Summary of Actinomyces massiliensis F0489, 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 01-June-2022 from the annotated genome of Actinomyces massiliensis F0489, 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_AKFT01000177	140	132	7	1	160,379	RefSeq:NZ_AKFT01000177
NZ_AKFT01000113	90	88	0	2	106,363	RefSeq:NZ_AKFT01000113
NZ_AKFT01000065	86	84	2	0	102,015	RefSeq:NZ_AKFT01000065
NZ_AKFT01000214	69	68	0	1	80,730	RefSeq:NZ_AKFT01000214
NZ_AKFT01000033	60	58	2	0	75,708	RefSeq:NZ_AKFT01000033
NZ_AKFT01000163	64	60	3	1	72,977	RefSeq:NZ_AKFT01000163
NZ_AKFT01000050	59	58	1	0	66,871	RefSeq:NZ_AKFT01000050
NZ_AKFT01000023	49	45	1	3	57,932	RefSeq:NZ_AKFT01000023
NZ_AKFT01000116	51	44	5	2	56,533	RefSeq:NZ_AKFT01000116
NZ_AKFT01000085	47	45	1	1	53,383	RefSeq:NZ_AKFT01000085
NZ_AKFT01000186	38	38	0	0	53,084	RefSeq:NZ_AKFT01000186
NZ_AKFT01000183	45	42	3	0	51,152	RefSeq:NZ_AKFT01000183
NZ_AKFT01000011	44	41	2	1	50,424	RefSeq:NZ_AKFT01000011
NZ_AKFT01000226	46	43	1	2	50,121	RefSeq:NZ_AKFT01000226
NZ_AKFT01000009	47	46	0	1	46,346	RefSeq:NZ_AKFT01000009
NZ_AKFT01000159	42	42	0	0	44,906	RefSeq:NZ_AKFT01000159
NZ_AKFT01000104	27	26	0	1	44,482	RefSeq:NZ_AKFT01000104
NZ_AKFT01000211	33	32	0	1	40,118	RefSeq:NZ_AKFT01000211
NZ_AKFT01000118	33	31	0	2	39,474	RefSeq:NZ_AKFT01000118
NZ_AKFT01000058	33	33	0	0	37,590	RefSeq:NZ_AKFT01000058
NZ_AKFT01000098	33	32	1	0	37,041	RefSeq:NZ_AKFT01000098
NZ_AKFT01000196	29	29	0	0	36,996	RefSeq:NZ_AKFT01000196
NZ_AKFT01000173	33	33	0	0	36,934	RefSeq:NZ_AKFT01000173
NZ_AKFT01000006	32	31	1	0	35,645	RefSeq:NZ_AKFT01000006
NZ_AKFT01000128	25	25	0	0	35,499	RefSeq:NZ_AKFT01000128
NZ_AKFT01000193	25	25	0	0	33,079	RefSeq:NZ_AKFT01000193
NZ_AKFT01000223	18	18	0	0	31,447	RefSeq:NZ_AKFT01000223
NZ_AKFT01000203	23	21	0	2	30,891	RefSeq:NZ_AKFT01000203
NZ_AKFT01000069	26	24	0	2	30,743	RefSeq:NZ_AKFT01000069
NZ_AKFT01000158	31	29	1	1	30,694	RefSeq:NZ_AKFT01000158
NZ_AKFT01000208	21	21	0	0	30,655	RefSeq:NZ_AKFT01000208
NZ_AKFT01000194	25	24	1	0	30,650	RefSeq:NZ_AKFT01000194
NZ_AKFT01000002	40	39	0	1	30,585	RefSeq:NZ_AKFT01000002
NZ_AKFT01000039	31	31	0	0	30,401	RefSeq:NZ_AKFT01000039
NZ_AKFT01000014	23	22	0	1	29,185	RefSeq:NZ_AKFT01000014
NZ_AKFT01000215	23	22	1	0	28,842	RefSeq:NZ_AKFT01000215
NZ_AKFT01000056	27	27	0	0	28,358	RefSeq:NZ_AKFT01000056
NZ_AKFT01000150	19	19	0	0	27,196	RefSeq:NZ_AKFT01000150
NZ_AKFT01000036	22	18	2	2	26,950	RefSeq:NZ_AKFT01000036
NZ_AKFT01000221	16	16	0	0	25,127	RefSeq:NZ_AKFT01000221
NZ_AKFT01000099	20	20	0	0	25,078	RefSeq:NZ_AKFT01000099
NZ_AKFT01000055	20	19	0	1	24,791	RefSeq:NZ_AKFT01000055
NZ_AKFT01000162	20	20	0	0	24,620	RefSeq:NZ_AKFT01000162
NZ_AKFT01000107	24	24	0	0	24,541	RefSeq:NZ_AKFT01000107
NZ_AKFT01000013	23	23	0	0	23,945	RefSeq:NZ_AKFT01000013
NZ_AKFT01000053	26	24	1	1	23,184	RefSeq:NZ_AKFT01000053
NZ_AKFT01000149	16	15	0	1	22,102	RefSeq:NZ_AKFT01000149
NZ_AKFT01000095	17	16	0	1	20,473	RefSeq:NZ_AKFT01000095
NZ_AKFT01000032	16	16	0	0	19,653	RefSeq:NZ_AKFT01000032
