Summary of Actinomadura logoneensis NEAU-G17, 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 08-Apr-2022 from the annotated genome of Actinomadura logoneensis NEAU-G17, 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_QURH01000338	63	60	0	3	91,209	RefSeq:NZ_QURH01000338
NZ_QURH01000180	65	60	5	0	68,032	RefSeq:NZ_QURH01000180
NZ_QURH01000199	62	61	0	1	65,958	RefSeq:NZ_QURH01000199
NZ_QURH01000316	67	66	0	1	64,812	RefSeq:NZ_QURH01000316
NZ_QURH01000099	68	62	4	2	64,519	RefSeq:NZ_QURH01000099
NZ_QURH01000110	68	65	3	0	63,613	RefSeq:NZ_QURH01000110
NZ_QURH01000226	54	52	1	1	61,577	RefSeq:NZ_QURH01000226
NZ_QURH01000200	49	48	1	0	59,573	RefSeq:NZ_QURH01000200
NZ_QURH01000037	47	44	1	2	57,473	RefSeq:NZ_QURH01000037
NZ_QURH01000312	40	40	0	0	55,139	RefSeq:NZ_QURH01000312
NZ_QURH01000211	55	51	2	2	54,905	RefSeq:NZ_QURH01000211
NZ_QURH01000336	48	44	3	1	50,829	RefSeq:NZ_QURH01000336
NZ_QURH01000114	51	50	0	1	47,444	RefSeq:NZ_QURH01000114
NZ_QURH01000215	43	42	0	1	46,776	RefSeq:NZ_QURH01000215
NZ_QURH01000299	44	40	2	2	44,053	RefSeq:NZ_QURH01000299
NZ_QURH01000008	39	38	0	1	43,140	RefSeq:NZ_QURH01000008
NZ_QURH01000115	35	35	0	0	40,853	RefSeq:NZ_QURH01000115
NZ_QURH01000177	36	36	0	0	39,035	RefSeq:NZ_QURH01000177
NZ_QURH01000146	38	38	0	0	38,588	RefSeq:NZ_QURH01000146
NZ_QURH01001054	29	29	0	0	38,191	RefSeq:NZ_QURH01001054
NZ_QURH01000236	34	32	0	2	37,485	RefSeq:NZ_QURH01000236
NZ_QURH01001053	27	25	0	2	37,322	RefSeq:NZ_QURH01001053
NZ_QURH01000070	29	29	0	0	36,946	RefSeq:NZ_QURH01000070
NZ_QURH01000224	32	32	0	0	36,392	RefSeq:NZ_QURH01000224
NZ_QURH01000247	29	28	0	1	35,261	RefSeq:NZ_QURH01000247
NZ_QURH01000326	32	29	1	2	34,579	RefSeq:NZ_QURH01000326
NZ_QURH01000121	33	32	0	1	34,249	RefSeq:NZ_QURH01000121
NZ_QURH01000255	36	36	0	0	34,012	RefSeq:NZ_QURH01000255
NZ_QURH01000034	27	26	0	1	33,689	RefSeq:NZ_QURH01000034
NZ_QURH01000332	27	26	0	1	32,610	RefSeq:NZ_QURH01000332
NZ_QURH01000097	32	32	0	0	31,390	RefSeq:NZ_QURH01000097
NZ_QURH01000144	30	29	0	1	31,253	RefSeq:NZ_QURH01000144
NZ_QURH01000205	24	24	0	0	30,888	RefSeq:NZ_QURH01000205
NZ_QURH01000322	30	27	3	0	30,600	RefSeq:NZ_QURH01000322
NZ_QURH01000039	35	35	0	0	29,931	RefSeq:NZ_QURH01000039
NZ_QURH01000231	26	24	0	2	29,569	RefSeq:NZ_QURH01000231
NZ_QURH01001049	28	26	1	1	29,543	RefSeq:NZ_QURH01001049
NZ_QURH01000010	27	24	1	2	29,126	RefSeq:NZ_QURH01000010
NZ_QURH01000287	25	23	0	2	29,012	RefSeq:NZ_QURH01000287
NZ_QURH01000078	24	24	0	0	28,860	RefSeq:NZ_QURH01000078
NZ_QURH01000011	28	27	1	0	28,796	RefSeq:NZ_QURH01000011
NZ_QURH01000050	27	27	0	0	28,742	RefSeq:NZ_QURH01000050
NZ_QURH01000026	30	29	0	1	28,735	RefSeq:NZ_QURH01000026
NZ_QURH01001051	20	20	0	0	28,411	RefSeq:NZ_QURH01001051
NZ_QURH01000259	30	28	0	2	28,140	RefSeq:NZ_QURH01000259
