Summary of Actinomadura sp. NEAU-Ht49, 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 12-July-2021 from the annotated genome of Actinomadura sp. NEAU-Ht49 NEAU-Ht49, 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 25.0) [Karp16, Karp11] using MetaCyc version 25.0 [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_RFFG01000001	210	199	4	7	228,591	RefSeq:NZ_RFFG01000001
NZ_RFFG01000002	225	216	4	5	213,302	RefSeq:NZ_RFFG01000002
NZ_RFFG01000003	185	178	4	3	205,023	RefSeq:NZ_RFFG01000003
NZ_RFFG01000004	165	161	1	3	189,948	RefSeq:NZ_RFFG01000004
NZ_RFFG01000005	136	132	1	3	164,384	RefSeq:NZ_RFFG01000005
NZ_RFFG01000006	139	135	0	4	161,435	RefSeq:NZ_RFFG01000006
NZ_RFFG01000007	154	147	6	1	154,259	RefSeq:NZ_RFFG01000007
NZ_RFFG01000008	153	150	3	0	150,891	RefSeq:NZ_RFFG01000008
NZ_RFFG01000009	138	135	1	2	150,553	RefSeq:NZ_RFFG01000009
NZ_RFFG01000010	123	120	1	2	135,421	RefSeq:NZ_RFFG01000010
NZ_RFFG01000011	106	104	2	0	134,318	RefSeq:NZ_RFFG01000011
NZ_RFFG01000012	125	121	2	2	128,299	RefSeq:NZ_RFFG01000012
NZ_RFFG01000013	130	127	0	3	127,522	RefSeq:NZ_RFFG01000013
NZ_RFFG01000014	120	116	2	2	127,380	RefSeq:NZ_RFFG01000014
NZ_RFFG01000015	124	124	0	0	126,702	RefSeq:NZ_RFFG01000015
NZ_RFFG01000016	124	120	0	4	125,356	RefSeq:NZ_RFFG01000016
NZ_RFFG01000017	123	122	0	1	120,935	RefSeq:NZ_RFFG01000017
NZ_RFFG01000018	109	107	1	1	117,577	RefSeq:NZ_RFFG01000018
NZ_RFFG01000019	83	82	0	1	114,764	RefSeq:NZ_RFFG01000019
NZ_RFFG01000020	97	97	0	0	113,674	RefSeq:NZ_RFFG01000020
NZ_RFFG01000021	94	93	1	0	108,078	RefSeq:NZ_RFFG01000021
NZ_RFFG01000022	91	86	0	5	105,699	RefSeq:NZ_RFFG01000022
NZ_RFFG01000023	93	93	0	0	103,653	RefSeq:NZ_RFFG01000023
NZ_RFFG01000024	101	99	0	2	103,645	RefSeq:NZ_RFFG01000024
NZ_RFFG01000025	102	97	1	4	100,695	RefSeq:NZ_RFFG01000025
NZ_RFFG01000026	108	104	1	3	99,836	RefSeq:NZ_RFFG01000026
NZ_RFFG01000027	80	80	0	0	97,390	RefSeq:NZ_RFFG01000027
NZ_RFFG01000028	89	86	3	0	94,913	RefSeq:NZ_RFFG01000028
NZ_RFFG01000029	90	88	0	2	94,839	RefSeq:NZ_RFFG01000029
NZ_RFFG01000030	59	58	0	1	93,894	RefSeq:NZ_RFFG01000030
NZ_RFFG01000031	83	82	0	1	89,182	RefSeq:NZ_RFFG01000031
NZ_RFFG01000032	83	82	0	1	88,300	RefSeq:NZ_RFFG01000032
NZ_RFFG01000033	88	86	1	1	86,390	RefSeq:NZ_RFFG01000033
NZ_RFFG01000034	80	78	0	2	83,315	RefSeq:NZ_RFFG01000034
NZ_RFFG01000035	76	75	1	0	83,237	RefSeq:NZ_RFFG01000035
NZ_RFFG01000036	75	72	0	3	82,227	RefSeq:NZ_RFFG01000036
NZ_RFFG01000037	77	75	0	2	80,723	RefSeq:NZ_RFFG01000037
NZ_RFFG01000038	67	65	1	1	78,004	RefSeq:NZ_RFFG01000038
NZ_RFFG01000039	75	73	0	2	76,638	RefSeq:NZ_RFFG01000039
NZ_RFFG01000040	68	65	0	3	73,701	RefSeq:NZ_RFFG01000040
NZ_RFFG01000041	71	71	0	0	71,825	RefSeq:NZ_RFFG01000041