NZ_AKFT01000218	16	16	0	0	19,314	RefSeq:NZ_AKFT01000218
NZ_AKFT01000140	12	12	0	0	18,083	RefSeq:NZ_AKFT01000140
NZ_AKFT01000045	15	14	1	0	17,958	RefSeq:NZ_AKFT01000045
NZ_AKFT01000134	17	15	0	2	17,889	RefSeq:NZ_AKFT01000134
NZ_AKFT01000209	16	16	0	0	17,817	RefSeq:NZ_AKFT01000209
NZ_AKFT01000005	14	13	0	1	17,550	RefSeq:NZ_AKFT01000005
NZ_AKFT01000037	13	13	0	0	17,464	RefSeq:NZ_AKFT01000037
NZ_AKFT01000123	19	18	0	1	17,439	RefSeq:NZ_AKFT01000123
NZ_AKFT01000109	14	14	0	0	17,338	RefSeq:NZ_AKFT01000109
NZ_AKFT01000007	25	23	0	2	17,288	RefSeq:NZ_AKFT01000007
NZ_AKFT01000079	16	15	0	1	16,948	RefSeq:NZ_AKFT01000079
NZ_AKFT01000146	14	14	0	0	16,713	RefSeq:NZ_AKFT01000146
NZ_AKFT01000057	17	15	0	2	16,698	RefSeq:NZ_AKFT01000057
NZ_AKFT01000021	13	12	0	1	16,349	RefSeq:NZ_AKFT01000021
NZ_AKFT01000028	11	11	0	0	16,174	RefSeq:NZ_AKFT01000028
NZ_AKFT01000175	13	13	0	0	16,141	RefSeq:NZ_AKFT01000175
NZ_AKFT01000131	16	15	0	1	15,737	RefSeq:NZ_AKFT01000131
NZ_AKFT01000188	15	13	0	2	15,726	RefSeq:NZ_AKFT01000188
NZ_AKFT01000105	10	10	0	0	15,650	RefSeq:NZ_AKFT01000105
NZ_AKFT01000010	12	12	0	0	15,528	RefSeq:NZ_AKFT01000010
NZ_AKFT01000012	17	16	0	1	15,457	RefSeq:NZ_AKFT01000012
NZ_AKFT01000100	14	13	1	0	15,206	RefSeq:NZ_AKFT01000100
NZ_AKFT01000001	14	13	0	1	15,183	RefSeq:NZ_AKFT01000001
NZ_AKFT01000156	11	11	0	0	14,774	RefSeq:NZ_AKFT01000156
NZ_AKFT01000043	11	10	0	1	13,229	RefSeq:NZ_AKFT01000043
NZ_AKFT01000125	18	17	0	1	13,206	RefSeq:NZ_AKFT01000125
NZ_AKFT01000171	14	14	0	0	13,172	RefSeq:NZ_AKFT01000171
NZ_AKFT01000063	11	10	0	1	13,109	RefSeq:NZ_AKFT01000063
NZ_AKFT01000088	13	12	0	1	13,087	RefSeq:NZ_AKFT01000088
NZ_AKFT01000199	12	9	3	0	11,126	RefSeq:NZ_AKFT01000199
NZ_AKFT01000027	15	14	0	1	11,057	RefSeq:NZ_AKFT01000027
NZ_AKFT01000082	13	10	0	3	8,613	RefSeq:NZ_AKFT01000082
152 Undisplayed Contigs/Replicons	547	533	16	50	793,524

Total:	2,867	2,705	57	105	3,416,440

Ortholog data available?	No

Database Contents

Genes	2,865
Pathways	176
Enzymatic Reactions	889
Transport Reactions	54
Polypeptides	2,843
Protein Complexes	89
Enzymes	533
Transporters	250
Compounds	667
Transcription Units	2,204
tRNAs	50
Protein Features	3,020
GO Terms	218

Database Version

29.0

Sequence Source	GCF_000296275.1
Synonyms	Actinomyces massiliensis strain F0489 Actinomyces massiliensis str. F0489 Actinomyces massiliensis F0489
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Terrabacteria group Actinomycetota Actinomycetes Actinomycetales Actinomycetaceae Actinomyces Actinomyces massiliensis Actinomyces massiliensis F0489
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN00792233
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1125718
Environment	biological product [ENVO:02000043]
Host	Homo sapiens
Human Microbiome Body Site	not-specified
Annotation Provider	NCBI RefSeq
Annotation Date	2021-12-22
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	5.3
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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