AMPDB_4231 | Big defensin

PEPTIDE SUMMARY

Big defensin

1 General Description

AMPDB ID: AMPDB_4231

Protein Names: Big defensin (RPD-1)

Protein Family: Big defensin family

Gene Name: Nil

Source Organism: Ruditapes philippinarum (Japanese littleneck clam) (Venerupis philippinarum)

Protein Length: 11 AA

Protein Existence: Evidence at protein level

2 Protein Sequence & Composition

2.1 Sequence

AVPDVAFNAYG

FASTA format

2.2 Composition

Counts of Amino Acids

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

Frequencies of Amino Acids

'A': 27.27%, 'R': 0%, 'N': 9.09%, 'D': 9.09%, 'C': 0%, 'Q': 0%, 'E': 0%, 'G': 9.09%, 'H': 0%, 'I': 0%, 'L': 0%, 'K': 0%, 'M': 0%, 'F': 9.09%, 'P': 9.09%, 'S': 0%, 'T': 0%, 'W': 0%, 'Y': 9.09%, 'V': 18.18%

Missing Amino Acid(s)

C, E, H, I, K, L, M, Q, R, S, T, W

Most Occurring Amino Acid(s)

Less Occurring Amino Acid(s)

D, F, G, N, P, Y

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	1123.23 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	80	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	12.027	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	0.573	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.232	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	3.75	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	-1.002	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.364, 0.273, 0.273 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.182	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	1490, 1490	Computed by ProtParam module (biopython 1.79)

4 Activity Details

4.1 Target Organism(s)

B.subtilis (Gram-positive), E.coli (Gram-negative), S.aureus (Gram-positive), V.anguillarum (Gram-negative), V.parahaemolyticus (Gram-negative)

4.2 Antimicrobial Activity

Antibiotic, Antimicrobial, Defensin, Fungicide, Anti-gram-negative, Anti-gram-Positive

4.3 Enzymatic Activity

Not found

4.4 Inhibitory Effect

Not found

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

5.1.1 PubMed

Citation 1: Wei YX, Guo DS, Li RG, et al. [Purification of a big defensin from Ruditapes philippinesis and its antibacterial activity]. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai). 2003;35(12):1145-8. Published 2003 Dec. doi:

PMID: 14673509

5.2 Protein Sequence Databases

UniProt: P86316

5.3 3D Structure Databases

No PDB Ids found

AlphaFoldDB: P86316

5.4 Nucleotide Sequence Databases

No entries found in GenBank or EMBL

CCDS: Not found

RefSeq: Not found

5.5 Protein-Protein Interaction Databases

STRING: Not found

IntAct: Not found

MINT: Not found

DIP: Not found

BioGRID: Not found

5.6 Ligand Databases

BindingDB: Not found

DrugBank: Not found

ChEMBL: Not found

5.7 Family & Domain Databases

InterPro: Not found

PANTHER: Not found

PROSITE: Not found

5.8 Genome Annotation Databases

Ensembl: Not found

KEGG: 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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