Summary of Prevotella sp. 109, version 29.0

Tier 3 Uncurated Organism Database

Database Authors

Pallavi Subhraveti¹, Peter Midford¹, Ingrid Keseler¹, Anamika Kothari¹, Ron Caspi¹, Peter D Karp¹

Summary

This Pathway/Genome Database (PGDB) was generated on 25-Oct-2020 from the annotated genome of Prevotella sp. 109 109, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_LFQU01000001	353	338	5	10	437,945	RefSeq:NZ_LFQU01000001
NZ_LFQU01000002	169	165	0	4	250,718	RefSeq:NZ_LFQU01000002
NZ_LFQU01000003	160	153	1	6	174,622	RefSeq:NZ_LFQU01000003
NZ_LFQU01000004	109	104	1	4	161,098	RefSeq:NZ_LFQU01000004
NZ_LFQU01000005	125	121	0	4	146,822	RefSeq:NZ_LFQU01000005
NZ_LFQU01000006	95	93	1	1	131,165	RefSeq:NZ_LFQU01000006
NZ_LFQU01000007	90	85	0	5	122,298	RefSeq:NZ_LFQU01000007
NZ_LFQU01000008	93	82	4	7	119,078	RefSeq:NZ_LFQU01000008
NZ_LFQU01000009	85	80	3	2	112,841	RefSeq:NZ_LFQU01000009
NZ_LFQU01000010	82	79	2	1	112,282	RefSeq:NZ_LFQU01000010
NZ_LFQU01000011	85	83	1	1	109,424	RefSeq:NZ_LFQU01000011
NZ_LFQU01000012	87	78	3	6	101,529	RefSeq:NZ_LFQU01000012
NZ_LFQU01000013	81	80	0	1	99,291	RefSeq:NZ_LFQU01000013
NZ_LFQU01000014	79	78	0	1	95,718	RefSeq:NZ_LFQU01000014
NZ_LFQU01000015	60	57	1	2	95,146	RefSeq:NZ_LFQU01000015
NZ_LFQU01000016	77	72	2	3	91,852	RefSeq:NZ_LFQU01000016
NZ_LFQU01000017	60	54	1	5	87,379	RefSeq:NZ_LFQU01000017
NZ_LFQU01000018	96	88	5	3	84,545	RefSeq:NZ_LFQU01000018
NZ_LFQU01000019	62	54	6	2	82,736	RefSeq:NZ_LFQU01000019
NZ_LFQU01000020	51	50	1	0	75,849	RefSeq:NZ_LFQU01000020
NZ_LFQU01000021	57	47	1	9	64,590	RefSeq:NZ_LFQU01000021
NZ_LFQU01000022	51	47	2	2	60,053	RefSeq:NZ_LFQU01000022
NZ_LFQU01000023	63	61	0	2	58,933	RefSeq:NZ_LFQU01000023
NZ_LFQU01000024	24	20	0	4	54,382	RefSeq:NZ_LFQU01000024
NZ_LFQU01000025	34	34	0	0	51,724	RefSeq:NZ_LFQU01000025
NZ_LFQU01000026	30	30	0	0	45,254	RefSeq:NZ_LFQU01000026
NZ_LFQU01000027	25	24	0	1	43,981	RefSeq:NZ_LFQU01000027
NZ_LFQU01000028	38	36	2	0	42,512	RefSeq:NZ_LFQU01000028
NZ_LFQU01000029	22	19	1	2	36,449	RefSeq:NZ_LFQU01000029
NZ_LFQU01000030	24	22	1	1	33,745	RefSeq:NZ_LFQU01000030
NZ_LFQU01000031	23	22	0	1	32,431	RefSeq:NZ_LFQU01000031
NZ_LFQU01000032	12	12	0	0	31,659	RefSeq:NZ_LFQU01000032
NZ_LFQU01000033	21	21	0	0	31,647	RefSeq:NZ_LFQU01000033
NZ_LFQU01000034	24	23	0	1	30,233	RefSeq:NZ_LFQU01000034
NZ_LFQU01000035	20	19	0	1	29,183	RefSeq:NZ_LFQU01000035
NZ_LFQU01000036	26	22	3	1	28,659	RefSeq:NZ_LFQU01000036
NZ_LFQU01000037	23	22	0	1	27,421	RefSeq:NZ_LFQU01000037
NZ_LFQU01000038	23	20	1	2	27,044	RefSeq:NZ_LFQU01000038
NZ_LFQU01000039	29	25	0	4	26,717	RefSeq:NZ_LFQU01000039
NZ_LFQU01000041	19	17	2	0	25,433	RefSeq:NZ_LFQU01000041
NZ_LFQU01000042	24	24	0	0	25,390	RefSeq:NZ_LFQU01000042
NZ_LFQU01000045	16	15	0	1	18,920	RefSeq:NZ_LFQU01000045
NZ_LFQU01000046	12	9	0	3	18,107	RefSeq:NZ_LFQU01000046
NZ_LFQU01000047	13	13	0	0	17,640	RefSeq:NZ_LFQU01000047
NZ_LFQU01000048	13	12	0	1	16,949	RefSeq:NZ_LFQU01000048
NZ_LFQU01000051	12	12	0	0	12,255	RefSeq:NZ_LFQU01000051
39 Undisplayed Contigs/Replicons	107	104	3	12	204,681

Total:	2,896	2,726	53	117	3,788,330

Ortholog data available?	Yes

Database Contents

Genes	2,895
Pathways	191
Enzymatic Reactions	977
Transport Reactions	42
Polypeptides	2,740
Protein Complexes	10
Enzymes	522
Transporters	193
Compounds	726
Transcription Units	1,963
tRNAs	46
Protein Features	3,285
GO Terms	10,053

Database Version

29.0

Sequence Source	GCF_001275135.1
Taxonomic Lineage	cellular organisms Bacteria <bacteria> FCB group Bacteroidota/Chlorobiota group Bacteroidota Bacteroidia Bacteroidales Prevotellaceae Prevotella unclassified Prevotella Prevotella sp. 109
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN03797675
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1676614
Environment	feces of 43-year-old healthy woman
Geographic Location	Russia
Collection Date	2013-03-21
Host	Homo sapiens
Human Microbiome Body Site	not-specified
Annotation Provider	NCBI RefSeq
Annotation Date	2020-03-3
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	4.11
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 Thu May 15, 2025, BIOCYC18A.

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