Summary of Actinomadura formosensis NBRC 14204, 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 formosensis NBRC 14204, 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_BCQQ01000001	122	122	0	0	135,934	RefSeq:NZ_BCQQ01000001
NZ_BCQQ01000002	81	79	0	2	101,231	RefSeq:NZ_BCQQ01000002
NZ_BCQQ01000003	98	93	2	3	98,496	RefSeq:NZ_BCQQ01000003
NZ_BCQQ01000004	91	89	1	1	97,431	RefSeq:NZ_BCQQ01000004
NZ_BCQQ01000005	86	85	1	0	93,483	RefSeq:NZ_BCQQ01000005
NZ_BCQQ01000006	79	79	0	0	92,356	RefSeq:NZ_BCQQ01000006
NZ_BCQQ01000007	94	93	0	1	91,844	RefSeq:NZ_BCQQ01000007
NZ_BCQQ01000008	92	89	3	0	88,691	RefSeq:NZ_BCQQ01000008
NZ_BCQQ01000009	79	78	0	1	88,453	RefSeq:NZ_BCQQ01000009
NZ_BCQQ01000010	71	65	2	4	85,469	RefSeq:NZ_BCQQ01000010
NZ_BCQQ01000011	89	80	6	3	82,582	RefSeq:NZ_BCQQ01000011
NZ_BCQQ01000012	77	77	0	0	80,114	RefSeq:NZ_BCQQ01000012
NZ_BCQQ01000013	65	61	0	4	78,851	RefSeq:NZ_BCQQ01000013
NZ_BCQQ01000014	66	63	2	1	78,732	RefSeq:NZ_BCQQ01000014
NZ_BCQQ01000015	64	62	0	2	76,458	RefSeq:NZ_BCQQ01000015
NZ_BCQQ01000016	65	64	0	1	75,636	RefSeq:NZ_BCQQ01000016
NZ_BCQQ01000017	65	61	4	0	72,596	RefSeq:NZ_BCQQ01000017
NZ_BCQQ01000018	68	65	1	2	71,587	RefSeq:NZ_BCQQ01000018
NZ_BCQQ01000019	70	70	0	0	70,942	RefSeq:NZ_BCQQ01000019
NZ_BCQQ01000020	67	66	0	1	67,831	RefSeq:NZ_BCQQ01000020
NZ_BCQQ01000021	66	64	0	2	66,753	RefSeq:NZ_BCQQ01000021
NZ_BCQQ01000022	63	62	0	1	66,375	RefSeq:NZ_BCQQ01000022
NZ_BCQQ01000023	61	49	4	8	65,474	RefSeq:NZ_BCQQ01000023
NZ_BCQQ01000024	55	55	0	0	64,833	RefSeq:NZ_BCQQ01000024
NZ_BCQQ01000025	64	64	0	0	64,738	RefSeq:NZ_BCQQ01000025
NZ_BCQQ01000026	54	51	1	2	63,977	RefSeq:NZ_BCQQ01000026
NZ_BCQQ01000027	59	57	1	1	63,640	RefSeq:NZ_BCQQ01000027
NZ_BCQQ01000028	56	56	0	0	61,685	RefSeq:NZ_BCQQ01000028
NZ_BCQQ01000029	59	59	0	0	61,506	RefSeq:NZ_BCQQ01000029
NZ_BCQQ01000030	57	55	1	1	60,260	RefSeq:NZ_BCQQ01000030
NZ_BCQQ01000031	58	58	0	0	59,791	RefSeq:NZ_BCQQ01000031
NZ_BCQQ01000032	52	51	1	0	59,649	RefSeq:NZ_BCQQ01000032
NZ_BCQQ01000033	53	51	0	2	56,040	RefSeq:NZ_BCQQ01000033
NZ_BCQQ01000034	46	46	0	0	55,941	RefSeq:NZ_BCQQ01000034
