13	13	0	0	15,102	RefSeq:NZ_AFGF01000051
NZ_AFGF01000198	15	15	0	0	14,870	RefSeq:NZ_AFGF01000198
NZ_AFGF01000116	12	12	0	0	14,620	RefSeq:NZ_AFGF01000116
NZ_AFGF01000158	12	12	0	0	14,237	RefSeq:NZ_AFGF01000158
NZ_AFGF01000263	14	13	1	0	13,534	RefSeq:NZ_AFGF01000263
NZ_AFGF01000243	12	12	0	0	12,982	RefSeq:NZ_AFGF01000243
NZ_AFGF01000186	12	12	0	0	12,467	RefSeq:NZ_AFGF01000186
NZ_AFGF01000073	12	10	0	2	10,662	RefSeq:NZ_AFGF01000073
NZ_AFGF01000068	12	12	0	0	10,038	RefSeq:NZ_AFGF01000068
NZ_AFGF01000258	11	11	0	0	8,512	RefSeq:NZ_AFGF01000258
215 Undisplayed Contigs/Replicons	396	381	17	33	516,507

Total:	4,011	3,844	72	95	4,323,011

Ortholog data available?	Yes

Database Contents

Genes	4,009
Pathways	246
Enzymatic Reactions	1,299
Transport Reactions	94
Polypeptides	3,993
Protein Complexes	107
Enzymes	803
Transporters	395
Compounds	1,010
Transcription Units	2,675
tRNAs	63
Protein Features	4,985
GO Terms	354

Database Version

29.0

Sequence Source	GCF_000219125.1
Synonyms	Acetonema longum APO-1 Acetonema longum strain DSM 6540 Acetonema longum str. DSM 6540 Acetonema longum DSM 6540
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Bacillota Negativicutes Selenomonadales Sporomusaceae Acetonema Acetonema longum Acetonema longum DSM 6540
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN02469409
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1009370
Environment	termite hindgut
Annotation Provider	NCBI RefSeq
Annotation Date	2022-02-15
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	6.0
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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