Summary of Actinobacteria bacterium OK074, version 29.0

Tier 3 Uncurated Organism Database

Database Authors

Pallavi Subhraveti¹, Quang Ong¹, Ingrid Keseler¹, Anamika Kothari¹, Ron Caspi¹, Peter D Karp¹

Summary

This Pathway/Genome Database (PGDB) was generated on 27-June-2017 from the annotated genome of Actinobacteria bacterium OK074 OK074, 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 21.5) [1, Karp11] using MetaCyc version 21.0 [Caspi16]. 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 Institutess of Health.

Genome

Contig	Total Genes	Protein Genes	RNA Genes	Pseudogenes	Size (bp)	NCBI Link
NZ_LJCV01000055	222	210	2	10	257,403	RefSeq:NZ_LJCV01000055
NZ_LJCV01000275	234	217	1	16	239,229	RefSeq:NZ_LJCV01000275
NZ_LJCV01000188	194	181	1	12	237,296	RefSeq:NZ_LJCV01000188
NZ_LJCV01000044	201	194	0	7	222,246	RefSeq:NZ_LJCV01000044
NZ_LJCV01000099	197	193	1	3	217,838	RefSeq:NZ_LJCV01000099
NZ_LJCV01000110	165	157	4	4	186,031	RefSeq:NZ_LJCV01000110
NZ_LJCV01000177	173	159	2	12	181,070	RefSeq:NZ_LJCV01000177
NZ_LJCV01000263	141	139	0	2	153,675	RefSeq:NZ_LJCV01000263
NZ_LJCV01000252	138	126	0	12	150,575	RefSeq:NZ_LJCV01000252
NZ_LJCV01000111	82	75	0	7	130,359	RefSeq:NZ_LJCV01000111
NZ_LJCV01000285	114	103	5	6	124,515	RefSeq:NZ_LJCV01000285
NZ_LJCV01000077	94	85	0	9	117,443	RefSeq:NZ_LJCV01000077
NZ_LJCV01000274	101	97	1	3	116,969	RefSeq:NZ_LJCV01000274
NZ_LJCV01000245	100	98	0	2	109,969	RefSeq:NZ_LJCV01000245
NZ_LJCV01000011	94	93	0	1	107,828	RefSeq:NZ_LJCV01000011
NZ_LJCV01000221	80	75	0	5	101,038	RefSeq:NZ_LJCV01000221
NZ_LJCV01000296	80	76	1	3	98,265	RefSeq:NZ_LJCV01000296
NZ_LJCV01000318	82	81	0	1	97,723	RefSeq:NZ_LJCV01000318
NZ_LJCV01000307	76	70	0	6	95,552	RefSeq:NZ_LJCV01000307
NZ_LJCV01000066	71	70	0	1	95,467	RefSeq:NZ_LJCV01000066
NZ_LJCV01000033	72	70	2	0	94,227	RefSeq:NZ_LJCV01000033
NZ_LJCV01000022	78	76	0	2	93,719	RefSeq:NZ_LJCV01000022
NZ_LJCV01000133	74	73	0	1	91,539	RefSeq:NZ_LJCV01000133
NZ_LJCV01000088	82	81	0	1	90,609	RefSeq:NZ_LJCV01000088
NZ_LJCV01000122	71	67	0	4	90,102	RefSeq:NZ_LJCV01000122
NZ_LJCV01000155	80	76	0	4	89,376	RefSeq:NZ_LJCV01000155
NZ_LJCV01000166	81	80	0	1	88,211	RefSeq:NZ_LJCV01000166
NZ_LJCV01000231	87	83	0	4	87,879	RefSeq:NZ_LJCV01000231
NZ_LJCV01000144	79	77	0	2	87,752	RefSeq:NZ_LJCV01000144
NZ_LJCV01000242	76	72	0	4	86,872	RefSeq:NZ_LJCV01000242
NZ_LJCV01000248	79	77	0	2	85,816	RefSeq:NZ_LJCV01000248
NZ_LJCV01000256	69	65	1	3	85,100	RefSeq:NZ_LJCV01000256
NZ_LJCV01000251	70	67	1	2	83,998	RefSeq:NZ_LJCV01000251