NZ_BCQQ01000035	55	53	0	2	55,609	RefSeq:NZ_BCQQ01000035
NZ_BCQQ01000036	62	60	0	2	54,729	RefSeq:NZ_BCQQ01000036
NZ_BCQQ01000037	56	54	0	2	53,429	RefSeq:NZ_BCQQ01000037
NZ_BCQQ01000038	60	58	1	1	53,132	RefSeq:NZ_BCQQ01000038
NZ_BCQQ01000039	49	48	0	1	52,628	RefSeq:NZ_BCQQ01000039
NZ_BCQQ01000041	38	37	1	0	52,007	RefSeq:NZ_BCQQ01000041
NZ_BCQQ01000040	54	50	2	2	51,845	RefSeq:NZ_BCQQ01000040
NZ_BCQQ01000042	45	44	0	1	50,096	RefSeq:NZ_BCQQ01000042
NZ_BCQQ01000043	59	58	0	1	49,911	RefSeq:NZ_BCQQ01000043
NZ_BCQQ01000044	45	43	0	2	47,889	RefSeq:NZ_BCQQ01000044
NZ_BCQQ01000045	29	28	0	1	45,951	RefSeq:NZ_BCQQ01000045
NZ_BCQQ01000046	36	34	0	2	44,753	RefSeq:NZ_BCQQ01000046
NZ_BCQQ01000047	45	45	0	0	43,677	RefSeq:NZ_BCQQ01000047
NZ_BCQQ01000048	37	36	0	1	43,050	RefSeq:NZ_BCQQ01000048
NZ_BCQQ01000049	22	22	0	0	42,900	RefSeq:NZ_BCQQ01000049
NZ_BCQQ01000050	37	36	0	1	42,898	RefSeq:NZ_BCQQ01000050
NZ_BCQQ01000051	39	37	0	2	42,599	RefSeq:NZ_BCQQ01000051
NZ_BCQQ01000052	38	37	0	1	42,183	RefSeq:NZ_BCQQ01000052
NZ_BCQQ01000053	42	41	0	1	42,154	RefSeq:NZ_BCQQ01000053
NZ_BCQQ01000054	37	34	1	2	42,023	RefSeq:NZ_BCQQ01000054
NZ_BCQQ01000055	38	38	0	0	41,848	RefSeq:NZ_BCQQ01000055
NZ_BCQQ01000056	40	39	0	1	41,815	RefSeq:NZ_BCQQ01000056
NZ_BCQQ01000057	43	42	0	1	41,246	RefSeq:NZ_BCQQ01000057
NZ_BCQQ01000058	38	36	1	1	40,885	RefSeq:NZ_BCQQ01000058
NZ_BCQQ01000059	34	34	0	0	40,205	RefSeq:NZ_BCQQ01000059
NZ_BCQQ01000060	47	43	0	4	40,041	RefSeq:NZ_BCQQ01000060
NZ_BCQQ01000061	44	41	0	3	38,116	RefSeq:NZ_BCQQ01000061
NZ_BCQQ01000062	32	31	1	0	38,075	RefSeq:NZ_BCQQ01000062
NZ_BCQQ01000063	32	31	0	1	37,846	RefSeq:NZ_BCQQ01000063
NZ_BCQQ01000064	32	32	0	0	37,638	RefSeq:NZ_BCQQ01000064
NZ_BCQQ01000065	41	40	0	1	37,488	RefSeq:NZ_BCQQ01000065
NZ_BCQQ01000066	35	35	0	0	37,445	RefSeq:NZ_BCQQ01000066
NZ_BCQQ01000067	36	35	1	0	37,272	RefSeq:NZ_BCQQ01000067
NZ_BCQQ01000068	31	31	0	0	37,021	RefSeq:NZ_BCQQ01000068
NZ_BCQQ01000069	33	33	0	0	36,990	RefSeq:NZ_BCQQ01000069
NZ_BCQQ01000070	35	34	0	1	36,653	RefSeq:NZ_BCQQ01000070
NZ_BCQQ01000071	39	38	0	1	36,620	RefSeq:NZ_BCQQ01000071
NZ_BCQQ01000072	36	35	0	1	36,353	RefSeq:NZ_BCQQ01000072