NZ_RFFG01000042	67	64	1	2	71,094	RefSeq:NZ_RFFG01000042
NZ_RFFG01000043	64	64	0	0	70,513	RefSeq:NZ_RFFG01000043
NZ_RFFG01000044	57	56	0	1	70,182	RefSeq:NZ_RFFG01000044
NZ_RFFG01000045	67	66	0	1	66,395	RefSeq:NZ_RFFG01000045
NZ_RFFG01000046	63	57	5	1	65,972	RefSeq:NZ_RFFG01000046
NZ_RFFG01000047	74	73	0	1	65,219	RefSeq:NZ_RFFG01000047
NZ_RFFG01000048	53	51	0	2	64,795	RefSeq:NZ_RFFG01000048
NZ_RFFG01000049	56	55	0	1	64,243	RefSeq:NZ_RFFG01000049
NZ_RFFG01000050	45	45	0	0	63,635	RefSeq:NZ_RFFG01000050
NZ_RFFG01000051	61	58	2	1	63,624	RefSeq:NZ_RFFG01000051
NZ_RFFG01000052	54	52	2	0	62,370	RefSeq:NZ_RFFG01000052
NZ_RFFG01000053	62	61	0	1	56,034	RefSeq:NZ_RFFG01000053
NZ_RFFG01000054	52	50	1	1	52,742	RefSeq:NZ_RFFG01000054
NZ_RFFG01000055	48	45	2	1	51,787	RefSeq:NZ_RFFG01000055
NZ_RFFG01000056	42	40	1	1	51,589	RefSeq:NZ_RFFG01000056
NZ_RFFG01000057	60	59	0	1	50,533	RefSeq:NZ_RFFG01000057
NZ_RFFG01000058	53	51	0	2	50,430	RefSeq:NZ_RFFG01000058
NZ_RFFG01000059	42	42	0	0	49,286	RefSeq:NZ_RFFG01000059
NZ_RFFG01000060	48	48	0	0	48,694	RefSeq:NZ_RFFG01000060
NZ_RFFG01000061	63	63	0	0	48,612	RefSeq:NZ_RFFG01000061
NZ_RFFG01000062	46	45	0	1	48,346	RefSeq:NZ_RFFG01000062
NZ_RFFG01000063	55	55	0	0	47,878	RefSeq:NZ_RFFG01000063
NZ_RFFG01000064	42	40	1	1	46,990	RefSeq:NZ_RFFG01000064
NZ_RFFG01000065	39	39	0	0	45,931	RefSeq:NZ_RFFG01000065
NZ_RFFG01000066	39	38	0	1	45,163	RefSeq:NZ_RFFG01000066
NZ_RFFG01000067	32	31	0	1	44,456	RefSeq:NZ_RFFG01000067
NZ_RFFG01000068	32	30	0	2	42,110	RefSeq:NZ_RFFG01000068
NZ_RFFG01000070	38	38	0	0	41,254	RefSeq:NZ_RFFG01000070
NZ_RFFG01000071	38	38	0	0	41,011	RefSeq:NZ_RFFG01000071
NZ_RFFG01000072	37	37	0	0	40,355	RefSeq:NZ_RFFG01000072
NZ_RFFG01000073	36	36	0	0	40,150	RefSeq:NZ_RFFG01000073
NZ_RFFG01000074	42	41	0	1	39,820	RefSeq:NZ_RFFG01000074
NZ_RFFG01000075	42	42	0	0	39,568	RefSeq:NZ_RFFG01000075
NZ_RFFG01000076	30	29	0	1	39,554	RefSeq:NZ_RFFG01000076
NZ_RFFG01000077	39	39	0	0	39,170	RefSeq:NZ_RFFG01000077
NZ_RFFG01000078	31	30	0	1	38,703	RefSeq:NZ_RFFG01000078
NZ_RFFG01000079	36	35	1	0	38,094	RefSeq:NZ_RFFG01000079
NZ_RFFG01000080	32	31	0	1	37,030	RefSeq:NZ_RFFG01000080
NZ_RFFG01000081	31	31	0	0	36,473	RefSeq:NZ_RFFG01000081
NZ_RFFG01000082	43	42	0	1	36,002	RefSeq:NZ_RFFG01000082
NZ_RFFG01000083	30	28	0	2	35,976	RefSeq:NZ_RFFG01000083
NZ_RFFG01000084	31	31	0	0	35,544	RefSeq:NZ_RFFG01000084
NZ_RFFG01000085	35	34	0	1	35,511	RefSeq:NZ_RFFG01000085
NZ_RFFG01000086	35	35	0	0	33,858	RefSeq:NZ_RFFG01000086
NZ_RFFG01000087	30	27	1	2	33,452	RefSeq:NZ_RFFG01000087
NZ_RFFG01000088	30	30	0	0	32,948	RefSeq:NZ_RFFG01000088
NZ_RFFG01000089	31	31	0	0	32,251	RefSeq:NZ_RFFG01000089
