Summary of Actinomadura hibisca NBRC 15177, 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 hibisca NBRC 15177, 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_BCRO01000011	366	361	0	5	368,308	RefSeq:NZ_BCRO01000011
NZ_BCRO01000012	318	311	5	2	332,054	RefSeq:NZ_BCRO01000012
NZ_BCRO01000001	244	238	4	2	265,231	RefSeq:NZ_BCRO01000001
NZ_BCRO01000019	228	225	2	1	255,322	RefSeq:NZ_BCRO01000019
NZ_BCRO01000026	238	236	0	2	230,087	RefSeq:NZ_BCRO01000026
NZ_BCRO01000027	214	207	0	7	221,765	RefSeq:NZ_BCRO01000027
NZ_BCRO01000031	197	197	0	0	215,278	RefSeq:NZ_BCRO01000031
NZ_BCRO01000039	196	186	7	3	205,950	RefSeq:NZ_BCRO01000039
NZ_BCRO01000040	186	182	0	4	200,249	RefSeq:NZ_BCRO01000040
NZ_BCRO01000010	196	192	0	4	184,622	RefSeq:NZ_BCRO01000010
NZ_BCRO01000018	184	180	1	3	183,502	RefSeq:NZ_BCRO01000018
NZ_BCRO01000002	142	139	1	2	138,797	RefSeq:NZ_BCRO01000002
NZ_BCRO01000022	138	135	1	2	136,181	RefSeq:NZ_BCRO01000022
NZ_BCRO01000043	128	124	4	0	130,593	RefSeq:NZ_BCRO01000043
NZ_BCRO01000044	111	110	0	1	130,225	RefSeq:NZ_BCRO01000044
NZ_BCRO01000042	112	112	0	0	130,186	RefSeq:NZ_BCRO01000042
NZ_BCRO01000045	120	119	0	1	126,046	RefSeq:NZ_BCRO01000045
NZ_BCRO01000051	146	141	1	4	123,169	RefSeq:NZ_BCRO01000051
NZ_BCRO01000037	108	104	2	2	116,304	RefSeq:NZ_BCRO01000037
NZ_BCRO01000025	108	107	0	1	114,884	RefSeq:NZ_BCRO01000025
NZ_BCRO01000054	102	100	0	2	105,283	RefSeq:NZ_BCRO01000054
NZ_BCRO01000007	88	87	0	1	101,463	RefSeq:NZ_BCRO01000007
NZ_BCRO01000020	92	90	2	0	101,418	RefSeq:NZ_BCRO01000020
NZ_BCRO01000033	94	94	0	0	96,483	RefSeq:NZ_BCRO01000033
NZ_BCRO01000049	81	80	1	0	92,406	RefSeq:NZ_BCRO01000049
NZ_BCRO01000077	111	105	4	2	90,901	RefSeq:NZ_BCRO01000077
NZ_BCRO01000060	78	76	2	0	88,978	RefSeq:NZ_BCRO01000060
NZ_BCRO01000063	82	78	3	1	84,861	RefSeq:NZ_BCRO01000063
NZ_BCRO01000064	75	74	0	1	84,491	RefSeq:NZ_BCRO01000064
NZ_BCRO01000032	66	61	4	1	84,192	RefSeq:NZ_BCRO01000032
NZ_BCRO01000024	76	75	0	1	78,978	RefSeq:NZ_BCRO01000024
NZ_BCRO01000030	66	66	0	0	76,944	RefSeq:NZ_BCRO01000030
NZ_BCRO01000070	68	66	1	1	76,729	RefSeq:NZ_BCRO01000070
NZ_BCRO01000071	77	75	1	1	76,580	RefSeq:NZ_BCRO01000071
NZ_BCRO01000028	53	49	1	3	74,879	RefSeq:NZ_BCRO01000028
NZ_BCRO01000053	72	71	1	0	72,759	RefSeq:NZ_BCRO01000053
NZ_BCRO01000062	66	62	4	0	71,581	RefSeq:NZ_BCRO01000062
NZ_BCRO01000072	74	74	0	0	70,429	RefSeq:NZ_BCRO01000072
NZ_BCRO01000055	68	68	0	0	68,070	RefSeq:NZ_BCRO01000055
NZ_BCRO01000029	60	60	0	0	67,108	RefSeq:NZ_BCRO01000029
NZ_BCRO01000073	67	62	3	2	66,529	RefSeq:NZ_BCRO01000073
NZ_BCRO01000036	63	63	0	0	64,624	RefSeq:NZ_BCRO01000036
NZ_BCRO01000074	62	62	0	0	64,174	RefSeq:NZ_BCRO01000074
NZ_BCRO01000075	57	54	2	1	63,847	RefSeq:NZ_BCRO01000075
NZ_BCRO01000076	52	50	0	2	63,216	RefSeq:NZ_BCRO01000076
NZ_BCRO01000078	53	53	0	0	62,826	RefSeq:NZ_BCRO01000078