NZ_BCQQ01000073	33	33	0	0	35,591	RefSeq:NZ_BCQQ01000073
NZ_BCQQ01000074	29	28	0	1	35,303	RefSeq:NZ_BCQQ01000074
NZ_BCQQ01000075	31	30	0	1	34,997	RefSeq:NZ_BCQQ01000075
NZ_BCQQ01000076	33	32	0	1	34,788	RefSeq:NZ_BCQQ01000076
NZ_BCQQ01000077	37	37	0	0	34,602	RefSeq:NZ_BCQQ01000077
NZ_BCQQ01000078	34	33	0	1	34,590	RefSeq:NZ_BCQQ01000078
NZ_BCQQ01000079	26	25	0	1	34,460	RefSeq:NZ_BCQQ01000079
NZ_BCQQ01000080	32	32	0	0	33,771	RefSeq:NZ_BCQQ01000080
NZ_BCQQ01000081	34	34	0	0	32,788	RefSeq:NZ_BCQQ01000081
NZ_BCQQ01000082	29	29	0	0	32,768	RefSeq:NZ_BCQQ01000082
NZ_BCQQ01000083	31	30	0	1	32,559	RefSeq:NZ_BCQQ01000083
NZ_BCQQ01000084	31	31	0	0	32,470	RefSeq:NZ_BCQQ01000084
NZ_BCQQ01000085	30	30	0	0	32,274	RefSeq:NZ_BCQQ01000085
NZ_BCQQ01000086	25	24	0	1	31,941	RefSeq:NZ_BCQQ01000086
NZ_BCQQ01000087	30	29	0	1	31,874	RefSeq:NZ_BCQQ01000087
NZ_BCQQ01000088	26	26	0	0	31,562	RefSeq:NZ_BCQQ01000088
NZ_BCQQ01000089	29	29	0	0	31,320	RefSeq:NZ_BCQQ01000089
NZ_BCQQ01000090	24	24	0	0	30,854	RefSeq:NZ_BCQQ01000090
NZ_BCQQ01000091	28	28	0	0	30,217	RefSeq:NZ_BCQQ01000091
NZ_BCQQ01000092	16	15	0	1	30,174	RefSeq:NZ_BCQQ01000092
NZ_BCQQ01000093	30	28	0	2	29,554	RefSeq:NZ_BCQQ01000093
NZ_BCQQ01000094	25	24	0	1	29,487	RefSeq:NZ_BCQQ01000094
NZ_BCQQ01000095	27	26	1	0	29,027	RefSeq:NZ_BCQQ01000095
NZ_BCQQ01000096	22	21	0	1	28,821	RefSeq:NZ_BCQQ01000096
NZ_BCQQ01000097	23	21	0	2	28,140	RefSeq:NZ_BCQQ01000097
NZ_BCQQ01000098	30	30	0	0	27,106	RefSeq:NZ_BCQQ01000098
NZ_BCQQ01000099	24	24	0	0	27,004	RefSeq:NZ_BCQQ01000099
NZ_BCQQ01000100	25	25	0	0	26,164	RefSeq:NZ_BCQQ01000100
NZ_BCQQ01000101	21	21	0	0	25,971	RefSeq:NZ_BCQQ01000101
NZ_BCQQ01000102	24	22	0	2	25,662	RefSeq:NZ_BCQQ01000102
NZ_BCQQ01000103	31	30	0	1	25,493	RefSeq:NZ_BCQQ01000103
NZ_BCQQ01000104	22	20	0	2	25,449	RefSeq:NZ_BCQQ01000104
NZ_BCQQ01000105	25	25	0	0	25,154	RefSeq:NZ_BCQQ01000105
NZ_BCQQ01000106	22	21	0	1	24,994	RefSeq:NZ_BCQQ01000106
NZ_BCQQ01000107	20	19	0	1	24,933	RefSeq:NZ_BCQQ01000107
NZ_BCQQ01000108	22	22	0	0	24,537	RefSeq:NZ_BCQQ01000108
NZ_BCQQ01000109	22	20	0	2	24,093	RefSeq:NZ_BCQQ01000109