NZ_RFFG01000090	25	23	0	2	32,175	RefSeq:NZ_RFFG01000090
NZ_RFFG01000091	28	27	1	0	30,767	RefSeq:NZ_RFFG01000091
NZ_RFFG01000092	29	27	2	0	30,758	RefSeq:NZ_RFFG01000092
NZ_RFFG01000093	34	32	2	0	30,545	RefSeq:NZ_RFFG01000093
NZ_RFFG01000094	24	23	0	1	30,402	RefSeq:NZ_RFFG01000094
NZ_RFFG01000095	26	26	0	0	28,877	RefSeq:NZ_RFFG01000095
NZ_RFFG01000096	19	18	1	0	28,773	RefSeq:NZ_RFFG01000096
NZ_RFFG01000097	30	29	0	1	28,694	RefSeq:NZ_RFFG01000097
NZ_RFFG01000098	23	21	0	2	28,639	RefSeq:NZ_RFFG01000098
NZ_RFFG01000099	27	27	0	0	28,557	RefSeq:NZ_RFFG01000099
NZ_RFFG01000100	26	26	0	0	28,303	RefSeq:NZ_RFFG01000100
NZ_RFFG01000101	23	22	0	1	28,137	RefSeq:NZ_RFFG01000101
NZ_RFFG01000102	27	26	0	1	28,086	RefSeq:NZ_RFFG01000102
NZ_RFFG01000103	28	28	0	0	28,023	RefSeq:NZ_RFFG01000103
NZ_RFFG01000104	21	20	0	1	27,922	RefSeq:NZ_RFFG01000104
NZ_RFFG01000105	35	35	0	0	27,775	RefSeq:NZ_RFFG01000105
NZ_RFFG01000106	23	23	0	0	27,575	RefSeq:NZ_RFFG01000106
NZ_RFFG01000107	18	17	0	1	27,005	RefSeq:NZ_RFFG01000107
NZ_RFFG01000108	21	21	0	0	26,111	RefSeq:NZ_RFFG01000108
NZ_RFFG01000109	23	23	0	0	25,587	RefSeq:NZ_RFFG01000109
NZ_RFFG01000110	13	13	0	0	25,301	RefSeq:NZ_RFFG01000110
NZ_RFFG01000111	19	19	0	0	24,362	RefSeq:NZ_RFFG01000111
NZ_RFFG01000113	15	14	0	1	23,258	RefSeq:NZ_RFFG01000113
NZ_RFFG01000114	23	22	0	1	23,174	RefSeq:NZ_RFFG01000114
NZ_RFFG01000115	19	18	0	1	23,031	RefSeq:NZ_RFFG01000115
NZ_RFFG01000116	24	23	0	1	22,838	RefSeq:NZ_RFFG01000116
NZ_RFFG01000117	14	14	0	0	22,489	RefSeq:NZ_RFFG01000117
NZ_RFFG01000118	19	17	1	1	22,364	RefSeq:NZ_RFFG01000118
NZ_RFFG01000119	19	19	0	0	22,269	RefSeq:NZ_RFFG01000119
NZ_RFFG01000120	22	21	0	1	21,641	RefSeq:NZ_RFFG01000120
NZ_RFFG01000121	17	17	0	0	21,166	RefSeq:NZ_RFFG01000121
NZ_RFFG01000122	20	19	0	1	20,897	RefSeq:NZ_RFFG01000122
NZ_RFFG01000123	16	14	0	2	20,727	RefSeq:NZ_RFFG01000123
NZ_RFFG01000124	21	19	0	2	20,464	RefSeq:NZ_RFFG01000124
NZ_RFFG01000125	12	12	0	0	20,137	RefSeq:NZ_RFFG01000125
NZ_RFFG01000126	13	13	0	0	20,032	RefSeq:NZ_RFFG01000126
NZ_RFFG01000127	21	20	0	1	19,873	RefSeq:NZ_RFFG01000127
NZ_RFFG01000128	16	16	0	0	19,525	RefSeq:NZ_RFFG01000128
NZ_RFFG01000129	15	15	0	0	19,132	RefSeq:NZ_RFFG01000129
NZ_RFFG01000130	15	15	0	0	18,550	RefSeq:NZ_RFFG01000130
NZ_RFFG01000131	20	20	0	0	18,180	RefSeq:NZ_RFFG01000131
NZ_RFFG01000132	17	17	0	0	18,151	RefSeq:NZ_RFFG01000132
NZ_RFFG01000133	16	16	0	0	18,084	RefSeq:NZ_RFFG01000133
NZ_RFFG01000134	16	16	0	0	17,948	RefSeq:NZ_RFFG01000134
NZ_RFFG01000135	18	16	0	2	17,774	RefSeq:NZ_RFFG01000135
NZ_RFFG01000136	12	10	0	2	17,634	RefSeq:NZ_RFFG01000136
NZ_RFFG01000137	17	15	0	2	17,418	RefSeq:NZ_RFFG01000137
NZ_RFFG01000138	16	15	0	1	17,230	RefSeq:NZ_RFFG01000138
