Summary of Actinomadura rubrobrunea NBRC 15275, 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 8-Mar-2022 from the annotated genome of Actinomadura rubrobrunea NBRC 15275, 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_BCQU01000001	161	154	2	5	198,437	RefSeq:NZ_BCQU01000001
NZ_BCQU01000002	125	123	0	2	143,879	RefSeq:NZ_BCQU01000002
NZ_BCQU01000003	101	100	0	1	127,610	RefSeq:NZ_BCQU01000003
NZ_BCQU01000004	110	107	0	3	126,813	RefSeq:NZ_BCQU01000004
NZ_BCQU01000005	95	95	0	0	123,430	RefSeq:NZ_BCQU01000005
NZ_BCQU01000006	96	94	0	2	115,218	RefSeq:NZ_BCQU01000006
NZ_BCQU01000007	103	101	0	2	114,452	RefSeq:NZ_BCQU01000007
NZ_BCQU01000008	88	86	1	1	104,331	RefSeq:NZ_BCQU01000008
NZ_BCQU01000009	78	73	4	1	104,163	RefSeq:NZ_BCQU01000009
NZ_BCQU01000010	79	74	2	3	95,769	RefSeq:NZ_BCQU01000010
NZ_BCQU01000011	67	65	0	2	92,674	RefSeq:NZ_BCQU01000011
NZ_BCQU01000012	86	84	1	1	92,431	RefSeq:NZ_BCQU01000012
NZ_BCQU01000013	78	75	3	0	90,706	RefSeq:NZ_BCQU01000013
NZ_BCQU01000014	73	72	0	1	89,045	RefSeq:NZ_BCQU01000014
NZ_BCQU01000015	71	71	0	0	87,678	RefSeq:NZ_BCQU01000015
NZ_BCQU01000016	85	85	0	0	86,681	RefSeq:NZ_BCQU01000016
NZ_BCQU01000017	82	79	1	2	86,538	RefSeq:NZ_BCQU01000017
NZ_BCQU01000018	72	70	1	1	85,702	RefSeq:NZ_BCQU01000018
NZ_BCQU01000019	68	67	0	1	85,536	RefSeq:NZ_BCQU01000019
NZ_BCQU01000020	70	67	2	1	83,986	RefSeq:NZ_BCQU01000020
NZ_BCQU01000021	72	72	0	0	82,979	RefSeq:NZ_BCQU01000021
NZ_BCQU01000022	75	73	0	2	81,987	RefSeq:NZ_BCQU01000022
NZ_BCQU01000023	66	66	0	0	80,606	RefSeq:NZ_BCQU01000023
NZ_BCQU01000024	58	56	0	2	76,269	RefSeq:NZ_BCQU01000024
NZ_BCQU01000025	80	78	0	2	73,728	RefSeq:NZ_BCQU01000025
NZ_BCQU01000026	61	60	0	1	71,853	RefSeq:NZ_BCQU01000026
NZ_BCQU01000027	64	61	0	3	71,265	RefSeq:NZ_BCQU01000027
NZ_BCQU01000028	69	67	1	1	68,940	RefSeq:NZ_BCQU01000028
NZ_BCQU01000029	67	61	4	2	67,459	RefSeq:NZ_BCQU01000029
NZ_BCQU01000030	56	55	0	1	66,235	RefSeq:NZ_BCQU01000030
NZ_BCQU01000031	68	60	4	4	64,246	RefSeq:NZ_BCQU01000031
NZ_BCQU01000032	38	37	1	0	62,632	RefSeq:NZ_BCQU01000032
NZ_BCQU01000033	56	52	1	3	62,499	RefSeq:NZ_BCQU01000033
NZ_BCQU01000034	51	50	0	1	62,231	RefSeq:NZ_BCQU01000034
NZ_BCQU01000035	51	47	2	2	61,352	RefSeq:NZ_BCQU01000035
NZ_BCQU01000036	41	40	0	1	60,550	RefSeq:NZ_BCQU01000036
NZ_BCQU01000037	35	35	0	0	60,312	RefSeq:NZ_BCQU01000037
NZ_BCQU01000038	52	50	2	0	59,999	RefSeq:NZ_BCQU01000038
NZ_BCQU01000039	47	47	0	0	59,160	RefSeq:NZ_BCQU01000039
NZ_BCQU01000040	57	55	0	2	58,892	RefSeq:NZ_BCQU01000040
NZ_BCQU01000041	45	43	0	2	56,704	RefSeq:NZ_BCQU01000041
NZ_BCQU01000042	47	47	0	0	54,948	RefSeq:NZ_BCQU01000042
NZ_BCQU01000043	51	50	0	1	53,423	RefSeq:NZ_BCQU01000043
NZ_BCQU01000044	48	48	0	0	53,249	RefSeq:NZ_BCQU01000044
NZ_BCQU01000045	54	52	0	2	51,653	RefSeq:NZ_BCQU01000045
NZ_BCQU01000046	49	47	0	2	50,906	RefSeq:NZ_BCQU01000046
NZ_BCQU01000047	43	43	0	0	50,542	RefSeq:NZ_BCQU01000047