NZ_QURH01000227	22	21	0	1	28,082	RefSeq:NZ_QURH01000227
NZ_QURH01000337	21	21	0	0	27,975	RefSeq:NZ_QURH01000337
NZ_QURH01000269	23	21	1	1	27,824	RefSeq:NZ_QURH01000269
NZ_QURH01000331	26	25	0	1	27,644	RefSeq:NZ_QURH01000331
NZ_QURH01000256	19	19	0	0	27,626	RefSeq:NZ_QURH01000256
NZ_QURH01000333	29	28	0	1	27,072	RefSeq:NZ_QURH01000333
NZ_QURH01000306	19	17	0	2	27,019	RefSeq:NZ_QURH01000306
NZ_QURH01000252	30	29	0	1	26,574	RefSeq:NZ_QURH01000252
NZ_QURH01000320	17	17	0	0	26,311	RefSeq:NZ_QURH01000320
NZ_QURH01001048	25	24	0	1	26,218	RefSeq:NZ_QURH01001048
NZ_QURH01000079	22	18	0	4	25,405	RefSeq:NZ_QURH01000079
NZ_QURH01001052	25	25	0	0	25,216	RefSeq:NZ_QURH01001052
NZ_QURH01000283	31	30	0	1	25,087	RefSeq:NZ_QURH01000283
NZ_QURH01000018	23	23	0	0	25,078	RefSeq:NZ_QURH01000018
NZ_QURH01000141	21	18	1	2	24,856	RefSeq:NZ_QURH01000141
NZ_QURH01001050	21	19	1	1	24,586	RefSeq:NZ_QURH01001050
NZ_QURH01001045	24	24	0	0	24,242	RefSeq:NZ_QURH01001045
NZ_QURH01000295	28	27	0	1	24,199	RefSeq:NZ_QURH01000295
NZ_QURH01000027	25	23	0	2	24,034	RefSeq:NZ_QURH01000027
NZ_QURH01000159	15	14	1	0	24,023	RefSeq:NZ_QURH01000159
NZ_QURH01000148	20	19	0	1	23,872	RefSeq:NZ_QURH01000148
NZ_QURH01001046	28	26	1	1	23,208	RefSeq:NZ_QURH01001046
NZ_QURH01000328	20	19	0	1	23,104	RefSeq:NZ_QURH01000328
NZ_QURH01000327	21	19	0	2	23,067	RefSeq:NZ_QURH01000327
NZ_QURH01000335	26	26	0	0	22,899	RefSeq:NZ_QURH01000335
NZ_QURH01000085	15	14	0	1	22,816	RefSeq:NZ_QURH01000085
NZ_QURH01000106	22	22	0	0	22,724	RefSeq:NZ_QURH01000106
NZ_QURH01001047	23	23	0	0	22,324	RefSeq:NZ_QURH01001047
NZ_QURH01001044	18	18	0	0	21,898	RefSeq:NZ_QURH01001044
NZ_QURH01000290	22	22	0	0	21,868	RefSeq:NZ_QURH01000290
NZ_QURH01001042	20	20	0	0	21,806	RefSeq:NZ_QURH01001042
NZ_QURH01000257	17	17	0	0	21,652	RefSeq:NZ_QURH01000257
NZ_QURH01000153	19	17	2	0	21,501	RefSeq:NZ_QURH01000153
NZ_QURH01000285	21	21	0	0	21,397	RefSeq:NZ_QURH01000285
NZ_QURH01000046	18	17	0	1	21,264	RefSeq:NZ_QURH01000046
NZ_QURH01000184	20	19	0	1	21,188	RefSeq:NZ_QURH01000184
NZ_QURH01001043	18	17	0	1	21,171	RefSeq:NZ_QURH01001043
NZ_QURH01000282	13	13	0	0	21,047	RefSeq:NZ_QURH01000282
NZ_QURH01000190	22	22	0	0	20,886	RefSeq:NZ_QURH01000190
NZ_QURH01000288	14	14	0	0	20,803	RefSeq:NZ_QURH01000288
NZ_QURH01001039	17	16	1	0	20,642	RefSeq:NZ_QURH01001039
NZ_QURH01000330	21	20	0	1	20,548	RefSeq:NZ_QURH01000330
NZ_QURH01000314	20	20	0	0	20,442	RefSeq:NZ_QURH01000314
NZ_QURH01001038	19	19	0	0	20,248	RefSeq:NZ_QURH01001038
NZ_QURH01000310	14	13	0	1	20,147	RefSeq:NZ_QURH01000310
NZ_QURH01000163	22	21	0	1	20,082	RefSeq:NZ_QURH01000163
NZ_QURH01001036	18	18	0	0	20,044	RefSeq:NZ_QURH01001036
NZ_QURH01001040	18	18	0	0	19,843	RefSeq:NZ_QURH01001040
NZ_QURH01000087	18	18	0	0	19,389	RefSeq:NZ_QURH01000087
NZ_QURH01000315	18	17	0	1	19,245	RefSeq:NZ_QURH01000315
