Summary of Actinokineospora inagensis DSM 44258, version 29.0

Tier 3 Uncurated Organism Database

Database Authors

Pallavi Subhraveti¹, Ingrid Keseler¹, Anamika Kothari¹, Ron Caspi¹, Peter D Karp¹

Summary

This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Actinokineospora inagensis DSM 44258, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_KI519516	383	375	2	6	423,085	RefSeq:NZ_KI519516
NZ_KI519517	287	281	0	6	352,186	RefSeq:NZ_KI519517
NZ_AXWW01000005	205	195	1	9	219,478	RefSeq:NZ_AXWW01000005
NZ_AXWW01000006	206	194	6	6	214,489	RefSeq:NZ_AXWW01000006
NZ_AXWW01000007	193	191	0	2	202,785	RefSeq:NZ_AXWW01000007
NZ_KI519518	195	189	4	2	193,924	RefSeq:NZ_KI519518
NZ_AXWW01000010	173	170	1	2	192,142	RefSeq:NZ_AXWW01000010
NZ_KI519519	126	125	0	1	187,511	RefSeq:NZ_KI519519
NZ_AXWW01000013	165	160	4	1	178,789	RefSeq:NZ_AXWW01000013
NZ_AXWW01000015	146	143	0	3	174,178	RefSeq:NZ_AXWW01000015
NZ_AXWW01000014	128	124	0	4	174,063	RefSeq:NZ_AXWW01000014
NZ_AXWW01000016	141	135	0	6	168,247	RefSeq:NZ_AXWW01000016
NZ_AXWW01000017	137	136	1	0	165,797	RefSeq:NZ_AXWW01000017
NZ_AXWW01000018	149	146	0	3	153,409	RefSeq:NZ_AXWW01000018
NZ_KI519520	89	87	0	2	129,795	RefSeq:NZ_KI519520
NZ_AXWW01000021	122	121	0	1	129,618	RefSeq:NZ_AXWW01000021
NZ_AXWW01000022	89	75	0	14	128,061	RefSeq:NZ_AXWW01000022
NZ_AXWW01000023	89	88	0	1	119,453	RefSeq:NZ_AXWW01000023
NZ_AXWW01000024	67	64	1	2	116,777	RefSeq:NZ_AXWW01000024
NZ_AXWW01000025	108	104	3	1	116,641	RefSeq:NZ_AXWW01000025
NZ_AXWW01000026	84	79	0	5	113,601	RefSeq:NZ_AXWW01000026
NZ_AXWW01000027	104	98	2	4	112,130	RefSeq:NZ_AXWW01000027
NZ_AXWW01000029	117	116	0	1	109,749	RefSeq:NZ_AXWW01000029
NZ_AXWW01000028	103	101	0	2	109,727	RefSeq:NZ_AXWW01000028
NZ_AXWW01000030	105	99	1	5	103,721	RefSeq:NZ_AXWW01000030
NZ_AXWW01000031	81	80	0	1	98,575	RefSeq:NZ_AXWW01000031
NZ_AXWW01000033	61	59	0	2	94,407	RefSeq:NZ_AXWW01000033
NZ_AXWW01000032	87	81	0	6	94,386	RefSeq:NZ_AXWW01000032
NZ_AXWW01000034	64	7	0	57	92,343	RefSeq:NZ_AXWW01000034
NZ_AXWW01000035	100	98	1	1	90,295	RefSeq:NZ_AXWW01000035
NZ_AXWW01000036	69	67	0	2	88,304	RefSeq:NZ_AXWW01000036
NZ_AXWW01000037	88	80	4	4	86,234	RefSeq:NZ_AXWW01000037
NZ_AXWW01000038	86	84	0	2	85,903	RefSeq:NZ_AXWW01000038
NZ_AXWW01000039	48	47	0	1	84,449	RefSeq:NZ_AXWW01000039
NZ_KI519521	73	71	0	2	83,571	RefSeq:NZ_KI519521
NZ_KI519522	67	66	1	0	78,049	RefSeq:NZ_KI519522
NZ_AXWW01000042	60	52	0	8	78,048	RefSeq:NZ_AXWW01000042
NZ_AXWW01000045	78	72	6	0	76,826	RefSeq:NZ_AXWW01000045
NZ_AXWW01000047	46	43	0	3	74,388	RefSeq:NZ_AXWW01000047
NZ_AXWW01000046	66	64	0	2	74,352	RefSeq:NZ_AXWW01000046
NZ_AXWW01000048	64	63	0	1	73,685	RefSeq:NZ_AXWW01000048
NZ_AXWW01000049	75	73	0	2	70,871	RefSeq:NZ_AXWW01000049
NZ_AXWW01000051	75	75	0	0	66,366	RefSeq:NZ_AXWW01000051
NZ_AXWW01000050	58	55	0	3	66,361	RefSeq:NZ_AXWW01000050
NZ_AXWW01000052	49	45	1	3	58,264	RefSeq:NZ_AXWW01000052
NZ_AXWW01000053	53	52	0	1	57,680	RefSeq:NZ_AXWW01000053
NZ_AXWW01000054	52	48	3	1	53,707	RefSeq:NZ_AXWW01000054
NZ_AXWW01000055	41	35	0	6	53,389	RefSeq:NZ_AXWW01000055
NZ_AXWW01000056	50	46	2	2	52,118	RefSeq:NZ_AXWW01000056