NZ_RFFG01000139	12	11	0	1	17,056	RefSeq:NZ_RFFG01000139
NZ_RFFG01000140	14	14	0	0	16,944	RefSeq:NZ_RFFG01000140
NZ_RFFG01000141	13	13	0	0	16,609	RefSeq:NZ_RFFG01000141
NZ_RFFG01000142	16	14	0	2	16,412	RefSeq:NZ_RFFG01000142
NZ_RFFG01000143	12	12	0	0	16,365	RefSeq:NZ_RFFG01000143
NZ_RFFG01000144	14	14	0	0	16,180	RefSeq:NZ_RFFG01000144
NZ_RFFG01000145	11	11	0	0	16,039	RefSeq:NZ_RFFG01000145
NZ_RFFG01000146	14	13	0	1	15,998	RefSeq:NZ_RFFG01000146
NZ_RFFG01000147	11	10	0	1	15,921	RefSeq:NZ_RFFG01000147
NZ_RFFG01000148	14	14	0	0	15,703	RefSeq:NZ_RFFG01000148
NZ_RFFG01000149	15	15	0	0	15,610	RefSeq:NZ_RFFG01000149
NZ_RFFG01000150	13	10	0	3	15,506	RefSeq:NZ_RFFG01000150
NZ_RFFG01000151	14	13	0	1	15,317	RefSeq:NZ_RFFG01000151
NZ_RFFG01000152	17	17	0	0	15,286	RefSeq:NZ_RFFG01000152
NZ_RFFG01000153	16	14	0	2	15,031	RefSeq:NZ_RFFG01000153
NZ_RFFG01000154	14	14	0	0	15,000	RefSeq:NZ_RFFG01000154
NZ_RFFG01000155	12	12	0	0	14,774	RefSeq:NZ_RFFG01000155
NZ_RFFG01000156	11	11	0	0	14,741	RefSeq:NZ_RFFG01000156
NZ_RFFG01000157	13	12	0	1	14,641	RefSeq:NZ_RFFG01000157
NZ_RFFG01000158	16	12	1	3	14,568	RefSeq:NZ_RFFG01000158
NZ_RFFG01000160	16	15	1	0	13,853	RefSeq:NZ_RFFG01000160
NZ_RFFG01000161	11	11	0	0	13,787	RefSeq:NZ_RFFG01000161
NZ_RFFG01000165	11	11	0	0	12,619	RefSeq:NZ_RFFG01000165
NZ_RFFG01000167	12	11	0	1	12,325	RefSeq:NZ_RFFG01000167
NZ_RFFG01000171	11	10	0	1	11,984	RefSeq:NZ_RFFG01000171
NZ_RFFG01000172	11	11	0	0	11,914	RefSeq:NZ_RFFG01000172
NZ_RFFG01000175	11	10	0	1	11,576	RefSeq:NZ_RFFG01000175
NZ_RFFG01000177	12	11	1	0	10,194	RefSeq:NZ_RFFG01000177
NZ_RFFG01000179	13	13	0	0	9,878	RefSeq:NZ_RFFG01000179
115 Undisplayed Contigs/Replicons	403	393	11	52	646,319

Total:	8,463	8,175	79	209	9,356,375

Ortholog data available?	No

Database Contents

Genes	8,460
Pathways	274
Enzymatic Reactions	1,380
Transport Reactions	58
Polypeptides	8,419
Protein Complexes	61
Enzymes	1,074
Transporters	707
Compounds	1,106
Transcription Units	6,441
tRNAs	66
Protein Features	8,898
GO Terms	22,264

Database Version

29.0

Sequence Source	GCF_003696215.1
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Actinomycetota Actinomycetes Streptosporangiales Thermomonosporaceae Actinomadura unclassified Actinomadura Actinomadura sp. NEAU-Ht49
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN10284833
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	2483351
Environment	soil
Geographic Location	China
Collection Date	2017-12-1
Annotation Provider	NCBI RefSeq
Annotation Date	2021-01-6
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	5.0
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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