NZ_QURH01000013	17	15	0	2	19,226	RefSeq:NZ_QURH01000013
NZ_QURH01000277	18	17	0	1	19,219	RefSeq:NZ_QURH01000277
NZ_QURH01000317	21	21	0	0	18,814	RefSeq:NZ_QURH01000317
NZ_QURH01000222	19	19	0	0	18,748	RefSeq:NZ_QURH01000222
NZ_QURH01000271	16	15	1	0	18,588	RefSeq:NZ_QURH01000271
NZ_QURH01000289	13	13	0	0	18,541	RefSeq:NZ_QURH01000289
NZ_QURH01001037	17	17	0	0	18,493	RefSeq:NZ_QURH01001037
NZ_QURH01000216	17	17	0	0	18,474	RefSeq:NZ_QURH01000216
NZ_QURH01000329	19	19	0	0	18,412	RefSeq:NZ_QURH01000329
NZ_QURH01000297	19	17	0	2	18,338	RefSeq:NZ_QURH01000297
NZ_QURH01000005	13	11	0	2	18,053	RefSeq:NZ_QURH01000005
NZ_QURH01000263	13	12	0	1	17,909	RefSeq:NZ_QURH01000263
NZ_QURH01000303	12	12	0	0	17,747	RefSeq:NZ_QURH01000303
NZ_QURH01000073	12	12	0	0	17,690	RefSeq:NZ_QURH01000073
NZ_QURH01000009	14	14	0	0	17,572	RefSeq:NZ_QURH01000009
NZ_QURH01000192	13	13	0	0	17,540	RefSeq:NZ_QURH01000192
NZ_QURH01001041	19	16	1	2	17,345	RefSeq:NZ_QURH01001041
NZ_QURH01000015	15	14	0	1	17,273	RefSeq:NZ_QURH01000015
NZ_QURH01000318	17	16	0	1	17,071	RefSeq:NZ_QURH01000318
NZ_QURH01000334	20	18	1	1	17,008	RefSeq:NZ_QURH01000334
NZ_QURH01000309	13	12	0	1	16,381	RefSeq:NZ_QURH01000309
NZ_QURH01000012	18	17	1	0	16,344	RefSeq:NZ_QURH01000012
NZ_QURH01001035	16	16	0	0	16,285	RefSeq:NZ_QURH01001035
NZ_QURH01000127	13	13	0	0	16,245	RefSeq:NZ_QURH01000127
NZ_QURH01000325	17	15	2	0	16,228	RefSeq:NZ_QURH01000325
NZ_QURH01000324	15	15	0	0	16,155	RefSeq:NZ_QURH01000324
NZ_QURH01001034	11	11	0	0	16,065	RefSeq:NZ_QURH01001034
NZ_QURH01000291	15	15	0	0	15,738	RefSeq:NZ_QURH01000291
NZ_QURH01000174	16	15	0	1	15,695	RefSeq:NZ_QURH01000174
NZ_QURH01001033	15	15	0	0	15,674	RefSeq:NZ_QURH01001033
NZ_QURH01000105	14	11	0	3	15,670	RefSeq:NZ_QURH01000105
NZ_QURH01001032	15	13	1	1	15,630	RefSeq:NZ_QURH01001032
NZ_QURH01000223	13	13	0	0	15,524	RefSeq:NZ_QURH01000223
NZ_QURH01000186	17	17	0	0	15,450	RefSeq:NZ_QURH01000186
NZ_QURH01001031	12	12	0	0	15,153	RefSeq:NZ_QURH01001031
NZ_QURH01000123	12	11	0	1	15,126	RefSeq:NZ_QURH01000123
NZ_QURH01001030	19	18	1	0	14,990	RefSeq:NZ_QURH01001030
NZ_QURH01000305	12	11	0	1	14,970	RefSeq:NZ_QURH01000305
NZ_QURH01000113	15	11	2	2	14,945	RefSeq:NZ_QURH01000113
NZ_QURH01000273	14	13	0	1	14,921	RefSeq:NZ_QURH01000273
NZ_QURH01001029	16	15	1	0	14,890	RefSeq:NZ_QURH01001029
NZ_QURH01000116	12	12	0	0	14,685	RefSeq:NZ_QURH01000116
NZ_QURH01000168	15	15	0	0	14,516	RefSeq:NZ_QURH01000168
NZ_QURH01001028	14	13	0	1	14,261	RefSeq:NZ_QURH01001028
NZ_QURH01000304	11	11	0	0	13,722	RefSeq:NZ_QURH01000304
NZ_QURH01001027	16	15	0	1	13,683	RefSeq:NZ_QURH01001027
NZ_QURH01001024	12	12	0	0	13,681	RefSeq:NZ_QURH01001024
NZ_QURH01000219	15	14	0	1	13,594	RefSeq:NZ_QURH01000219
NZ_QURH01000292	11	11	0	0	13,560	RefSeq:NZ_QURH01000292
