AMPDB_3566 | Colicin-Ib

PEPTIDE SUMMARY

Colicin-Ib

1 General Description

AMPDB ID: AMPDB_3566

Protein Names: Colicin-Ib

Protein Family: Channel forming colicin family

Gene Name: cib

Source Organism: Escherichia coli

Protein Length: 626 AA

Protein Existence: Inferred from homology

2 Protein Sequence & Composition

2.1 Sequence

MSDPVRITNPGAESLGYDSDGHEIMAVDIYVNPPRVDVFHGTPPAWSSFGNKTIWGGNEWVDDSPTRSDIEKRDKEITAYKNTLSAQQKENENKRTEAGKRLSAAIAAREKDENTLKTLRAGNADAADITRQEFRLLQAELREYGFRTEIAGYDALRLHTESRMLFADADSLRISPREARSLIEQAEKRQKDAQNADKKAADMLAEYERRKGILDTRLSELEKNGGAALAVLDAQQARLLGQQTRNDRAISEARNKLSSVTESLKTARNALTRAEQQLTQQKNTPDGKTIVSPEKFPGRSSTNHSIVVSGDPRFAGTIKITTSAVIDNRANLNYLLTHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAEWDKLRQRLLDARNKITSAESAINSARNNVSARTNEQKHANDALNALLKEKENIRSQLADINQKIAEEKRKRDEINMVKDAIKLTSDFYRTIYDEFGKQASELAKELASVSQGKQIKSVDDALNAFDKFRNNLNKKYNIQDRMAISKALEAINQVHMAENFKLFSKAFGFTGKVIERYDVAVELQKAVKTDNWRPFFVKLESLAAGRAASAVTAWAFSVMLGTPVGILGFAIIMAAVSALVNDKFIEQVNKLIGI

FASTA format

2.2 Composition

Counts of Amino Acids

'A': 75, 'R': 46, 'N': 43, 'D': 43, 'C': 0, 'Q': 26, 'E': 46, 'G': 30, 'H': 7, 'I': 39, 'L': 51, 'K': 50, 'M': 9, 'F': 20, 'P': 15, 'S': 41, 'T': 34, 'W': 6, 'Y': 13, 'V': 32

Frequencies of Amino Acids

'A': 11.98%, 'R': 7.35%, 'N': 6.87%, 'D': 6.87%, 'C': 0%, 'Q': 4.15%, 'E': 7.35%, 'G': 4.79%, 'H': 1.12%, 'I': 6.23%, 'L': 8.15%, 'K': 7.99%, 'M': 1.44%, 'F': 3.19%, 'P': 2.4%, 'S': 6.55%, 'T': 5.43%, 'W': 0.96%, 'Y': 2.08%, 'V': 5.11%

Missing Amino Acid(s)

Most Occurring Amino Acid(s)

Less Occurring Amino Acid(s)

Hydrophobic Amino Acid(s) Count

277

Hydrophilic Amino Acid(s) Count

349

Basic Amino Acid(s) Count

Acidic Amino Acid(s) Count

103

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	69923.7 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	82.875	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	38.17	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	-0.608	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.755	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	9.596	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	7.709	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.257, 0.206, 0.289 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.062	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	52370, 52370	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: Mankovich JA, Hsu CH, Konisky J, et al. DNA and amino acid sequence analysis of structural and immunity genes of colicins Ia and Ib. J Bacteriol. 1986;168(1):228-36. Published 1986 Oct. doi:10.1128/jb.168.1.228-236.1986

PMID: 3531169

Citation 2: Mankovich JA, Lai PH, Gokul N, et al. Organization of the colicin Ib gene. Promoter structure and immunity domain. J Biol Chem. 1984;259(14):8764-8. Published 1984 Jul 25. doi:

PMID: 6204975

Citation 3: Varley JM, Boulnois GJ, Boulnois GJ. Analysis of a cloned colicin Ib gene: complete nucleotide sequence and implications for regulation of expression. Nucleic Acids Res. 1984;12(17):6727-39. Published 1984 Sep 11. doi:10.1093/nar/12.17.6727

PMID: 6091036

5.2 Protein Sequence Databases

UniProt: P04479

5.3 3D Structure Databases

No PDB Ids found

AlphaFoldDB: P04479

5.4 Nucleotide Sequence Databases

Sl. no.	Accession(s)	Access Link(s)
1.	K02071	GenBank \|\| EMBL
2.	X01009	GenBank \|\| EMBL
3.	M13820	GenBank \|\| 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: IPR000293, IPR038283, IPR014740, IPR014739

PANTHER: Not found

PROSITE: PS00276

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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