Summary of Actinomadura madurae LIID-AJ290, 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 madurae LIID-AJ290, 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_AWOO02000001	402	392	0	10	507,970	RefSeq:NZ_AWOO02000001
NZ_AWOO02000002	380	374	2	4	394,126	RefSeq:NZ_AWOO02000002
NZ_AWOO02000003	322	307	5	10	301,719	RefSeq:NZ_AWOO02000003
NZ_AWOO02000004	269	263	0	6	275,686	RefSeq:NZ_AWOO02000004
NZ_AWOO02000005	219	217	1	1	258,314	RefSeq:NZ_AWOO02000005
NZ_AWOO02000006	242	236	3	3	257,596	RefSeq:NZ_AWOO02000006
NZ_AWOO02000007	214	206	4	4	240,455	RefSeq:NZ_AWOO02000007
NZ_AWOO02000008	214	211	1	2	239,821	RefSeq:NZ_AWOO02000008
NZ_AWOO02000009	225	214	1	10	227,583	RefSeq:NZ_AWOO02000009
NZ_AWOO02000010	194	191	0	3	205,626	RefSeq:NZ_AWOO02000010
NZ_AWOO02000011	196	190	3	3	190,899	RefSeq:NZ_AWOO02000011
NZ_AWOO02000012	147	139	0	8	189,523	RefSeq:NZ_AWOO02000012
NZ_AWOO02000013	173	168	3	2	182,412	RefSeq:NZ_AWOO02000013
NZ_AWOO02000014	148	148	0	0	179,783	RefSeq:NZ_AWOO02000014
NZ_AWOO02000015	152	145	4	3	178,552	RefSeq:NZ_AWOO02000015
NZ_AWOO02000016	156	150	1	5	177,263	RefSeq:NZ_AWOO02000016
NZ_AWOO02000017	165	160	2	3	174,279	RefSeq:NZ_AWOO02000017
NZ_AWOO02000018	149	146	1	2	170,212	RefSeq:NZ_AWOO02000018
NZ_AWOO02000019	157	149	4	4	163,935	RefSeq:NZ_AWOO02000019
NZ_AWOO02000020	151	150	0	1	157,986	RefSeq:NZ_AWOO02000020
NZ_AWOO02000021	117	115	1	1	156,676	RefSeq:NZ_AWOO02000021
NZ_AWOO02000022	139	136	1	2	150,484	RefSeq:NZ_AWOO02000022
NZ_AWOO02000023	150	145	2	3	146,335	RefSeq:NZ_AWOO02000023
NZ_AWOO02000024	117	114	1	2	140,184	RefSeq:NZ_AWOO02000024
NZ_AWOO02000025	138	125	6	7	133,823	RefSeq:NZ_AWOO02000025
NZ_AWOO02000026	149	128	20	1	133,660	RefSeq:NZ_AWOO02000026
NZ_AWOO02000027	116	114	0	2	119,325	RefSeq:NZ_AWOO02000027
NZ_AWOO02000028	112	110	1	1	117,072	RefSeq:NZ_AWOO02000028
NZ_AWOO02000029	114	112	0	2	116,090	RefSeq:NZ_AWOO02000029
NZ_AWOO02000030	99	95	1	3	115,917	RefSeq:NZ_AWOO02000030
NZ_AWOO02000031	75	72	0	3	115,523	RefSeq:NZ_AWOO02000031
NZ_AWOO02000032	105	101	0	4	111,871	RefSeq:NZ_AWOO02000032
NZ_AWOO02000033	105	105	0	0	110,573	RefSeq:NZ_AWOO02000033
NZ_AWOO02000034	101	97	0	4	103,014	RefSeq:NZ_AWOO02000034
NZ_AWOO02000035	101	93	4	4	102,591	RefSeq:NZ_AWOO02000035
NZ_AWOO02000036	87	86	1	0	102,566	RefSeq:NZ_AWOO02000036
NZ_AWOO02000037	94	88	0	6	102,294	RefSeq:NZ_AWOO02000037
NZ_AWOO02000038	100	97	0	3	101,453	RefSeq:NZ_AWOO02000038
NZ_AWOO02000039	92	86	2	4	100,766	RefSeq:NZ_AWOO02000039
NZ_AWOO02000040	80	77	0	3	96,060	RefSeq:NZ_AWOO02000040