NZ_LJCV01000198	77	75	0	2	83,928	RefSeq:NZ_LJCV01000198
NZ_LJCV01000209	57	54	0	3	81,148	RefSeq:NZ_LJCV01000209
NZ_LJCV01000247	59	57	1	1	80,511	RefSeq:NZ_LJCV01000247
NZ_LJCV01000220	70	66	0	4	79,942	RefSeq:NZ_LJCV01000220
NZ_LJCV01000244	65	62	0	3	78,621	RefSeq:NZ_LJCV01000244
NZ_LJCV01000250	86	79	4	3	76,599	RefSeq:NZ_LJCV01000250
NZ_LJCV01000260	87	84	0	3	75,423	RefSeq:NZ_LJCV01000260
NZ_LJCV01000246	52	51	0	1	74,542	RefSeq:NZ_LJCV01000246
NZ_LJCV01000255	65	63	0	2	73,523	RefSeq:NZ_LJCV01000255
NZ_LJCV01000253	61	60	0	1	71,147	RefSeq:NZ_LJCV01000253
NZ_LJCV01000292	57	55	0	2	70,385	RefSeq:NZ_LJCV01000292
NZ_LJCV01000254	52	51	0	1	69,344	RefSeq:NZ_LJCV01000254
NZ_LJCV01000249	55	53	0	2	68,377	RefSeq:NZ_LJCV01000249
NZ_LJCV01000258	59	59	0	0	68,172	RefSeq:NZ_LJCV01000258
NZ_LJCV01000259	61	59	0	2	67,869	RefSeq:NZ_LJCV01000259
NZ_LJCV01000269	54	50	1	3	66,794	RefSeq:NZ_LJCV01000269
NZ_LJCV01000286	60	58	0	2	66,723	RefSeq:NZ_LJCV01000286
NZ_LJCV01000262	60	60	0	0	66,282	RefSeq:NZ_LJCV01000262
NZ_LJCV01000265	56	51	1	4	63,918	RefSeq:NZ_LJCV01000265
NZ_LJCV01000266	60	58	0	2	62,223	RefSeq:NZ_LJCV01000266
NZ_LJCV01000267	37	33	1	3	57,893	RefSeq:NZ_LJCV01000267
NZ_LJCV01000257	54	50	0	4	57,346	RefSeq:NZ_LJCV01000257
NZ_LJCV01000268	53	50	0	3	57,003	RefSeq:NZ_LJCV01000268
NZ_LJCV01000273	59	50	4	5	55,482	RefSeq:NZ_LJCV01000273
NZ_LJCV01000261	26	24	0	2	55,068	RefSeq:NZ_LJCV01000261
NZ_LJCV01000272	38	35	0	3	54,289	RefSeq:NZ_LJCV01000272
NZ_LJCV01000280	46	38	0	8	51,359	RefSeq:NZ_LJCV01000280
NZ_LJCV01000271	42	41	0	1	50,839	RefSeq:NZ_LJCV01000271
NZ_LJCV01000270	56	47	0	9	50,721	RefSeq:NZ_LJCV01000270
NZ_LJCV01000284	44	42	0	2	50,637	RefSeq:NZ_LJCV01000284
NZ_LJCV01000279	47	40	2	5	49,618	RefSeq:NZ_LJCV01000279
NZ_LJCV01000002	44	42	0	2	47,614	RefSeq:NZ_LJCV01000002
NZ_LJCV01000277	44	42	0	2	46,342	RefSeq:NZ_LJCV01000277
NZ_LJCV01000303	38	37	0	1	46,269	RefSeq:NZ_LJCV01000303
NZ_LJCV01000276	45	44	0	1	45,445	RefSeq:NZ_LJCV01000276
NZ_LJCV01000293	42	41	0	1	45,211	RefSeq:NZ_LJCV01000293
NZ_LJCV01000278	42	39	1	2	44,836	RefSeq:NZ_LJCV01000278
NZ_LJCV01000288	42	37	1	4	44,733	RefSeq:NZ_LJCV01000288
NZ_LJCV01000281	41	41	0	0	44,361	RefSeq:NZ_LJCV01000281
NZ_LJCV01000282	34	33	0	1	44,019	RefSeq:NZ_LJCV01000282
NZ_LJCV01000283	39	38	0	1	43,718	RefSeq:NZ_LJCV01000283
NZ_LJCV01000287	35	34	0	1	43,372	RefSeq:NZ_LJCV01000287
NZ_LJCV01000295	51	49	0	2	43,321	RefSeq:NZ_LJCV01000295
NZ_LJCV01000290	39	36	0	3	43,244	RefSeq:NZ_LJCV01000290
NZ_LJCV01000289	43	40	0	3	42,761	RefSeq:NZ_LJCV01000289
