Summary of Acidisphaera rubrifaciens HS-AP3, 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 Acidisphaera rubrifaciens HS-AP3, 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_BANB01000045	49	47	1	1	51,703	RefSeq:NZ_BANB01000045
NZ_BANB01000009	43	42	0	1	51,127	RefSeq:NZ_BANB01000009
NZ_BANB01000165	42	42	0	0	49,852	RefSeq:NZ_BANB01000165
NZ_BANB01000086	45	44	0	1	39,868	RefSeq:NZ_BANB01000086
NZ_BANB01000143	29	28	0	1	37,753	RefSeq:NZ_BANB01000143
NZ_BANB01000240	23	23	0	0	25,233	RefSeq:NZ_BANB01000240
NZ_BANB01000076	30	30	0	0	25,123	RefSeq:NZ_BANB01000076
NZ_BANB01000006	20	20	0	0	24,942	RefSeq:NZ_BANB01000006
NZ_BANB01000084	26	23	0	3	23,437	RefSeq:NZ_BANB01000084
NZ_BANB01000088	17	15	0	2	23,006	RefSeq:NZ_BANB01000088
NZ_BANB01000410	15	15	0	0	21,639	RefSeq:NZ_BANB01000410
NZ_BANB01000090	18	17	0	1	21,527	RefSeq:NZ_BANB01000090
NZ_BANB01000220	18	17	0	1	21,031	RefSeq:NZ_BANB01000220
NZ_BANB01000104	24	22	1	1	19,424	RefSeq:NZ_BANB01000104
NZ_BANB01000425	17	17	0	0	19,186	RefSeq:NZ_BANB01000425
NZ_BANB01000081	18	15	2	1	18,601	RefSeq:NZ_BANB01000081
NZ_BANB01000256	14	13	0	1	17,908	RefSeq:NZ_BANB01000256
NZ_BANB01000238	12	12	0	0	17,051	RefSeq:NZ_BANB01000238
NZ_BANB01000213	19	17	0	2	16,211	RefSeq:NZ_BANB01000213
NZ_BANB01000047	14	13	1	0	16,180	RefSeq:NZ_BANB01000047
NZ_BANB01000303	17	17	0	0	15,672	RefSeq:NZ_BANB01000303
NZ_BANB01000010	12	12	0	0	15,555	RefSeq:NZ_BANB01000010
NZ_BANB01000050	14	12	0	2	15,431	RefSeq:NZ_BANB01000050
NZ_BANB01000085	13	11	0	2	15,383	RefSeq:NZ_BANB01000085
NZ_BANB01000051	17	17	0	0	15,209	RefSeq:NZ_BANB01000051
NZ_BANB01000079	12	12	0	0	15,162	RefSeq:NZ_BANB01000079
NZ_BANB01000278	16	15	0	1	15,081	RefSeq:NZ_BANB01000278
NZ_BANB01000119	16	14	0	2	14,714	RefSeq:NZ_BANB01000119
NZ_BANB01000067	13	13	0	0	14,586	RefSeq:NZ_BANB01000067
NZ_BANB01000120	14	13	0	1	13,807	RefSeq:NZ_BANB01000120
NZ_BANB01000478	12	10	0	2	13,637	RefSeq:NZ_BANB01000478
NZ_BANB01000302	10	10	0	0	13,148	RefSeq:NZ_BANB01000302
NZ_BANB01000024	12	11	0	1	13,011	RefSeq:NZ_BANB01000024
NZ_BANB01000025	11	10	0	1	12,714	RefSeq:NZ_BANB01000025
NZ_BANB01000193	12	11	0	1	12,621	RefSeq:NZ_BANB01000193
NZ_BANB01000160	15	12	0	3	12,470	RefSeq:NZ_BANB01000160
NZ_BANB01000295	12	11	0	1	12,431	RefSeq:NZ_BANB01000295
NZ_BANB01000335	11	11	0	0	12,056	RefSeq:NZ_BANB01000335
NZ_BANB01000164	15	14	0	1	12,042	RefSeq:NZ_BANB01000164
NZ_BANB01000011	11	10	1	0	11,754	RefSeq:NZ_BANB01000011
NZ_BANB01000259	14	11	0	3	11,739	RefSeq:NZ_BANB01000259
NZ_BANB01000097	11	11	0	0	11,612	RefSeq:NZ_BANB01000097
NZ_BANB01000265	12	12	0	0	10,616	RefSeq:NZ_BANB01000265
NZ_BANB01000359	11	9	1	1	9,942	RefSeq:NZ_BANB01000359
1,195 Undisplayed Contigs/Replicons	2,057	2,016	43	635	3,001,078

Total:	3,500	2,777	50	673	3,862,273

Ortholog data available?	No

Database Contents

Genes	3,498
Pathways	226
Enzymatic Reactions	1,227
Transport Reactions	45
Polypeptides	3,539
Protein Complexes	53
Enzymes	685
Transporters	330
Compounds	946
Transcription Units	2,954
tRNAs	42
Protein Features	3,382
GO Terms	8,374

Database Version

29.0

Sequence Source	GCF_000964365.1
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Alphaproteobacteria Rhodospirillales Acetobacteraceae Acidisphaera Acidisphaera rubrifaciens Acidisphaera rubrifaciens HS-AP3
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMD00036637
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	1231350
Environment	G_DNA_Anterior nares
Annotation Provider	NCBI RefSeq
Annotation Date	2020-01-7
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	4.10
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, BIOCYC17A.

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