AMPDB_55653 | Similar to pyocin s2 and s1

PEPTIDE SUMMARY

Similar to pyocin s2 and s1

1 General Description

AMPDB ID: AMPDB_55653

Protein Names: Similar to pyocin s2 and s1

Protein Family: Nil

Gene Name: usp PAU_01214 PA-RVA2-4271

Source Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 3105-77) (Xenorhabdus luminescens (strain 2))

Protein Length: 557 AA

Protein Existence: Predicted

2 Protein Sequence & Composition

2.1 Sequence

MAIGYFLLVGDKTTCGGQIITGDHTMTFNGRATAREGDKVTCGKHPGTYMIVGGVSDVFDMGRKLAGTLDSVSTCPCRARFINSERDSYEKQEQPNHPATAPVNMAAQNVSSPVKEAESVQSGPPPVIKAPPPTPVFTKSCLRGKGCTDAGTDAEPADNFGRMGIYQVSSSPAPVTTPKPEPPPQGGKHSPKPDKPQDKKLPWYKRWLSDGKDKTEAAATAMAATARSAVAEGEALAMRYIGGSAISAGRWLVAPNPVTVGLMGLFYSPSLNQGEEDYLSEYQLRQIAEQFGKVPTRVRFRWIRDEESGRMTVQGYHVSPESGLDEVPVHVMRLNQTTGNYEFWEPGENRPTILWTPNEQEFKVPAHTGNEEPPFIPSQITVLPIPDKVGSDIESLPMPEEKDFRDYILVLPIPNMPPVYVYLSKPPVKLFEVDLYRNFAGRLRNGTHADHMPSAAAVKARLKALYPKLLPSELNSDSKNVSAIIIPEEVHKKLSQTYGGRNSAEQIERDSQDLRAALDRNFDAIKPSLKSYGATEVQLENARHRMHKLNEEQGLYK

FASTA format

2.2 Composition

Counts of Amino Acids

'A': 45, 'R': 31, 'N': 22, 'D': 28, 'C': 6, 'Q': 21, 'E': 39, 'G': 43, 'H': 12, 'I': 23, 'L': 37, 'K': 34, 'M': 15, 'F': 16, 'P': 53, 'S': 38, 'T': 32, 'W': 6, 'Y': 19, 'V': 37

Frequencies of Amino Acids

'A': 8.08%, 'R': 5.57%, 'N': 3.95%, 'D': 5.03%, 'C': 1.08%, 'Q': 3.77%, 'E': 7%, 'G': 7.72%, 'H': 2.15%, 'I': 4.13%, 'L': 6.64%, 'K': 6.1%, 'M': 2.69%, 'F': 2.87%, 'P': 9.52%, 'S': 6.82%, 'T': 5.75%, 'W': 1.08%, 'Y': 3.41%, 'V': 6.64%

Missing Amino Acid(s)

No Amino Acid(s) are missing in this protein

Most Occurring Amino Acid(s)

Less Occurring Amino Acid(s)

C, W

Hydrophobic Amino Acid(s) Count

275

Hydrophilic Amino Acid(s) Count

282

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	61282.4 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	69.354	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	52.577	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	-0.559	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.749	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	7.135	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	-1.228	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.248, 0.28, 0.244 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.074	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	61310, 61685	Computed by ProtParam module (biopython 1.79)

4 Activity Details

4.1 Target Organism(s)

E.coli (Gram-negative)

4.2 Antimicrobial Activity

Antibiotic, Antimicrobial, Bacteriocin, Anti-gram-negative

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: Waterfield NR, Sanchez-Contreras M, Eleftherianos I, et al. Rapid Virulence Annotation (RVA): identification of virulence factors using a bacterial genome library and multiple invertebrate hosts. Proc Natl Acad Sci U S A. 2008;105(41):15967-72. Published 2008 Oct 14. doi:10.1073/pnas.0711114105

PMID: 18838673

Citation 2: Wilkinson P, Waterfield NR, Crossman L, et al. Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens. BMC Genomics. 2009;10:302. Published 2009 Jul 7. doi:10.1186/1471-2164-10-302

PMID: 19583835

5.2 Protein Sequence Databases

UniProt: B6VKC9

5.3 3D Structure Databases

No PDB Ids found

AlphaFoldDB: B6VKC9

5.4 Nucleotide Sequence Databases

Sl. no.	Accession(s)	Access Link(s)
1.	FM162591	GenBank \|\| EMBL
2.	FM211044	GenBank \|\| EMBL

CCDS: Not found

RefSeq: Not found

5.5 Protein-Protein Interaction Databases

STRING: 291112.PAU_01214

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: IPR008727, IPR016128, IPR036302

PANTHER: Not found

PROSITE: Not found

5.8 Genome Annotation Databases

Ensembl: Not found

KEGG: pay:PAU_01214

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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