AMPDB_3746 | Colicin-D

PEPTIDE SUMMARY

Colicin-D

1 General Description

AMPDB ID: AMPDB_3746

Protein Names: Colicin-D

Protein Family: Cloacin colicin family

Gene Name: cda

Source Organism: Escherichia coli

Protein Length: 697 AA

Protein Existence: Evidence at protein level

2 Protein Sequence & Composition

2.1 Sequence

MSDYEGSGPTEGIDYGHSMVVWPSTGLISGGDVKPGGSSGIAPSMPPGWGDYSPQGIALVQSVLFPGIIRRIILDKELEEGDWSGWSVSVHSPWGNEKVSAARTVLENGLRGGLPEPSRPAAVSFARLEPASGNEQKIIRLMVTQQLEQVTDIPASQLPAAGNNVPVKYRLMDLMQNGTQYMAIIGGIPMTVPVVDAVPVPDRSRPGTNIKDVYSAPVSPNLPDLVLSVGQMNTPVLSNPEIQEEGVIAETGNYVEAGYTMSSNNHDVIVRFPEGSDVSPLYISTVEILDSNGLSQRQEAENKAKDDFRVKKEEAVARAEAEKAKAELFSKAGVNQPPVYTQEMMERANSVMNEQGALVLNNTASSVQLAMTGTGVWTAAGDIAGNISKFFSNALEKVTIPEVSPLLMRISLGALWFHSEEAGAGSDIVPGRNLEAMFSLSAQMLAGQGVVIEPGATSVNLPVRGQLINSNGQLALDLLKTGNESIPAAVPVLNAVRDTATGLDKITLPAVVGAPSRTILVNPVPQPSVPTDTGNHQPVPVTPVHTGTEVKSVEMPVTTITPVSDVGGLRDFIYWRPDAAGTGVEAVYVMLNDPLDSGRFSRKQLDKKYKHAGDFGISDTKKNRETLTKFRDAIEEHLSDKDTVEKGTYRREKGSKVYFNPNTMNVVIIKSNGEFLSGWKINPDADNGRIYLETGEL

FASTA format

2.2 Composition

Counts of Amino Acids

'A': 53, 'R': 29, 'N': 38, 'D': 36, 'C': 0, 'Q': 24, 'E': 46, 'G': 65, 'H': 8, 'I': 38, 'L': 52, 'K': 31, 'M': 20, 'F': 15, 'P': 52, 'S': 57, 'T': 40, 'W': 9, 'Y': 16, 'V': 68

Frequencies of Amino Acids

'A': 7.6%, 'R': 4.16%, 'N': 5.45%, 'D': 5.16%, 'C': 0%, 'Q': 3.44%, 'E': 6.6%, 'G': 9.33%, 'H': 1.15%, 'I': 5.45%, 'L': 7.46%, 'K': 4.45%, 'M': 2.87%, 'F': 2.15%, 'P': 7.46%, 'S': 8.18%, 'T': 5.74%, 'W': 1.29%, 'Y': 2.3%, 'V': 9.76%

Missing Amino Acid(s)

Most Occurring Amino Acid(s)

Less Occurring Amino Acid(s)

Hydrophobic Amino Acid(s) Count

372

Hydrophilic Amino Acid(s) Count

325

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	74688.4 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	86.255	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	36.161	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	-0.234	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.643	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	4.704	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	-21.2	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.284, 0.304, 0.245 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.057	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	73340, 73340	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: Roos U, Harkness RE, Braun V, et al. Assembly of colicin genes from a few DNA fragments. Nucleotide sequence of colicin D. Mol Microbiol. 1989;3(7):891-902. Published 1989 Jul. doi:10.1111/j.1365-2958.1989.tb00238.x

PMID: 2677603

5.2 Protein Sequence Databases

UniProt: P17998

5.3 3D Structure Databases

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

AlphaFoldDB: P17998

5.4 Nucleotide Sequence Databases

Sl. no.	Accession(s)	Access Link(s)
1.	X14941	GenBank \|\| EMBL

CCDS: Not found

RefSeq: WP_016245160.1

5.5 Protein-Protein Interaction Databases

STRING: Not found

IntAct: P17998

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: IPR024575, IPR038233, IPR024440, IPR037178, IPR016128, IPR036302

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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