Summary of Actinomadura chibensis NBRC 106107, 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 chibensis NBRC 106107, 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_BCQP01000010	458	449	3	6	487,924	RefSeq:NZ_BCQP01000010
NZ_BCQP01000017	472	457	4	11	466,108	RefSeq:NZ_BCQP01000017
NZ_BCQP01000004	346	342	3	1	378,532	RefSeq:NZ_BCQP01000004
NZ_BCQP01000016	258	255	3	0	287,929	RefSeq:NZ_BCQP01000016
NZ_BCQP01000024	140	119	0	21	221,887	RefSeq:NZ_BCQP01000024
NZ_BCQP01000015	180	173	5	2	201,085	RefSeq:NZ_BCQP01000015
NZ_BCQP01000002	168	167	0	1	196,147	RefSeq:NZ_BCQP01000002
NZ_BCQP01000027	161	158	1	2	185,314	RefSeq:NZ_BCQP01000027
NZ_BCQP01000028	175	172	3	0	184,912	RefSeq:NZ_BCQP01000028
NZ_BCQP01000029	168	166	1	1	181,993	RefSeq:NZ_BCQP01000029
NZ_BCQP01000030	158	152	0	6	180,846	RefSeq:NZ_BCQP01000030
NZ_BCQP01000001	172	166	6	0	174,799	RefSeq:NZ_BCQP01000001
NZ_BCQP01000036	156	153	1	2	169,679	RefSeq:NZ_BCQP01000036
NZ_BCQP01000012	161	159	1	1	169,207	RefSeq:NZ_BCQP01000012
NZ_BCQP01000025	153	150	0	3	151,108	RefSeq:NZ_BCQP01000025
NZ_BCQP01000037	157	151	4	2	151,087	RefSeq:NZ_BCQP01000037
NZ_BCQP01000038	121	119	1	1	131,312	RefSeq:NZ_BCQP01000038
NZ_BCQP01000039	95	94	1	0	130,606	RefSeq:NZ_BCQP01000039
NZ_BCQP01000040	118	117	0	1	128,217	RefSeq:NZ_BCQP01000040
NZ_BCQP01000041	122	120	1	1	127,005	RefSeq:NZ_BCQP01000041
NZ_BCQP01000042	114	113	0	1	123,142	RefSeq:NZ_BCQP01000042
NZ_BCQP01000043	95	94	0	1	122,868	RefSeq:NZ_BCQP01000043
NZ_BCQP01000044	98	95	1	2	122,050	RefSeq:NZ_BCQP01000044
NZ_BCQP01000045	107	106	0	1	118,151	RefSeq:NZ_BCQP01000045
NZ_BCQP01000019	84	82	0	2	117,171	RefSeq:NZ_BCQP01000019
NZ_BCQP01000048	116	116	0	0	117,061	RefSeq:NZ_BCQP01000048
NZ_BCQP01000032	111	106	4	1	114,916	RefSeq:NZ_BCQP01000032
NZ_BCQP01000035	102	100	0	2	114,856	RefSeq:NZ_BCQP01000035
NZ_BCQP01000049	105	101	1	3	113,875	RefSeq:NZ_BCQP01000049
NZ_BCQP01000050	94	92	1	1	111,275	RefSeq:NZ_BCQP01000050
NZ_BCQP01000051	87	87	0	0	107,341	RefSeq:NZ_BCQP01000051
NZ_BCQP01000052	88	88	0	0	104,972	RefSeq:NZ_BCQP01000052
NZ_BCQP01000008	90	87	2	1	95,162	RefSeq:NZ_BCQP01000008
NZ_BCQP01000053	93	91	1	1	94,912	RefSeq:NZ_BCQP01000053
NZ_BCQP01000054	92	92	0	0	94,305	RefSeq:NZ_BCQP01000054
NZ_BCQP01000055	83	83	0	0	92,409	RefSeq:NZ_BCQP01000055
NZ_BCQP01000056	75	74	1	0	88,384	RefSeq:NZ_BCQP01000056
NZ_BCQP01000022	65	63	0	2	88,262	RefSeq:NZ_BCQP01000022
NZ_BCQP01000047	77	77	0	0	87,671	RefSeq:NZ_BCQP01000047
NZ_BCQP01000009	75	72	3	0	86,953	RefSeq:NZ_BCQP01000009
NZ_BCQP01000020	57	52	0	5	86,182	RefSeq:NZ_BCQP01000020
NZ_BCQP01000057	76	75	1	0	83,851	RefSeq:NZ_BCQP01000057
NZ_BCQP01000058	71	71	0	0	82,679	RefSeq:NZ_BCQP01000058
NZ_BCQP01000059	74	73	0	1	82,482	RefSeq:NZ_BCQP01000059
NZ_BCQP01000060	72	70	2	0	80,263	RefSeq:NZ_BCQP01000060
NZ_BCQP01000061	78	77	0	1	79,037	RefSeq:NZ_BCQP01000061
NZ_BCQP01000062	68	67	0	1	78,815	RefSeq:NZ_BCQP01000062
NZ_BCQP01000063	66	65	0	1	75,745	RefSeq:NZ_BCQP01000063
NZ_BCQP01000064	54	54	0	0	75,627	RefSeq:NZ_BCQP01000064
NZ_BCQP01000065	69	66	1	2	75,391	RefSeq:NZ_BCQP01000065
NZ_BCQP01000066	69	65	2	2	74,451	RefSeq:NZ_BCQP01000066
NZ_BCQP01000067	70	69	0	1	72,229	RefSeq:NZ_BCQP01000067
NZ_BCQP01000068	64	64	0	0	70,537	RefSeq:NZ_BCQP01000068
NZ_BCQP01000069	60	57	1	2	68,717	RefSeq:NZ_BCQP01000069