NZ_BCQU01000048	40	39	1	0	50,338	RefSeq:NZ_BCQU01000048
NZ_BCQU01000049	48	45	0	3	50,205	RefSeq:NZ_BCQU01000049
NZ_BCQU01000050	46	43	1	2	50,077	RefSeq:NZ_BCQU01000050
NZ_BCQU01000051	42	42	0	0	47,662	RefSeq:NZ_BCQU01000051
NZ_BCQU01000052	41	40	0	1	47,591	RefSeq:NZ_BCQU01000052
NZ_BCQU01000053	40	36	4	0	46,083	RefSeq:NZ_BCQU01000053
NZ_BCQU01000054	40	40	0	0	45,460	RefSeq:NZ_BCQU01000054
NZ_BCQU01000055	41	41	0	0	44,784	RefSeq:NZ_BCQU01000055
NZ_BCQU01000056	41	40	0	1	44,775	RefSeq:NZ_BCQU01000056
NZ_BCQU01000057	36	34	1	1	44,336	RefSeq:NZ_BCQU01000057
NZ_BCQU01000058	33	32	0	1	43,943	RefSeq:NZ_BCQU01000058
NZ_BCQU01000059	29	29	0	0	42,352	RefSeq:NZ_BCQU01000059
NZ_BCQU01000060	40	37	2	1	41,488	RefSeq:NZ_BCQU01000060
NZ_BCQU01000061	39	33	3	3	40,304	RefSeq:NZ_BCQU01000061
NZ_BCQU01000062	36	36	0	0	39,352	RefSeq:NZ_BCQU01000062
NZ_BCQU01000063	34	33	0	1	39,155	RefSeq:NZ_BCQU01000063
NZ_BCQU01000064	35	34	0	1	39,072	RefSeq:NZ_BCQU01000064
NZ_BCQU01000065	40	40	0	0	38,348	RefSeq:NZ_BCQU01000065
NZ_BCQU01000066	35	34	0	1	38,185	RefSeq:NZ_BCQU01000066
NZ_BCQU01000067	35	34	0	1	37,668	RefSeq:NZ_BCQU01000067
NZ_BCQU01000068	38	37	1	0	37,002	RefSeq:NZ_BCQU01000068
NZ_BCQU01000069	32	30	2	0	35,871	RefSeq:NZ_BCQU01000069
NZ_BCQU01000070	27	27	0	0	35,786	RefSeq:NZ_BCQU01000070
NZ_BCQU01000071	39	36	2	1	35,595	RefSeq:NZ_BCQU01000071
NZ_BCQU01000072	30	30	0	0	33,626	RefSeq:NZ_BCQU01000072
NZ_BCQU01000073	33	33	0	0	33,363	RefSeq:NZ_BCQU01000073
NZ_BCQU01000074	26	24	0	2	31,366	RefSeq:NZ_BCQU01000074
NZ_BCQU01000075	26	25	0	1	31,112	RefSeq:NZ_BCQU01000075
NZ_BCQU01000076	27	26	0	1	30,352	RefSeq:NZ_BCQU01000076
NZ_BCQU01000077	27	26	0	1	29,799	RefSeq:NZ_BCQU01000077
NZ_BCQU01000078	26	24	1	1	29,776	RefSeq:NZ_BCQU01000078
NZ_BCQU01000079	23	23	0	0	29,293	RefSeq:NZ_BCQU01000079
NZ_BCQU01000080	33	29	3	1	28,912	RefSeq:NZ_BCQU01000080
NZ_BCQU01000081	23	21	0	2	28,759	RefSeq:NZ_BCQU01000081
NZ_BCQU01000082	26	25	0	1	28,753	RefSeq:NZ_BCQU01000082
NZ_BCQU01000083	28	26	1	1	28,231	RefSeq:NZ_BCQU01000083
NZ_BCQU01000084	28	27	0	1	28,185	RefSeq:NZ_BCQU01000084
NZ_BCQU01000085	22	20	0	2	27,833	RefSeq:NZ_BCQU01000085
NZ_BCQU01000086	22	21	1	0	27,034	RefSeq:NZ_BCQU01000086
NZ_BCQU01000087	23	22	0	1	26,947	RefSeq:NZ_BCQU01000087
NZ_BCQU01000088	20	19	0	1	26,504	RefSeq:NZ_BCQU01000088
NZ_BCQU01000089	23	22	0	1	26,498	RefSeq:NZ_BCQU01000089
NZ_BCQU01000090	25	23	0	2	25,971	RefSeq:NZ_BCQU01000090
NZ_BCQU01000091	23	22	0	1	25,874	RefSeq:NZ_BCQU01000091
NZ_BCQU01000092	23	22	0	1	25,790	RefSeq:NZ_BCQU01000092
NZ_BCQU01000093	21	20	0	1	24,867	RefSeq:NZ_BCQU01000093
NZ_BCQU01000094	20	18	0	2	24,846	RefSeq:NZ_BCQU01000094
NZ_BCQU01000095	20	20	0	0	24,557	RefSeq:NZ_BCQU01000095
NZ_BCQU01000096	22	19	0	3	24,430	RefSeq:NZ_BCQU01000096
NZ_BCQU01000097	25	25	0	0	24,391	RefSeq:NZ_BCQU01000097
NZ_BCQU01000098	23	22	0	1	23,664	RefSeq:NZ_BCQU01000098
NZ_BCQU01000099	21	20	0	1	23,606	RefSeq:NZ_BCQU01000099