NZ_LJCV01000291	38	37	0	1	42,582	RefSeq:NZ_LJCV01000291
NZ_LJCV01000298	31	30	0	1	42,386	RefSeq:NZ_LJCV01000298
NZ_LJCV01000092	38	36	0	2	42,371	RefSeq:NZ_LJCV01000092
NZ_LJCV01000297	40	39	0	1	42,195	RefSeq:NZ_LJCV01000297
NZ_LJCV01000314	46	45	1	0	41,674	RefSeq:NZ_LJCV01000314
NZ_LJCV01000301	37	34	0	3	41,315	RefSeq:NZ_LJCV01000301
NZ_LJCV01000299	32	30	0	2	40,945	RefSeq:NZ_LJCV01000299
NZ_LJCV01000294	32	32	0	0	40,606	RefSeq:NZ_LJCV01000294
NZ_LJCV01000304	28	26	1	1	40,587	RefSeq:NZ_LJCV01000304
NZ_LJCV01000310	27	27	0	0	39,249	RefSeq:NZ_LJCV01000310
NZ_LJCV01000300	29	27	0	2	39,107	RefSeq:NZ_LJCV01000300
NZ_LJCV01000308	35	34	0	1	38,995	RefSeq:NZ_LJCV01000308
NZ_LJCV01000313	37	37	0	0	37,913	RefSeq:NZ_LJCV01000313
NZ_LJCV01000305	33	32	0	1	37,834	RefSeq:NZ_LJCV01000305
NZ_LJCV01000306	33	32	0	1	37,323	RefSeq:NZ_LJCV01000306
NZ_LJCV01000015	30	29	0	1	37,170	RefSeq:NZ_LJCV01000015
NZ_LJCV01000311	34	32	1	1	37,169	RefSeq:NZ_LJCV01000311
NZ_LJCV01000309	36	36	0	0	37,145	RefSeq:NZ_LJCV01000309
NZ_LJCV01000302	28	21	0	7	36,175	RefSeq:NZ_LJCV01000302
NZ_LJCV01000010	32	29	0	3	36,022	RefSeq:NZ_LJCV01000010
NZ_LJCV01000004	37	29	4	4	35,883	RefSeq:NZ_LJCV01000004
NZ_LJCV01000312	26	22	0	4	35,715	RefSeq:NZ_LJCV01000312
NZ_LJCV01000006	27	27	0	0	35,481	RefSeq:NZ_LJCV01000006
NZ_LJCV01000315	31	25	1	5	35,337	RefSeq:NZ_LJCV01000315
NZ_LJCV01000030	23	20	3	0	35,155	RefSeq:NZ_LJCV01000030
NZ_LJCV01000001	24	22	0	2	34,693	RefSeq:NZ_LJCV01000001
NZ_LJCV01000316	24	23	0	1	33,285	RefSeq:NZ_LJCV01000316
NZ_LJCV01000317	18	16	0	2	32,528	RefSeq:NZ_LJCV01000317
NZ_LJCV01000029	31	27	2	2	32,304	RefSeq:NZ_LJCV01000029
NZ_LJCV01000005	23	22	0	1	32,019	RefSeq:NZ_LJCV01000005
NZ_LJCV01000007	32	30	0	2	31,828	RefSeq:NZ_LJCV01000007
NZ_LJCV01000003	32	26	0	6	31,693	RefSeq:NZ_LJCV01000003
NZ_LJCV01000009	27	27	0	0	31,547	RefSeq:NZ_LJCV01000009
NZ_LJCV01000013	30	28	0	2	31,483	RefSeq:NZ_LJCV01000013
NZ_LJCV01000014	32	30	0	2	31,247	RefSeq:NZ_LJCV01000014
NZ_LJCV01000012	27	26	0	1	30,841	RefSeq:NZ_LJCV01000012
NZ_LJCV01000008	34	27	7	0	30,117	RefSeq:NZ_LJCV01000008
NZ_LJCV01000025	23	23	0	0	30,109	RefSeq:NZ_LJCV01000025
NZ_LJCV01000017	27	24	0	3	29,831	RefSeq:NZ_LJCV01000017
NZ_LJCV01000016	25	23	0	2	29,330	RefSeq:NZ_LJCV01000016
NZ_LJCV01000049	20	19	0	1	28,824	RefSeq:NZ_LJCV01000049
NZ_LJCV01000018	24	23	1	0	28,714	RefSeq:NZ_LJCV01000018
NZ_LJCV01000024	23	22	0	1	27,985	RefSeq:NZ_LJCV01000024
NZ_LJCV01000041	24	22	0	2	27,717	RefSeq:NZ_LJCV01000041
NZ_LJCV01000021	11	7	0	4	27,498	RefSeq:NZ_LJCV01000021