NZ_BCRO01000058	51	51	0	0	62,654	RefSeq:NZ_BCRO01000058
NZ_BCRO01000079	67	65	0	2	60,879	RefSeq:NZ_BCRO01000079
NZ_BCRO01000006	69	65	3	1	59,883	RefSeq:NZ_BCRO01000006
NZ_BCRO01000080	58	58	0	0	59,390	RefSeq:NZ_BCRO01000080
NZ_BCRO01000081	47	45	0	2	58,673	RefSeq:NZ_BCRO01000081
NZ_BCRO01000069	57	57	0	0	57,771	RefSeq:NZ_BCRO01000069
NZ_BCRO01000082	48	45	3	0	57,715	RefSeq:NZ_BCRO01000082
NZ_BCRO01000086	54	54	0	0	55,314	RefSeq:NZ_BCRO01000086
NZ_BCRO01000087	53	50	0	3	55,276	RefSeq:NZ_BCRO01000087
NZ_BCRO01000088	44	43	0	1	54,632	RefSeq:NZ_BCRO01000088
NZ_BCRO01000089	55	54	0	1	54,403	RefSeq:NZ_BCRO01000089
NZ_BCRO01000092	34	33	0	1	53,996	RefSeq:NZ_BCRO01000092
NZ_BCRO01000093	49	49	0	0	53,496	RefSeq:NZ_BCRO01000093
NZ_BCRO01000094	50	50	0	0	53,254	RefSeq:NZ_BCRO01000094
NZ_BCRO01000095	45	44	0	1	52,714	RefSeq:NZ_BCRO01000095
NZ_BCRO01000066	44	44	0	0	52,205	RefSeq:NZ_BCRO01000066
NZ_BCRO01000048	61	61	0	0	50,550	RefSeq:NZ_BCRO01000048
NZ_BCRO01000046	55	54	0	1	49,054	RefSeq:NZ_BCRO01000046
NZ_BCRO01000098	47	45	1	1	48,170	RefSeq:NZ_BCRO01000098
NZ_BCRO01000099	43	41	2	0	48,050	RefSeq:NZ_BCRO01000099
NZ_BCRO01000100	39	39	0	0	47,971	RefSeq:NZ_BCRO01000100
NZ_BCRO01000083	35	34	0	1	43,809	RefSeq:NZ_BCRO01000083
NZ_BCRO01000103	40	39	0	1	43,500	RefSeq:NZ_BCRO01000103
NZ_BCRO01000104	36	35	1	0	42,998	RefSeq:NZ_BCRO01000104
NZ_BCRO01000105	49	47	1	1	42,332	RefSeq:NZ_BCRO01000105
NZ_BCRO01000091	32	30	0	2	41,319	RefSeq:NZ_BCRO01000091
NZ_BCRO01000108	37	37	0	0	41,099	RefSeq:NZ_BCRO01000108
NZ_BCRO01000109	36	36	0	0	40,466	RefSeq:NZ_BCRO01000109
NZ_BCRO01000023	37	37	0	0	40,423	RefSeq:NZ_BCRO01000023
NZ_BCRO01000110	33	33	0	0	40,370	RefSeq:NZ_BCRO01000110
NZ_BCRO01000052	38	38	0	0	39,948	RefSeq:NZ_BCRO01000052
NZ_BCRO01000111	42	42	0	0	38,820	RefSeq:NZ_BCRO01000111
NZ_BCRO01000112	44	44	0	0	38,679	RefSeq:NZ_BCRO01000112
NZ_BCRO01000115	38	38	0	0	38,153	RefSeq:NZ_BCRO01000115
NZ_BCRO01000041	34	34	0	0	38,098	RefSeq:NZ_BCRO01000041
NZ_BCRO01000009	33	33	0	0	38,009	RefSeq:NZ_BCRO01000009
NZ_BCRO01000003	38	38	0	0	37,742	RefSeq:NZ_BCRO01000003
NZ_BCRO01000008	32	31	0	1	36,491	RefSeq:NZ_BCRO01000008
NZ_BCRO01000096	34	33	0	1	36,484	RefSeq:NZ_BCRO01000096
NZ_BCRO01000116	29	27	2	0	35,708	RefSeq:NZ_BCRO01000116
NZ_BCRO01000056	34	33	1	0	34,909	RefSeq:NZ_BCRO01000056
NZ_BCRO01000117	34	33	0	1	34,416	RefSeq:NZ_BCRO01000117
NZ_BCRO01000120	32	31	0	1	33,001	RefSeq:NZ_BCRO01000120
NZ_BCRO01000121	36	35	0	1	32,080	RefSeq:NZ_BCRO01000121
NZ_BCRO01000014	29	28	0	1	31,985	RefSeq:NZ_BCRO01000014
NZ_BCRO01000122	25	23	0	2	31,835	RefSeq:NZ_BCRO01000122
NZ_BCRO01000050	33	33	0	0	31,614	RefSeq:NZ_BCRO01000050
NZ_BCRO01000123	23	23	0	0	30,819	RefSeq:NZ_BCRO01000123
NZ_BCRO01000124	34	34	0	0	30,694	RefSeq:NZ_BCRO01000124
NZ_BCRO01000125	31	31	0	0	30,506	RefSeq:NZ_BCRO01000125
NZ_BCRO01000128	29	29	0	0	29,684	RefSeq:NZ_BCRO01000128