NZ_BCQU01000100	13	12	0	1	23,599	RefSeq:NZ_BCQU01000100
NZ_BCQU01000101	18	18	0	0	23,520	RefSeq:NZ_BCQU01000101
NZ_BCQU01000102	22	20	0	2	23,422	RefSeq:NZ_BCQU01000102
NZ_BCQU01000103	18	18	0	0	23,358	RefSeq:NZ_BCQU01000103
NZ_BCQU01000104	19	19	0	0	23,078	RefSeq:NZ_BCQU01000104
NZ_BCQU01000105	20	17	2	1	22,966	RefSeq:NZ_BCQU01000105
NZ_BCQU01000106	21	21	0	0	22,919	RefSeq:NZ_BCQU01000106
NZ_BCQU01000107	20	18	0	2	22,888	RefSeq:NZ_BCQU01000107
NZ_BCQU01000108	18	18	0	0	22,857	RefSeq:NZ_BCQU01000108
NZ_BCQU01000109	19	19	0	0	22,319	RefSeq:NZ_BCQU01000109
NZ_BCQU01000110	19	19	0	0	21,637	RefSeq:NZ_BCQU01000110
NZ_BCQU01000111	22	22	0	0	21,531	RefSeq:NZ_BCQU01000111
NZ_BCQU01000112	17	16	0	1	21,318	RefSeq:NZ_BCQU01000112
NZ_BCQU01000113	21	21	0	0	21,301	RefSeq:NZ_BCQU01000113
NZ_BCQU01000114	15	14	1	0	21,256	RefSeq:NZ_BCQU01000114
NZ_BCQU01000115	13	12	0	1	19,640	RefSeq:NZ_BCQU01000115
NZ_BCQU01000116	14	13	1	0	19,531	RefSeq:NZ_BCQU01000116
NZ_BCQU01000117	18	17	0	1	18,499	RefSeq:NZ_BCQU01000117
NZ_BCQU01000118	21	17	3	1	18,305	RefSeq:NZ_BCQU01000118
NZ_BCQU01000119	13	13	0	0	17,704	RefSeq:NZ_BCQU01000119
NZ_BCQU01000120	14	14	0	0	17,571	RefSeq:NZ_BCQU01000120
NZ_BCQU01000121	15	14	0	1	17,426	RefSeq:NZ_BCQU01000121
NZ_BCQU01000122	17	14	2	1	17,017	RefSeq:NZ_BCQU01000122
NZ_BCQU01000123	15	15	0	0	16,928	RefSeq:NZ_BCQU01000123
NZ_BCQU01000124	11	10	0	1	16,288	RefSeq:NZ_BCQU01000124
NZ_BCQU01000126	14	13	0	1	15,689	RefSeq:NZ_BCQU01000126
NZ_BCQU01000128	14	13	0	1	15,061	RefSeq:NZ_BCQU01000128
NZ_BCQU01000130	16	15	0	1	14,785	RefSeq:NZ_BCQU01000130
NZ_BCQU01000132	15	15	0	0	14,274	RefSeq:NZ_BCQU01000132
NZ_BCQU01000136	13	12	0	1	13,216	RefSeq:NZ_BCQU01000136
NZ_BCQU01000137	12	11	0	1	12,947	RefSeq:NZ_BCQU01000137
NZ_BCQU01000138	11	10	1	0	11,394	RefSeq:NZ_BCQU01000138
97 Undisplayed Contigs/Replicons	301	297	7	43	460,454

Total:	5,760	5,517	72	171	6,724,167

Ortholog data available?	Yes

Database Contents

Genes	5,756
Pathways	275
Enzymatic Reactions	1,464
Transport Reactions	47
Polypeptides	5,679
Protein Complexes	5
Enzymes	1,012
Transporters	497
Compounds	1,108
Transcription Units	4,467
tRNAs	63
Protein Features	6,661
GO Terms	338

Database Version

29.0

Sequence Source	GCF_001552235.1
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Actinomycetota Actinomycetes Streptosporangiales Thermomonosporaceae Actinomadura Actinomadura rubrobrunea Actinomadura rubrobrunea NBRC 15275
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMD00046516
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1220567
Annotation Provider	NCBI RefSeq
Annotation Date	2021-07-10
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	5.2
Annotation Comment	Best-placed reference protein set; GeneMarkS-2+
NCBI Genome Type	representative

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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