NZ_LJCV01000019	27	24	0	3	26,945	RefSeq:NZ_LJCV01000019
NZ_LJCV01000020	25	21	0	4	26,237	RefSeq:NZ_LJCV01000020
NZ_LJCV01000034	27	26	0	1	26,189	RefSeq:NZ_LJCV01000034
NZ_LJCV01000032	20	19	0	1	26,033	RefSeq:NZ_LJCV01000032
NZ_LJCV01000045	26	21	0	5	25,869	RefSeq:NZ_LJCV01000045
NZ_LJCV01000023	17	17	0	0	25,478	RefSeq:NZ_LJCV01000023
NZ_LJCV01000028	20	20	0	0	25,425	RefSeq:NZ_LJCV01000028
NZ_LJCV01000036	19	18	0	1	25,255	RefSeq:NZ_LJCV01000036
NZ_LJCV01000035	20	20	0	0	25,099	RefSeq:NZ_LJCV01000035
NZ_LJCV01000038	21	20	1	0	25,001	RefSeq:NZ_LJCV01000038
NZ_LJCV01000027	19	18	0	1	24,927	RefSeq:NZ_LJCV01000027
NZ_LJCV01000037	23	21	0	2	24,892	RefSeq:NZ_LJCV01000037
NZ_LJCV01000043	22	22	0	0	24,146	RefSeq:NZ_LJCV01000043
NZ_LJCV01000053	20	19	0	1	23,757	RefSeq:NZ_LJCV01000053
NZ_LJCV01000046	23	21	1	1	23,495	RefSeq:NZ_LJCV01000046
NZ_LJCV01000071	23	21	0	2	23,485	RefSeq:NZ_LJCV01000071
NZ_LJCV01000039	20	20	0	0	23,447	RefSeq:NZ_LJCV01000039
NZ_LJCV01000048	23	22	0	1	23,275	RefSeq:NZ_LJCV01000048
NZ_LJCV01000093	22	21	0	1	23,263	RefSeq:NZ_LJCV01000093
NZ_LJCV01000040	20	19	0	1	22,818	RefSeq:NZ_LJCV01000040
NZ_LJCV01000042	15	15	0	0	22,672	RefSeq:NZ_LJCV01000042
NZ_LJCV01000052	22	21	0	1	22,645	RefSeq:NZ_LJCV01000052
NZ_LJCV01000047	16	16	0	0	22,413	RefSeq:NZ_LJCV01000047
NZ_LJCV01000054	26	20	0	6	22,203	RefSeq:NZ_LJCV01000054
NZ_LJCV01000064	22	20	0	2	22,143	RefSeq:NZ_LJCV01000064
NZ_LJCV01000051	17	16	0	1	21,906	RefSeq:NZ_LJCV01000051
NZ_LJCV01000058	20	20	0	0	21,820	RefSeq:NZ_LJCV01000058
NZ_LJCV01000056	21	18	1	2	21,727	RefSeq:NZ_LJCV01000056
NZ_LJCV01000050	17	17	0	0	21,587	RefSeq:NZ_LJCV01000050
NZ_LJCV01000061	13	13	0	0	21,469	RefSeq:NZ_LJCV01000061
NZ_LJCV01000060	26	23	1	2	21,362	RefSeq:NZ_LJCV01000060
NZ_LJCV01000057	17	14	2	1	21,042	RefSeq:NZ_LJCV01000057
NZ_LJCV01000062	15	14	0	1	20,944	RefSeq:NZ_LJCV01000062
NZ_LJCV01000059	16	15	0	1	20,915	RefSeq:NZ_LJCV01000059
NZ_LJCV01000238	17	15	1	1	20,687	RefSeq:NZ_LJCV01000238
NZ_LJCV01000068	20	20	0	0	20,361	RefSeq:NZ_LJCV01000068
NZ_LJCV01000065	13	13	0	0	20,023	RefSeq:NZ_LJCV01000065
NZ_LJCV01000074	15	14	0	1	19,996	RefSeq:NZ_LJCV01000074
NZ_LJCV01000075	18	17	0	1	19,985	RefSeq:NZ_LJCV01000075
NZ_LJCV01000076	15	14	0	1	19,813	RefSeq:NZ_LJCV01000076
NZ_LJCV01000069	15	12	2	1	19,775	RefSeq:NZ_LJCV01000069
NZ_LJCV01000084	23	21	0	2	19,563	RefSeq:NZ_LJCV01000084
NZ_LJCV01000067	15	15	0	0	18,628	RefSeq:NZ_LJCV01000067
NZ_LJCV01000072	18	17	0	1	18,582	RefSeq:NZ_LJCV01000072
NZ_LJCV01000082	22	21	0	1	18,195	RefSeq:NZ_LJCV01000082