NZ_BCQP01000070	47	45	0	2	63,649	RefSeq:NZ_BCQP01000070
NZ_BCQP01000071	55	55	0	0	62,459	RefSeq:NZ_BCQP01000071
NZ_BCQP01000011	57	57	0	0	62,291	RefSeq:NZ_BCQP01000011
NZ_BCQP01000031	48	46	1	1	62,242	RefSeq:NZ_BCQP01000031
NZ_BCQP01000072	63	61	1	1	61,787	RefSeq:NZ_BCQP01000072
NZ_BCQP01000073	68	68	0	0	61,642	RefSeq:NZ_BCQP01000073
NZ_BCQP01000074	55	54	0	1	59,381	RefSeq:NZ_BCQP01000074
NZ_BCQP01000075	47	45	1	1	58,735	RefSeq:NZ_BCQP01000075
NZ_BCQP01000076	57	56	0	1	58,166	RefSeq:NZ_BCQP01000076
NZ_BCQP01000077	51	51	0	0	52,603	RefSeq:NZ_BCQP01000077
NZ_BCQP01000078	44	40	2	2	52,279	RefSeq:NZ_BCQP01000078
NZ_BCQP01000079	43	41	1	1	49,339	RefSeq:NZ_BCQP01000079
NZ_BCQP01000080	34	34	0	0	47,350	RefSeq:NZ_BCQP01000080
NZ_BCQP01000081	32	32	0	0	43,782	RefSeq:NZ_BCQP01000081
NZ_BCQP01000033	41	40	0	1	42,927	RefSeq:NZ_BCQP01000033
NZ_BCQP01000026	37	36	0	1	42,810	RefSeq:NZ_BCQP01000026
NZ_BCQP01000083	35	34	0	1	42,473	RefSeq:NZ_BCQP01000083
NZ_BCQP01000084	43	40	0	3	42,030	RefSeq:NZ_BCQP01000084
NZ_BCQP01000003	36	35	0	1	41,771	RefSeq:NZ_BCQP01000003
NZ_BCQP01000085	36	29	0	7	41,324	RefSeq:NZ_BCQP01000085
NZ_BCQP01000086	32	32	0	0	40,018	RefSeq:NZ_BCQP01000086
NZ_BCQP01000087	40	39	0	1	38,894	RefSeq:NZ_BCQP01000087
NZ_BCQP01000088	39	38	0	1	38,581	RefSeq:NZ_BCQP01000088
NZ_BCQP01000023	37	36	0	1	37,245	RefSeq:NZ_BCQP01000023
NZ_BCQP01000089	44	40	3	1	36,110	RefSeq:NZ_BCQP01000089
NZ_BCQP01000090	30	30	0	0	36,083	RefSeq:NZ_BCQP01000090
NZ_BCQP01000091	37	36	1	0	35,384	RefSeq:NZ_BCQP01000091
NZ_BCQP01000092	26	26	0	0	34,211	RefSeq:NZ_BCQP01000092
NZ_BCQP01000007	29	28	1	0	33,610	RefSeq:NZ_BCQP01000007
NZ_BCQP01000014	29	28	0	1	33,240	RefSeq:NZ_BCQP01000014
NZ_BCQP01000093	24	24	0	0	30,943	RefSeq:NZ_BCQP01000093
NZ_BCQP01000094	27	25	1	1	30,017	RefSeq:NZ_BCQP01000094
NZ_BCQP01000046	28	28	0	0	29,500	RefSeq:NZ_BCQP01000046
NZ_BCQP01000095	17	16	0	1	25,638	RefSeq:NZ_BCQP01000095
NZ_BCQP01000096	24	24	0	0	23,313	RefSeq:NZ_BCQP01000096
NZ_BCQP01000097	20	18	1	1	20,570	RefSeq:NZ_BCQP01000097
NZ_BCQP01000005	24	24	0	0	19,843	RefSeq:NZ_BCQP01000005
NZ_BCQP01000034	21	20	0	1	17,916	RefSeq:NZ_BCQP01000034
NZ_BCQP01000101	12	11	0	1	14,819	RefSeq:NZ_BCQP01000101
NZ_BCQP01000102	12	12	0	0	14,468	RefSeq:NZ_BCQP01000102
NZ_BCQP01000103	14	13	1	0	14,195	RefSeq:NZ_BCQP01000103
NZ_BCQP01000104	12	12	0	0	13,257	RefSeq:NZ_BCQP01000104
NZ_BCQP01000109	11	10	1	0	9,093	RefSeq:NZ_BCQP01000109
36 Undisplayed Contigs/Replicons	132	129	10	11	225,465

Total:	8,406	8,181	84	141	9,408,892

Ortholog data available?	Yes

Database Contents

Genes	8,398
Pathways	293
Enzymatic Reactions	1,533
Transport Reactions	45
Polypeptides	8,271
Protein Complexes	6
Enzymes	1,216
Transporters	831
Compounds	1,178
Transcription Units	5,727
tRNAs	70
Protein Features	9,841
GO Terms	555

Database Version

29.0

Sequence Source	GCF_001552135.1
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Actinomycetota Actinomycetes Streptosporangiales Thermomonosporaceae Actinomadura Actinomadura chibensis Actinomadura chibensis NBRC 106107
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMD00046498
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1220554
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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