NZ_AXWW01000057	54	52	1	1	50,711	RefSeq:NZ_AXWW01000057
NZ_AXWW01000058	38	35	0	3	46,888	RefSeq:NZ_AXWW01000058
NZ_AXWW01000059	40	37	1	2	44,672	RefSeq:NZ_AXWW01000059
NZ_AXWW01000060	39	39	0	0	44,528	RefSeq:NZ_AXWW01000060
NZ_AXWW01000061	39	39	0	0	44,019	RefSeq:NZ_AXWW01000061
NZ_AXWW01000062	33	33	0	0	40,961	RefSeq:NZ_AXWW01000062
NZ_AXWW01000063	37	37	0	0	40,462	RefSeq:NZ_AXWW01000063
NZ_AXWW01000064	38	35	1	2	40,322	RefSeq:NZ_AXWW01000064
NZ_AXWW01000065	43	42	0	1	38,411	RefSeq:NZ_AXWW01000065
NZ_KI519523	27	27	0	0	36,910	RefSeq:NZ_KI519523
NZ_AXWW01000068	27	25	1	1	36,879	RefSeq:NZ_AXWW01000068
NZ_AXWW01000069	41	41	0	0	35,607	RefSeq:NZ_AXWW01000069
NZ_AXWW01000070	34	33	0	1	35,430	RefSeq:NZ_AXWW01000070
NZ_AXWW01000071	31	29	0	2	34,655	RefSeq:NZ_AXWW01000071
NZ_AXWW01000072	23	22	1	0	33,284	RefSeq:NZ_AXWW01000072
NZ_AXWW01000073	29	28	1	0	32,300	RefSeq:NZ_AXWW01000073
NZ_AXWW01000074	29	29	0	0	31,334	RefSeq:NZ_AXWW01000074
NZ_AXWW01000075	29	29	0	0	29,398	RefSeq:NZ_AXWW01000075
NZ_AXWW01000076	21	15	0	6	27,470	RefSeq:NZ_AXWW01000076
NZ_AXWW01000077	27	27	0	0	27,005	RefSeq:NZ_AXWW01000077
NZ_AXWW01000078	29	28	0	1	25,818	RefSeq:NZ_AXWW01000078
NZ_AXWW01000079	17	15	0	2	25,005	RefSeq:NZ_AXWW01000079
NZ_AXWW01000080	19	18	0	1	24,358	RefSeq:NZ_AXWW01000080
NZ_AXWW01000081	21	21	0	0	22,979	RefSeq:NZ_AXWW01000081
NZ_AXWW01000082	22	21	0	1	22,337	RefSeq:NZ_AXWW01000082
NZ_AXWW01000083	20	20	0	0	22,253	RefSeq:NZ_AXWW01000083
NZ_AXWW01000084	16	16	0	0	21,349	RefSeq:NZ_AXWW01000084
NZ_AXWW01000085	20	19	0	1	21,227	RefSeq:NZ_AXWW01000085
NZ_AXWW01000086	19	17	1	1	20,224	RefSeq:NZ_AXWW01000086
NZ_AXWW01000087	24	23	0	1	15,640	RefSeq:NZ_AXWW01000087
NZ_AXWW01000088	17	15	1	1	14,866	RefSeq:NZ_AXWW01000088
NZ_AXWW01000090	12	12	0	0	13,822	RefSeq:NZ_AXWW01000090
NZ_AXWW01000093	13	13	0	0	12,341	RefSeq:NZ_AXWW01000093
NZ_AXWW01000101	12	9	3	0	8,056	RefSeq:NZ_AXWW01000101
15 Undisplayed Contigs/Replicons	102	100	4	12	135,311

Total:	6,358	6,060	59	239	7,278,759

Ortholog data available?	Yes

Database Contents

Genes	6,352
Pathways	264
Enzymatic Reactions	1,353
Transport Reactions	56
Polypeptides	6,068
Protein Complexes	48
Enzymes	1,008
Transporters	413
Compounds	1,075
Transcription Units	4,263
tRNAs	49
Protein Features	6,980
GO Terms	1

Database Version

29.0

Sequence Source	GCF_000482865.1
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Actinomycetota Actinomycetes Pseudonocardiales Pseudonocardiaceae Actinokineospora Actinokineospora inagensis Actinokineospora inagensis DSM 44258
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN02441427
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1120935
Environment	Plants; Fresh water; Aquatic
Geographic Location	Japan
Relationship to Oxygen	aerobe
Temperature Range	mesophile
Annotation Provider	NCBI
Annotation Date	2017-04-15
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version	4.1
Annotation Comment	Best-placed reference protein set; GeneMarkS+
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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