NZ_LJCV01000070	13	13	0	0	17,796	RefSeq:NZ_LJCV01000070
NZ_LJCV01000073	17	16	0	1	17,540	RefSeq:NZ_LJCV01000073
NZ_LJCV01000079	18	17	0	1	17,513	RefSeq:NZ_LJCV01000079
NZ_LJCV01000078	17	16	0	1	17,343	RefSeq:NZ_LJCV01000078
NZ_LJCV01000240	16	14	0	2	16,949	RefSeq:NZ_LJCV01000240
NZ_LJCV01000106	15	12	2	1	16,934	RefSeq:NZ_LJCV01000106
NZ_LJCV01000081	14	14	0	0	16,757	RefSeq:NZ_LJCV01000081
NZ_LJCV01000086	14	13	1	0	16,377	RefSeq:NZ_LJCV01000086
NZ_LJCV01000085	14	14	0	0	16,354	RefSeq:NZ_LJCV01000085
NZ_LJCV01000083	12	12	0	0	16,065	RefSeq:NZ_LJCV01000083
NZ_LJCV01000091	16	16	0	0	15,818	RefSeq:NZ_LJCV01000091
NZ_LJCV01000087	12	11	0	1	15,425	RefSeq:NZ_LJCV01000087
NZ_LJCV01000096	13	11	0	2	15,095	RefSeq:NZ_LJCV01000096
NZ_LJCV01000090	17	17	0	0	14,991	RefSeq:NZ_LJCV01000090
NZ_LJCV01000098	15	14	1	0	14,509	RefSeq:NZ_LJCV01000098
NZ_LJCV01000095	11	11	0	0	14,069	RefSeq:NZ_LJCV01000095
NZ_LJCV01000143	12	8	2	2	13,482	RefSeq:NZ_LJCV01000143
NZ_LJCV01000102	11	11	0	0	13,431	RefSeq:NZ_LJCV01000102
NZ_LJCV01000151	13	12	0	1	11,181	RefSeq:NZ_LJCV01000151
NZ_LJCV01000138	12	12	0	0	11,054	RefSeq:NZ_LJCV01000138
NZ_LJCV01000115	14	13	0	1	10,783	RefSeq:NZ_LJCV01000115
NZ_LJCV01000123	12	9	2	1	10,593	RefSeq:NZ_LJCV01000123
NZ_LJCV01000119	12	11	0	1	10,455	RefSeq:NZ_LJCV01000119
127 Undisplayed Contigs/Replicons	497	491	9	99	875,511

Total:	9,112	8,525	85	502	10,668,107

Ortholog data available?	Yes

Database Contents

Genes	9,108
Pathways	287
Enzymatic Reactions	1,675
Transport Reactions	97
Polypeptides	8,579
Protein Complexes	48
Enzymes	1,592
Transporters	750
Compounds	1,408
Transcription Units	6,862
tRNAs	68
Protein Features	9,855
GO Terms	28,493

Database Version

29.0

Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Actinomycetota Actinomycetes unclassified Actinobacteria (class) unclassified Actinobacteria (class) (miscellaneous) Actinobacteria bacterium OK074
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN03275768
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1592327
Environment	Endosphere of plant Populus trichocarpa
Geographic Location	USA
Collection Date	2012-05
Host	Populus trichocarpa

References

Caspi16: Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Karp PD (2016). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases." Nucleic Acids Res 44(D1);D471-80. PMID: 26527732

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

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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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