NZ_BCRO01000129	27	25	2	0	29,657	RefSeq:NZ_BCRO01000129
NZ_BCRO01000034	24	24	0	0	29,456	RefSeq:NZ_BCRO01000034
NZ_BCRO01000102	28	28	0	0	29,345	RefSeq:NZ_BCRO01000102
NZ_BCRO01000130	22	22	0	0	29,163	RefSeq:NZ_BCRO01000130
NZ_BCRO01000131	31	30	0	1	28,001	RefSeq:NZ_BCRO01000131
NZ_BCRO01000114	27	26	0	1	27,698	RefSeq:NZ_BCRO01000114
NZ_BCRO01000132	22	22	0	0	27,626	RefSeq:NZ_BCRO01000132
NZ_BCRO01000013	22	21	1	0	26,474	RefSeq:NZ_BCRO01000013
NZ_BCRO01000047	27	25	1	1	25,530	RefSeq:NZ_BCRO01000047
NZ_BCRO01000133	25	25	0	0	24,993	RefSeq:NZ_BCRO01000133
NZ_BCRO01000134	19	19	0	0	24,179	RefSeq:NZ_BCRO01000134
NZ_BCRO01000106	23	23	0	0	23,933	RefSeq:NZ_BCRO01000106
NZ_BCRO01000004	19	19	0	0	22,216	RefSeq:NZ_BCRO01000004
NZ_BCRO01000127	18	18	0	0	22,127	RefSeq:NZ_BCRO01000127
NZ_BCRO01000137	17	16	0	1	20,743	RefSeq:NZ_BCRO01000137
NZ_BCRO01000059	14	14	0	0	20,690	RefSeq:NZ_BCRO01000059
NZ_BCRO01000065	23	23	0	0	20,040	RefSeq:NZ_BCRO01000065
NZ_BCRO01000068	14	14	0	0	19,926	RefSeq:NZ_BCRO01000068
NZ_BCRO01000118	17	17	0	0	19,683	RefSeq:NZ_BCRO01000118
NZ_BCRO01000140	21	21	0	0	17,744	RefSeq:NZ_BCRO01000140
NZ_BCRO01000107	16	14	2	0	17,605	RefSeq:NZ_BCRO01000107
NZ_BCRO01000139	16	16	0	0	16,894	RefSeq:NZ_BCRO01000139
NZ_BCRO01000101	14	14	0	0	16,431	RefSeq:NZ_BCRO01000101
NZ_BCRO01000061	14	12	0	2	16,040	RefSeq:NZ_BCRO01000061
NZ_BCRO01000141	12	12	0	0	15,443	RefSeq:NZ_BCRO01000141
NZ_BCRO01000143	15	15	0	0	15,206	RefSeq:NZ_BCRO01000143
NZ_BCRO01000038	17	16	0	1	14,756	RefSeq:NZ_BCRO01000038
NZ_BCRO01000146	12	12	0	0	14,705	RefSeq:NZ_BCRO01000146
NZ_BCRO01000119	14	14	0	0	13,970	RefSeq:NZ_BCRO01000119
NZ_BCRO01000017	13	13	0	0	13,367	RefSeq:NZ_BCRO01000017
NZ_BCRO01000090	11	11	0	0	12,947	RefSeq:NZ_BCRO01000090
NZ_BCRO01000035	12	12	0	0	12,656	RefSeq:NZ_BCRO01000035
NZ_BCRO01000150	15	15	0	0	11,975	RefSeq:NZ_BCRO01000150
NZ_BCRO01000144	12	12	0	0	11,316	RefSeq:NZ_BCRO01000144
NZ_BCRO01000057	13	13	0	0	10,164	RefSeq:NZ_BCRO01000057
41 Undisplayed Contigs/Replicons	162	159	5	6	210,732

Total:	8,506	8,319	82	105	9,023,974

Ortholog data available?	Yes

Database Contents

Genes	8,503
Pathways	295
Enzymatic Reactions	1,547
Transport Reactions	45
Polypeptides	8,366
Protein Complexes	5
Enzymes	1,188
Transporters	726
Compounds	1,171
Transcription Units	5,991
tRNAs	70
Protein Features	9,293
GO Terms	490

Database Version

29.0

Sequence Source	GCF_001552635.1
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Actinomycetota Actinomycetes Streptosporangiales Thermomonosporaceae Actinomadura Actinomadura hibisca Actinomadura hibisca NBRC 15177
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMD00046515
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1220559
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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