Sequence patterns and HMM profiles to predict proteome wide zinc finger motifs

Rathinavelan, Thenmalarchelvi (2023) Sequence patterns and HMM profiles to predict proteome wide zinc finger motifs. Pattern Recognition, 135. p. 109134. ISSN 0031-3203

Text
1-s2.0-S0031320322006148-main.pdf - Published Version
Download (4MB)

Abstract

Zinc finger (ZnF) is an important class of nucleic acid and protein recognition domain, wherein, zinc ion is the inorganic co-factor that forms a tetrahedral geometry with the cysteine and/or histidine residues. ZnF domains take up diverse architectures with different ZnF motifs and have a wide range of biological functions. Nonetheless, predicting the ZnF motif(s) from the sequence is quite challenging. To this end, 74 unique ZnF sequence patterns are collected from the literature and classified into 32 different classes. Since the shorter length of ZnF sequence patterns leads to inaccurate predictions, ZnF domain Pfam HMM profiles defined under 6 ZnF Pfam clans (215 HMM profiles) and a few undefined Pfam clans (74 HMM profiles) are used for the prediction. A web server, namely, ZnF-Prot (https://project.iith.ac.in/znprot/) is developed which can predict the presence of 31 ZnF domains in a protein/proteome sequence of any organism. The use of ZnF sequence patterns and Pfam HMM profiles resulted in an accurate prediction of 610 test cases (taken randomly from 249 organisms) considered here. Additionally, the application of ZnF-Prot is demonstrated by considering Arabidopsis thaliana, Homo sapiens, Saccharomyces cerevisiae, Caenorhabditis elegans and Ciona intestinalis proteomes as test cases, wherein, 87–96% of the predicted ZnF motifs are cross-validated.

[error in script]

IITH Creators:

IITH Creators	ORCiD
Rathinavelan, Thenmalarchelvi	http://orcid.org/0000-0002-1142-0583

Item Type:

Article

Uncontrolled Keywords:

Pfam HMM profile; Zinc finger classification; Zinc finger motif; Zinc finger prediction; Zinc finger proteome; Finger classifications; Pfam HMM profile; Sequence patterns; Zinc finger; Zinc finger classification; Zinc finger motifs; Zinc finger prediction; Zinc finger proteome; Amino acids; Forecasting; HTTP; Nucleic acids; Yeast; Zinc; Proteins

Subjects:

Others > Biotechnology

Divisions:

Department of Biotechnology

Depositing User:

Mr Nigam Prasad Bisoyi

Date Deposited:

24 Aug 2023 10:52

Last Modified:

24 Aug 2023 10:52

URI:

http://raiithold.iith.ac.in/id/eprint/11615