NZ_BCQQ01000110	23	22	0	1	24,025	RefSeq:NZ_BCQQ01000110
NZ_BCQQ01000111	30	26	3	1	24,008	RefSeq:NZ_BCQQ01000111
NZ_BCQQ01000112	21	21	0	0	23,583	RefSeq:NZ_BCQQ01000112
NZ_BCQQ01000113	21	21	0	0	23,493	RefSeq:NZ_BCQQ01000113
NZ_BCQQ01000114	25	24	0	1	23,243	RefSeq:NZ_BCQQ01000114
NZ_BCQQ01000115	20	20	0	0	23,119	RefSeq:NZ_BCQQ01000115
NZ_BCQQ01000116	22	22	0	0	23,075	RefSeq:NZ_BCQQ01000116
NZ_BCQQ01000117	24	22	0	2	22,430	RefSeq:NZ_BCQQ01000117
NZ_BCQQ01000118	25	25	0	0	22,424	RefSeq:NZ_BCQQ01000118
NZ_BCQQ01000119	14	13	0	1	22,125	RefSeq:NZ_BCQQ01000119
NZ_BCQQ01000120	15	15	0	0	21,624	RefSeq:NZ_BCQQ01000120
NZ_BCQQ01000121	22	22	0	0	21,519	RefSeq:NZ_BCQQ01000121
NZ_BCQQ01000122	24	22	1	1	21,519	RefSeq:NZ_BCQQ01000122
NZ_BCQQ01000123	25	23	0	2	21,395	RefSeq:NZ_BCQQ01000123
NZ_BCQQ01000124	19	19	0	0	20,897	RefSeq:NZ_BCQQ01000124
NZ_BCQQ01000125	17	17	0	0	20,704	RefSeq:NZ_BCQQ01000125
NZ_BCQQ01000126	23	22	0	1	20,610	RefSeq:NZ_BCQQ01000126
NZ_BCQQ01000127	17	17	0	0	20,469	RefSeq:NZ_BCQQ01000127
NZ_BCQQ01000128	22	20	0	2	20,362	RefSeq:NZ_BCQQ01000128
NZ_BCQQ01000129	17	16	0	1	19,654	RefSeq:NZ_BCQQ01000129
NZ_BCQQ01000130	21	19	1	1	19,281	RefSeq:NZ_BCQQ01000130
NZ_BCQQ01000131	20	20	0	0	19,120	RefSeq:NZ_BCQQ01000131
NZ_BCQQ01000132	19	17	1	1	18,669	RefSeq:NZ_BCQQ01000132
NZ_BCQQ01000133	15	15	0	0	18,504	RefSeq:NZ_BCQQ01000133
NZ_BCQQ01000134	20	19	0	1	18,151	RefSeq:NZ_BCQQ01000134
NZ_BCQQ01000135	16	15	0	1	17,838	RefSeq:NZ_BCQQ01000135
NZ_BCQQ01000136	16	14	2	0	17,808	RefSeq:NZ_BCQQ01000136
NZ_BCQQ01000137	18	15	3	0	17,702	RefSeq:NZ_BCQQ01000137
NZ_BCQQ01000138	17	15	0	2	17,484	RefSeq:NZ_BCQQ01000138
NZ_BCQQ01000139	16	16	0	0	17,359	RefSeq:NZ_BCQQ01000139
NZ_BCQQ01000140	15	14	0	1	17,331	RefSeq:NZ_BCQQ01000140
NZ_BCQQ01000141	15	15	0	0	17,300	RefSeq:NZ_BCQQ01000141
NZ_BCQQ01000142	20	20	0	0	17,025	RefSeq:NZ_BCQQ01000142
NZ_BCQQ01000143	17	14	2	1	16,871	RefSeq:NZ_BCQQ01000143
NZ_BCQQ01000144	14	14	0	0	16,869	RefSeq:NZ_BCQQ01000144
NZ_BCQQ01000145	14	13	1	0	16,573	RefSeq:NZ_BCQQ01000145
NZ_BCQQ01000146	14	14	0	0	16,157	RefSeq:NZ_BCQQ01000146
NZ_BCQQ01000147	12	11	0	1	16,041	RefSeq:NZ_BCQQ01000147
