Summary of Salmonella enterica enterica serovar Enteritidis str. 77-2659, version 29.0

Tier 3 Uncurated Organism Database

Database Authors

Pallavi Subhraveti¹, Quang Ong¹, Ingrid Keseler¹, Tim Holland¹, Anamika Kothari¹, Ron Caspi¹, Peter D Karp¹

Summary

This Pathway/Genome Database (PGDB) was generated by the PathoLogic program [Karp02, Dale10, Karp11, Caspi12] using Pathway Tools software version 18.5 and MetaCyc version 18.5 on 10-Aug-2014 18:43:19 from the annotated genome of Salmonella enterica serovar Enteritidis str. 77-2659 as obtained from RefSeq downloaded on 21-May-2014.

This BioCyc Tier 3 PGDB was computationally generated. It has not undergone any manual curation nor manual review, and thus may contain errors. Development of this PGDB was supported by grant GM080746 from the NIH.

Genome

Replicon	Total Genes	Protein Genes	RNA Genes	Pseudogenes	Size (bp)	NCBI Link
NZ_ALEV01000023 chromosome	534	525	9	0	546,163	RefSeq:NZ_ALEV01000023
NZ_ALEV01000041 chromosome	399	392	7	0	410,558	RefSeq:NZ_ALEV01000041
NZ_ALEV01000014 chromosome	415	410	5	0	408,662	RefSeq:NZ_ALEV01000014
NZ_ALEV01000032 chromosome	332	327	5	0	316,860	RefSeq:NZ_ALEV01000032
NZ_ALEV01000013 chromosome	280	275	5	0	304,141	RefSeq:NZ_ALEV01000013
NZ_ALEV01000027 chromosome	288	281	7	0	299,197	RefSeq:NZ_ALEV01000027
NZ_ALEV01000012 chromosome	285	285	0	0	296,404	RefSeq:NZ_ALEV01000012
NZ_ALEV01000022 chromosome	198	198	0	0	227,885	RefSeq:NZ_ALEV01000022
NZ_ALEV01000007 chromosome	187	186	1	0	216,764	RefSeq:NZ_ALEV01000007
NZ_ALEV01000009 chromosome	154	154	0	0	190,218	RefSeq:NZ_ALEV01000009
NZ_ALEV01000031 chromosome	170	165	5	0	183,426	RefSeq:NZ_ALEV01000031
NZ_ALEV01000015 chromosome	145	145	0	0	152,957	RefSeq:NZ_ALEV01000015
NZ_ALEV01000037 chromosome	139	139	0	0	150,204	RefSeq:NZ_ALEV01000037
NZ_ALEV01000033 chromosome	115	114	1	0	122,969	RefSeq:NZ_ALEV01000033
NZ_ALEV01000011 chromosome	95	94	1	0	106,161	RefSeq:NZ_ALEV01000011
NZ_ALEV01000025 chromosome	92	85	7	0	89,047	RefSeq:NZ_ALEV01000025
NZ_ALEV01000005 chromosome	77	77	0	0	79,732	RefSeq:NZ_ALEV01000005
NZ_ALEV01000024 chromosome	66	66	0	0	76,957	RefSeq:NZ_ALEV01000024
NZ_ALEV01000006 chromosome	64	61	3	0	67,504	RefSeq:NZ_ALEV01000006
NZ_ALEV01000001 chromosome	61	60	1	0	65,920	RefSeq:NZ_ALEV01000001
NZ_ALEV01000028 chromosome	59	58	1	0	62,661	RefSeq:NZ_ALEV01000028
NZ_ALEV01000008 chromosome	78	78	0	0	58,386	RefSeq:NZ_ALEV01000008
NZ_ALEV01000036 chromosome	50	50	0	0	55,301	RefSeq:NZ_ALEV01000036
NZ_ALEV01000039 chromosome	43	42	1	0	46,947	RefSeq:NZ_ALEV01000039
NZ_ALEV01000019 chromosome	38	37	1	0	37,448	RefSeq:NZ_ALEV01000019
NZ_ALEV01000042 chromosome	32	32	0	0	32,962	RefSeq:NZ_ALEV01000042
NZ_ALEV01000002 chromosome	33	33	0	0	30,632	RefSeq:NZ_ALEV01000002
NZ_ALEV01000029 chromosome	48	48	0	0	26,370	RefSeq:NZ_ALEV01000029
NZ_ALEV01000035 chromosome	11	11	0	0	10,499	RefSeq:NZ_ALEV01000035
NZ_ALEV01000038 chromosome	6	6	0	0	6,085	RefSeq:NZ_ALEV01000038
NZ_ALEV01000018 chromosome	7	3	4	0	4,576	RefSeq:NZ_ALEV01000018
NZ_ALEV01000010 chromosome	2	2	0	0	2,442	RefSeq:NZ_ALEV01000010
NZ_ALEV01000004 chromosome	0	0	0	0	2,383	RefSeq:NZ_ALEV01000004
NZ_ALEV01000026 chromosome	1	0	1	0	1,739	RefSeq:NZ_ALEV01000026
NZ_ALEV01000030 chromosome	1	1	0	0	1,719	RefSeq:NZ_ALEV01000030
NZ_ALEV01000021 chromosome	1	1	0	0	986	RefSeq:NZ_ALEV01000021
NZ_ALEV01000043 chromosome	1	0	1	0	664	RefSeq:NZ_ALEV01000043
NZ_ALEV01000020 chromosome	0	0	0	0	554	RefSeq:NZ_ALEV01000020
NZ_ALEV01000040 chromosome	0	0	0	0	521	RefSeq:NZ_ALEV01000040
NZ_ALEV01000016 chromosome	0	0	0	0	488	RefSeq:NZ_ALEV01000016
NZ_ALEV01000034 chromosome	2	0	2	0	367	RefSeq:NZ_ALEV01000034
NZ_ALEV01000003 chromosome	2	0	2	0	342	RefSeq:NZ_ALEV01000003
NZ_ALEV01000017 chromosome	0	0	0	0	211	RefSeq:NZ_ALEV01000017

Total:	4,511	4,441	70	0	4,696,012

Ortholog data available?	Yes

Database Contents

Genes	4,509
Pathways	449
Enzymatic Reactions	1,822
Transport Reactions	88
Polypeptides	4,474
Protein Complexes	3
Enzymes	1,249
Transporters	584
Compounds	1,223
Transcription Units	2,970
tRNAs	64
Protein Features	5,946

Database Version

29.0

Synonyms	Salmonella enterica subsp. enterica serovar Enteritidis strain 77-2659 Salmonella enterica subsp. enterica serovar Enteritidis str. 77-2659
Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Salmonella Salmonella enterica Salmonella enterica enterica Salmonella enterica enterica serovar Enteritidis Salmonella enterica enterica serovar Enteritidis str. 77-2659
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD	0023408
NCBI-Taxonomy	926035
Environment	clinical
Geographic Location	USA
Collection Date	1977

References

Caspi12: Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD (2012). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases." Nucleic Acids Res 40(D1);D742-D753. PMID: 22102576

Dale10: Dale JM, Popescu L, Karp PD (2010). "Machine learning methods for metabolic pathway prediction." BMC Bioinformatics 11;15. PMID: 20064214

Karp02: Karp PD, Paley S, Romero P (2002). "The Pathway Tools software." Bioinformatics 18 Suppl 1;S225-32. PMID: 12169551

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 9, 2025, BIOCYC16.

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