Summary of Actinomadura latina NBRC 106108, 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 latina NBRC 106108, 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_BCQS01000003	1,064	1,039	12	13	1,074,402	RefSeq:NZ_BCQS01000003
NZ_BCQS01000005	879	864	9	6	932,179	RefSeq:NZ_BCQS01000005
NZ_BCQS01000011	336	333	1	2	398,182	RefSeq:NZ_BCQS01000011
NZ_BCQS01000012	354	344	3	7	380,047	RefSeq:NZ_BCQS01000012
NZ_BCQS01000007	331	324	2	5	336,372	RefSeq:NZ_BCQS01000007
NZ_BCQS01000013	275	271	0	4	324,448	RefSeq:NZ_BCQS01000013
NZ_BCQS01000006	276	269	1	6	300,191	RefSeq:NZ_BCQS01000006
NZ_BCQS01000018	259	258	0	1	268,219	RefSeq:NZ_BCQS01000018
NZ_BCQS01000008	255	250	3	2	260,257	RefSeq:NZ_BCQS01000008
NZ_BCQS01000019	204	201	0	3	248,668	RefSeq:NZ_BCQS01000019
NZ_BCQS01000020	198	195	1	2	232,277	RefSeq:NZ_BCQS01000020
NZ_BCQS01000017	205	197	5	3	216,524	RefSeq:NZ_BCQS01000017
NZ_BCQS01000009	193	185	1	7	200,852	RefSeq:NZ_BCQS01000009
NZ_BCQS01000026	183	176	1	6	185,886	RefSeq:NZ_BCQS01000026
NZ_BCQS01000027	180	174	2	4	180,456	RefSeq:NZ_BCQS01000027
NZ_BCQS01000032	122	109	1	12	130,079	RefSeq:NZ_BCQS01000032
NZ_BCQS01000035	116	111	2	3	121,906	RefSeq:NZ_BCQS01000035
NZ_BCQS01000001	125	120	2	3	118,928	RefSeq:NZ_BCQS01000001
NZ_BCQS01000028	114	113	0	1	116,681	RefSeq:NZ_BCQS01000028
NZ_BCQS01000033	89	87	0	2	114,632	RefSeq:NZ_BCQS01000033
NZ_BCQS01000036	101	94	4	3	107,471	RefSeq:NZ_BCQS01000036
NZ_BCQS01000004	90	89	0	1	93,310	RefSeq:NZ_BCQS01000004
NZ_BCQS01000031	87	86	0	1	92,647	RefSeq:NZ_BCQS01000031
NZ_BCQS01000039	65	62	0	3	89,041	RefSeq:NZ_BCQS01000039
NZ_BCQS01000023	84	83	0	1	88,462	RefSeq:NZ_BCQS01000023
NZ_BCQS01000016	76	75	0	1	81,562	RefSeq:NZ_BCQS01000016
NZ_BCQS01000040	56	53	0	3	67,082	RefSeq:NZ_BCQS01000040
NZ_BCQS01000041	63	61	1	1	66,440	RefSeq:NZ_BCQS01000041
NZ_BCQS01000015	56	54	1	1	63,269	RefSeq:NZ_BCQS01000015
NZ_BCQS01000042	56	54	2	0	61,054	RefSeq:NZ_BCQS01000042
NZ_BCQS01000043	57	55	1	1	59,486	RefSeq:NZ_BCQS01000043
NZ_BCQS01000044	57	53	2	2	58,661	RefSeq:NZ_BCQS01000044
NZ_BCQS01000030	48	48	0	0	54,376	RefSeq:NZ_BCQS01000030
NZ_BCQS01000038	54	53	0	1	54,030	RefSeq:NZ_BCQS01000038
NZ_BCQS01000045	35	34	0	1	54,021	RefSeq:NZ_BCQS01000045
NZ_BCQS01000046	45	42	1	2	53,110	RefSeq:NZ_BCQS01000046
NZ_BCQS01000047	45	44	0	1	52,805	RefSeq:NZ_BCQS01000047
NZ_BCQS01000048	40	40	0	0	46,846	RefSeq:NZ_BCQS01000048
NZ_BCQS01000024	50	50	0	0	46,168	RefSeq:NZ_BCQS01000024
NZ_BCQS01000025	48	48	0	0	41,228	RefSeq:NZ_BCQS01000025
NZ_BCQS01000014	41	41	0	0	40,372	RefSeq:NZ_BCQS01000014
NZ_BCQS01000049	25	24	0	1	38,973	RefSeq:NZ_BCQS01000049
NZ_BCQS01000037	35	35	0	0	37,382	RefSeq:NZ_BCQS01000037
NZ_BCQS01000029	33	31	2	0	34,635	RefSeq:NZ_BCQS01000029
NZ_BCQS01000010	31	30	1	0	33,090	RefSeq:NZ_BCQS01000010
NZ_BCQS01000002	26	25	0	1	27,469	RefSeq:NZ_BCQS01000002
NZ_BCQS01000022	24	23	0	1	26,867	RefSeq:NZ_BCQS01000022
NZ_BCQS01000021	19	19	0	0	22,510	RefSeq:NZ_BCQS01000021
NZ_BCQS01000034	13	13	0	0	15,240	RefSeq:NZ_BCQS01000034
NZ_BCQS01000052	9	7	2	0	11,048	RefSeq:NZ_BCQS01000052
NZ_BCQS01000055	11	8	3	0	9,951	RefSeq:NZ_BCQS01000055
25 Undisplayed Contigs/Replicons	45	44	3	10	97,856

Total:	7,295	7,098	69	128	7,867,648

Ortholog data available?	Yes

Database Contents

Genes	7,292
Pathways	288
Enzymatic Reactions	1,520
Transport Reactions	50
Polypeptides	7,152
Protein Complexes	5
Enzymes	1,134
Transporters	640
Compounds	1,184
Transcription Units	5,057
tRNAs	58
Protein Features	8,518
GO Terms	427

Database Version

29.0

Sequence Source	GCF_001552195.1
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Actinomycetota Actinomycetes Streptosporangiales Thermomonosporaceae Actinomadura Actinomadura latina Actinomadura latina NBRC 106108
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMD00046499
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1220563
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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