NZ_BCQQ01000148	13	13	0	0	15,479	RefSeq:NZ_BCQQ01000148
NZ_BCQQ01000149	12	12	0	0	15,475	RefSeq:NZ_BCQQ01000149
NZ_BCQQ01000151	14	13	1	0	14,926	RefSeq:NZ_BCQQ01000151
NZ_BCQQ01000152	17	16	0	1	14,910	RefSeq:NZ_BCQQ01000152
NZ_BCQQ01000153	26	26	0	0	14,902	RefSeq:NZ_BCQQ01000153
NZ_BCQQ01000154	12	12	0	0	14,851	RefSeq:NZ_BCQQ01000154
NZ_BCQQ01000155	16	15	0	1	14,229	RefSeq:NZ_BCQQ01000155
NZ_BCQQ01000156	12	11	0	1	14,113	RefSeq:NZ_BCQQ01000156
NZ_BCQQ01000159	17	17	0	0	13,168	RefSeq:NZ_BCQQ01000159
NZ_BCQQ01000160	12	11	0	1	13,009	RefSeq:NZ_BCQQ01000160
NZ_BCQQ01000161	12	12	0	0	12,998	RefSeq:NZ_BCQQ01000161
NZ_BCQQ01000162	17	16	1	0	12,950	RefSeq:NZ_BCQQ01000162
NZ_BCQQ01000164	11	10	0	1	12,716	RefSeq:NZ_BCQQ01000164
NZ_BCQQ01000166	14	12	1	1	12,496	RefSeq:NZ_BCQQ01000166
NZ_BCQQ01000167	14	12	2	0	12,491	RefSeq:NZ_BCQQ01000167
NZ_BCQQ01000168	12	12	0	0	12,422	RefSeq:NZ_BCQQ01000168
NZ_BCQQ01000169	11	11	0	0	12,197	RefSeq:NZ_BCQQ01000169
NZ_BCQQ01000171	12	12	0	0	11,566	RefSeq:NZ_BCQQ01000171
NZ_BCQQ01000173	11	10	0	1	11,193	RefSeq:NZ_BCQQ01000173
NZ_BCQQ01000179	11	11	0	0	9,386	RefSeq:NZ_BCQQ01000179
NZ_BCQQ01000185	12	12	0	0	8,651	RefSeq:NZ_BCQQ01000185
171 Undisplayed Contigs/Replicons	480	478	7	54	692,348

Total:	6,498	6,243	65	190	7,079,728

Ortholog data available?	Yes

Database Contents

Genes	6,492
Pathways	279
Enzymatic Reactions	1,490
Transport Reactions	44
Polypeptides	6,509
Protein Complexes	5
Enzymes	1,078
Transporters	525
Compounds	1,141
Transcription Units	4,754
tRNAs	55
Protein Features	7,302
GO Terms	333

Database Version

29.0

Sequence Source	GCF_001552155.1
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Actinomycetota Actinomycetes Streptosporangiales Thermomonosporaceae Actinomadura Actinomadura formosensis Actinomadura formosensis NBRC 14204
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMD00046511
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1220557
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+

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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