AMPDB_723 | Bacteriocin pediocin PA-1

1 General Description

AMPDB ID: AMPDB_723

Protein Names: Bacteriocin pediocin PA-1 (Pediocin ACH)

Protein Family: Bacteriocin class IIA YGNGV family

Gene Name: pedA pap papA

Source Organism: Pediococcus acidilactici

Protein Length: 62 AA

Protein Existence: Evidence at protein level

2 Protein Sequence & Composition

MKKIEKLTEKEMANIIGGKYYGNGVTCGKHSCSVDWGKATTCIINNGAMAWATGGHQGNHKC

FASTA format

Counts of Amino Acids

'A': 5, 'R': 0, 'N': 5, 'D': 1, 'C': 4, 'Q': 1, 'E': 3, 'G': 10, 'H': 3, 'I': 5, 'L': 1, 'K': 8, 'M': 3, 'F': 0, 'P': 0, 'S': 2, 'T': 5, 'W': 2, 'Y': 2, 'V': 2

Frequencies of Amino Acids

'A': 8.06%, 'R': 0%, 'N': 8.06%, 'D': 1.61%, 'C': 6.45%, 'Q': 1.61%, 'E': 4.84%, 'G': 16.13%, 'H': 4.84%, 'I': 8.06%, 'L': 1.61%, 'K': 12.9%, 'M': 4.84%, 'F': 0%, 'P': 0%, 'S': 3.23%, 'T': 8.06%, 'W': 3.23%, 'Y': 3.23%, 'V': 3.23%

Missing Amino Acid(s)

F, P, R

Most Occurring Amino Acid(s)

Less Occurring Amino Acid(s)

D, L, Q

Hydrophobic Amino Acid(s) Count

Hydrophilic Amino Acid(s) Count

Basic Amino Acid(s) Count

Acidic Amino Acid(s) Count

Modified Amino Acid(s) Count

Modified Amino Acid(s) Frequencies

Computed by biopython (version 1.79) & proteinAnalysis (version 1)

3 Physicochemical Properties

Sl. No.	Properties	Values	Reference
1.	Molecular Mass	6643.64 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	55.161	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	19.716	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	-0.482	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.563	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	8.994	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	4.025	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.194, 0.274, 0.194 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.065	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	13980, 14230	Computed by ProtParam module (biopython 1.79)

4.1 Target Organism(s)

L.monocytogenes (Gram-positive)

4.2 Antimicrobial Activity

Antibiotic, Antimicrobial, Bacteriocin, Anti-gram-Positive

4.3 Enzymatic Activity

4.4 Inhibitory Effect

4.5 Other Biological Activity

Non-hemolytic, Non-ribosomal

Activity data manually curated from Literature and UniProt

5 Database Cross-references

5.1 Literature Database

Citation 1: Marugg JD, Gonzalez CF, Kunka BS, et al. Cloning, expression, and nucleotide sequence of genes involved in production of pediocin PA-1, and bacteriocin from Pediococcus acidilactici PAC1.0. Appl Environ Microbiol. 1992;58(8):2360-7. Published 1992 Aug. doi:10.1128/aem.58.8.2360-2367.1992

PMID: 1514784

Citation 2: Motlagh A, Bukhtiyarova M, Ray B, et al. Complete nucleotide sequence of pSMB 74, a plasmid encoding the production of pediocin AcH in Pediococcus acidilactici. Lett Appl Microbiol. 1994;18(6):305-12. Published 1994 Jun. doi:10.1111/j.1472-765x.1994.tb00876.x

PMID: 7764941

Citation 3: Henderson JT, Chopko AL, van Wassenaar PD, et al. Purification and primary structure of pediocin PA-1 produced by Pediococcus acidilactici PAC-1.0. Arch Biochem Biophys. 1992;295(1):5-12. Published 1992 May 15. doi:10.1016/0003-9861(92)90480-k

PMID: 1575516

Citation 4: Nieto Lozano JC, Meyer JN, Sletten K, et al. Purification and amino acid sequence of a bacteriocin produced by Pediococcus acidilactici. J Gen Microbiol. 1992;138(9):1985-90. Published 1992 Sep. doi:10.1099/00221287-138-9-1985

PMID: 1402795

5.2 Protein Sequence Databases

5.3 3D Structure Databases

	Sl. no.	PDB ID	Method	Resolution	Access Links	3D View

AlphaFoldDB: P29430

5.4 Nucleotide Sequence Databases

Sl. no.	Accession(s)	Access Link(s)
1.	M83924	GenBank \|\| EMBL
2.	M90679	GenBank \|\| EMBL
3.	U02482	GenBank \|\| EMBL

5.5 Protein-Protein Interaction Databases

STRING: Not found

IntAct: Not found

BioGRID: Not found

5.6 Ligand Databases

BindingDB: Not found

DrugBank: Not found

ChEMBL: Not found

5.7 Family & Domain Databases

PANTHER: Not found

PROSITE: PS60030

5.8 Genome Annotation Databases

Ensembl: Not found

5.9 Phylogenomic Databases

GeneTree: Not found

5.10 Enzyme & Pathway Databases

BRENDA: Not found

BioCyc: Not found

5.11 Protein-RNA Interaction Databases

RNAct: Not found

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