NZ_QURH01000250	13	12	0	1	13,537	RefSeq:NZ_QURH01000250
NZ_QURH01000313	17	17	0	0	13,308	RefSeq:NZ_QURH01000313
NZ_QURH01000207	14	14	0	0	13,248	RefSeq:NZ_QURH01000207
NZ_QURH01000086	15	15	0	0	13,128	RefSeq:NZ_QURH01000086
NZ_QURH01001019	14	13	0	1	13,050	RefSeq:NZ_QURH01001019
NZ_QURH01001018	14	13	0	1	13,029	RefSeq:NZ_QURH01001018
NZ_QURH01000158	14	14	0	0	13,020	RefSeq:NZ_QURH01000158
NZ_QURH01001020	14	13	0	1	13,006	RefSeq:NZ_QURH01001020
NZ_QURH01001015	13	12	0	1	12,959	RefSeq:NZ_QURH01001015
NZ_QURH01001016	14	12	1	1	12,929	RefSeq:NZ_QURH01001016
NZ_QURH01001017	11	11	0	0	12,928	RefSeq:NZ_QURH01001017
NZ_QURH01000244	12	10	0	2	12,922	RefSeq:NZ_QURH01000244
NZ_QURH01000300	11	11	0	0	12,906	RefSeq:NZ_QURH01000300
NZ_QURH01000212	15	15	0	0	12,858	RefSeq:NZ_QURH01000212
NZ_QURH01000234	12	12	0	0	12,624	RefSeq:NZ_QURH01000234
NZ_QURH01001009	15	13	1	1	12,588	RefSeq:NZ_QURH01001009
NZ_QURH01000071	12	11	0	1	12,552	RefSeq:NZ_QURH01000071
NZ_QURH01000194	12	9	2	1	11,900	RefSeq:NZ_QURH01000194
NZ_QURH01001003	12	11	0	1	11,882	RefSeq:NZ_QURH01001003
NZ_QURH01001002	11	11	0	0	11,804	RefSeq:NZ_QURH01001002
NZ_QURH01000284	12	10	0	2	11,681	RefSeq:NZ_QURH01000284
NZ_QURH01000229	15	13	2	0	11,676	RefSeq:NZ_QURH01000229
NZ_QURH01000201	13	13	0	0	11,189	RefSeq:NZ_QURH01000201
NZ_QURH01000264	12	11	0	1	11,016	RefSeq:NZ_QURH01000264
NZ_QURH01000992	11	11	0	0	10,717	RefSeq:NZ_QURH01000992
NZ_QURH01000238	12	11	0	1	10,509	RefSeq:NZ_QURH01000238
NZ_QURH01000235	10	10	0	0	10,447	RefSeq:NZ_QURH01000235
NZ_QURH01000294	13	12	0	1	10,106	RefSeq:NZ_QURH01000294
NZ_QURH01000974	11	11	0	0	9,178	RefSeq:NZ_QURH01000974
NZ_QURH01000068	11	11	0	0	6,932	RefSeq:NZ_QURH01000068
NZ_QURH01000874	14	13	0	1	5,808	RefSeq:NZ_QURH01000874
879 Undisplayed Contigs/Replicons	2,593	2,572	22	369	3,874,846

Total:	6,871	6,310	76	485	8,093,581

Ortholog data available?	No

Database Contents

Genes	6,870
Pathways	264
Enzymatic Reactions	1,420
Transport Reactions	43
Polypeptides	7,126
Protein Complexes	3
Enzymes	1,021
Transporters	648
Compounds	1,089
Transcription Units	6,044
tRNAs	68
Protein Features	7,182
GO Terms	453

Database Version

29.0

Sequence Source	GCF_003428695.1
Synonyms	Actinomadura sp. NEAU-G17
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Actinomycetota Actinomycetes Streptosporangiales Thermomonosporaceae Actinomadura Actinomadura logoneensis
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN09770274
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	2293572
Environment	soil
Geographic Location	Chad
Collection Date	2017-06-23
Annotation Provider	NCBI RefSeq
Annotation Date	2021-03-19
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	5.1
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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