NZ_AWOO02000041	100	97	0	3	94,120	RefSeq:NZ_AWOO02000041
NZ_AWOO02000042	94	92	1	1	89,182	RefSeq:NZ_AWOO02000042
NZ_AWOO02000043	88	88	0	0	88,797	RefSeq:NZ_AWOO02000043
NZ_AWOO02000044	77	76	0	1	86,868	RefSeq:NZ_AWOO02000044
NZ_AWOO02000045	63	59	3	1	85,430	RefSeq:NZ_AWOO02000045
NZ_AWOO02000046	92	91	0	1	81,670	RefSeq:NZ_AWOO02000046
NZ_AWOO02000047	62	60	1	1	77,806	RefSeq:NZ_AWOO02000047
NZ_AWOO02000048	75	71	2	2	76,405	RefSeq:NZ_AWOO02000048
NZ_AWOO02000049	72	70	0	2	74,516	RefSeq:NZ_AWOO02000049
NZ_AWOO02000050	64	63	0	1	73,409	RefSeq:NZ_AWOO02000050
NZ_AWOO02000051	63	62	1	0	72,549	RefSeq:NZ_AWOO02000051
NZ_AWOO02000052	66	63	1	2	72,299	RefSeq:NZ_AWOO02000052
NZ_AWOO02000053	62	61	0	1	69,433	RefSeq:NZ_AWOO02000053
NZ_AWOO02000054	63	58	0	5	67,905	RefSeq:NZ_AWOO02000054
NZ_AWOO02000055	66	65	0	1	65,843	RefSeq:NZ_AWOO02000055
NZ_AWOO02000056	62	59	0	3	65,611	RefSeq:NZ_AWOO02000056
NZ_AWOO02000057	65	64	0	1	61,413	RefSeq:NZ_AWOO02000057
NZ_AWOO02000058	53	53	0	0	60,717	RefSeq:NZ_AWOO02000058
NZ_AWOO02000059	61	59	0	2	60,322	RefSeq:NZ_AWOO02000059
NZ_AWOO02000060	59	59	0	0	57,587	RefSeq:NZ_AWOO02000060
NZ_AWOO02000061	49	48	0	1	55,372	RefSeq:NZ_AWOO02000061
NZ_AWOO02000062	48	48	0	0	53,268	RefSeq:NZ_AWOO02000062
NZ_AWOO02000063	47	47	0	0	52,935	RefSeq:NZ_AWOO02000063
NZ_AWOO02000064	40	39	0	1	52,346	RefSeq:NZ_AWOO02000064
NZ_AWOO02000065	44	43	0	1	51,365	RefSeq:NZ_AWOO02000065
NZ_AWOO02000066	48	47	0	1	50,267	RefSeq:NZ_AWOO02000066
NZ_AWOO02000067	45	45	0	0	48,274	RefSeq:NZ_AWOO02000067
NZ_AWOO02000068	43	43	0	0	46,729	RefSeq:NZ_AWOO02000068
NZ_AWOO02000069	47	47	0	0	46,645	RefSeq:NZ_AWOO02000069
NZ_AWOO02000070	40	38	1	1	46,273	RefSeq:NZ_AWOO02000070
NZ_AWOO02000071	40	40	0	0	46,030	RefSeq:NZ_AWOO02000071
NZ_AWOO02000072	47	43	0	4	44,413	RefSeq:NZ_AWOO02000072
NZ_AWOO02000073	46	46	0	0	44,333	RefSeq:NZ_AWOO02000073
NZ_AWOO02000074	34	34	0	0	41,890	RefSeq:NZ_AWOO02000074
NZ_AWOO02000075	40	40	0	0	40,460	RefSeq:NZ_AWOO02000075
NZ_AWOO02000076	38	36	0	2	39,696	RefSeq:NZ_AWOO02000076
NZ_AWOO02000077	37	37	0	0	39,076	RefSeq:NZ_AWOO02000077
NZ_AWOO02000078	40	40	0	0	36,547	RefSeq:NZ_AWOO02000078
NZ_AWOO02000079	43	39	3	1	35,867	RefSeq:NZ_AWOO02000079
NZ_AWOO02000080	32	31	0	1	33,959	RefSeq:NZ_AWOO02000080
NZ_AWOO02000081	32	28	0	4	33,618	RefSeq:NZ_AWOO02000081
NZ_AWOO02000082	32	28	0	4	32,398	RefSeq:NZ_AWOO02000082
NZ_AWOO02000083	25	24	1	0	31,882	RefSeq:NZ_AWOO02000083
NZ_AWOO02000084	30	28	0	2	31,860	RefSeq:NZ_AWOO02000084
NZ_AWOO02000085	32	31	0	1	31,608	RefSeq:NZ_AWOO02000085
NZ_AWOO02000086	26	26	0	0	31,210	RefSeq:NZ_AWOO02000086
NZ_AWOO02000087	29	29	0	0	28,753	RefSeq:NZ_AWOO02000087
NZ_AWOO02000088	21	21	0	0	28,549	RefSeq:NZ_AWOO02000088
NZ_AWOO02000089	24	23	0	1	28,533	RefSeq:NZ_AWOO02000089
NZ_AWOO02000090	26	24	0	2	28,267	RefSeq:NZ_AWOO02000090
NZ_AWOO02000091	21	20	0	1	28,134	RefSeq:NZ_AWOO02000091
NZ_AWOO02000092	27	26	0	1	27,634	RefSeq:NZ_AWOO02000092
NZ_AWOO02000093	25	25	0	0	26,184	RefSeq:NZ_AWOO02000093
NZ_AWOO02000094	21	21	0	0	25,940	RefSeq:NZ_AWOO02000094
NZ_AWOO02000095	18	18	0	0	25,503	RefSeq:NZ_AWOO02000095
NZ_AWOO02000096	26	24	0	2	25,367	RefSeq:NZ_AWOO02000096
NZ_AWOO02000097	27	27	0	0	24,784	RefSeq:NZ_AWOO02000097
NZ_AWOO02000098	20	20	0	0	23,607	RefSeq:NZ_AWOO02000098
NZ_AWOO02000099	16	15	0	1	21,373	RefSeq:NZ_AWOO02000099
NZ_AWOO02000100	24	23	0	1	21,224	RefSeq:NZ_AWOO02000100
NZ_AWOO02000101	16	16	0	0	18,894	RefSeq:NZ_AWOO02000101
NZ_AWOO02000102	18	18	0	0	18,469	RefSeq:NZ_AWOO02000102
NZ_AWOO02000103	15	14	1	0	18,094	RefSeq:NZ_AWOO02000103
NZ_AWOO02000104	14	13	0	1	18,008	RefSeq:NZ_AWOO02000104
NZ_AWOO02000105	13	12	0	1	17,409	RefSeq:NZ_AWOO02000105
NZ_AWOO02000106	17	16	0	1	16,322	RefSeq:NZ_AWOO02000106
NZ_AWOO02000107	15	15	0	0	15,561	RefSeq:NZ_AWOO02000107
NZ_AWOO02000108	10	10	0	0	15,458	RefSeq:NZ_AWOO02000108
NZ_AWOO02000109	16	15	0	1	15,089	RefSeq:NZ_AWOO02000109
NZ_AWOO02000110	14	11	1	2	13,766	RefSeq:NZ_AWOO02000110
NZ_AWOO02000113	13	11	0	2	11,728	RefSeq:NZ_AWOO02000113
NZ_AWOO02000112	18	18	0	0	11,727	RefSeq:NZ_AWOO02000112
37 Undisplayed Contigs/Replicons	68	66	4	11	124,269

Total:	9,483	9,169	95	219	10,308,866

Ortholog data available?	Yes

Database Contents

Genes	9,481
Pathways	289
Enzymatic Reactions	1,541
Transport Reactions	47
Polypeptides	9,316
Protein Complexes	4
Enzymes	1,240
Transporters	909
Compounds	1,199
Transcription Units	6,518
tRNAs	88
Protein Features	10,902
GO Terms	620

Database Version

29.0

Sequence Source	GCF_000468475.2
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Actinomycetota Actinomycetes Streptosporangiales Thermomonosporaceae Actinomadura Actinomadura madurae Actinomadura madurae LIID-AJ290
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN02640231
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1394178
Environment	mycetoma of the foot
Geographic Location	Mexico
Collection Date	2011
Host	Homo sapiens
Annotation Provider	NCBI RefSeq
Annotation Date	2022-01-20
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	5.3
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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