scholarly journals TMpro web server and web service: transmembrane helix prediction through amino acid property analysis

2007 ◽  
Vol 23 (20) ◽  
pp. 2795-2796 ◽  
Author(s):  
M. Ganapathiraju ◽  
C. J. Jursa ◽  
H. A. Karimi ◽  
J. Klein-Seetharaman
Keyword(s):  
Amino Acid ◽  
Web Service ◽  
Transmembrane Helix ◽  
Web Server ◽  
Amino Acid Property ◽  
Acid Property ◽  
Property Analysis ◽  
Transmembrane Helix Prediction

HIV-1 protease cleavage site prediction based on amino acid property

2009 ◽  
Vol 30 (1) ◽  
pp. 33-39 ◽  
Author(s):  
Bing Niu ◽  
Lin Lu ◽  
Liang Liu ◽  
Tian Hong Gu ◽  
Kai-Yan Feng ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cleavage Site ◽  
Amino Acid Property ◽  
Acid Property ◽  
Site Prediction ◽  
Protease Cleavage Site ◽  
Protease Cleavage ◽  
Cleavage Site Prediction ◽  
Hiv 1

scholarly journals Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information

2008 ◽  
Vol 4 (9) ◽  
pp. e1000181 ◽  
Author(s):  
Kai Wang ◽  
Jeremy A. Horst ◽  
Gong Cheng ◽  
David C. Nickle ◽  
Ram Samudrala
Keyword(s):  
Amino Acid ◽  
Amino Acid Property ◽  
Structure Evolution ◽  
Acid Property ◽  
Sequence Structure

scholarly journals Fe(2)OG: an integrated HMM profile-based web server to predict and analyze putative non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenase function in protein sequences

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Siddhartha Kundu
Keyword(s):  
Amino Acid ◽  
Water Molecule ◽  
Active Site ◽  
Ferrous Iron ◽  
Web Server ◽  
Protein Sequences ◽  
Diverse Group ◽  
And Function ◽  
Functionally Diverse ◽  
Haem Iron

Abstract Objective Non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenases (i2OGdd), are a taxonomically and functionally diverse group of enzymes. The active site comprises ferrous iron in a hexa-coordinated distorted octahedron with the apoenzyme, 2-oxoglutarate and a displaceable water molecule. Current information on novel i2OGdd members is sparse and relies on computationally-derived annotation schema. The dissimilar amino acid composition and variable active site geometry thereof, results in differing reaction chemistries amongst i2OGdd members. An additional need of researchers is a curated list of sequences with putative i2OGdd function which can be probed further for empirical data. Results This work reports the implementation of $$Fe\left(2\right)OG$$ F e 2 O G , a web server with dual functionality and an extension of previous work on i2OGdd enzymes $$\left(Fe\left(2\right)OG\equiv \{H2OGpred,DB2OG\}\right)$$ F e 2 O G ≡ { H 2 O G p r e d , D B 2 O G } . $$Fe\left(2\right)OG$$ F e 2 O G , in this form is completely revised, updated (URL, scripts, repository) and will strengthen the knowledge base of investigators on i2OGdd biochemistry and function. $$Fe\left(2\right)OG$$ F e 2 O G , utilizes the superior predictive propensity of HMM-profiles of laboratory validated i2OGdd members to predict probable active site geometries in user-defined protein sequences. $$Fe\left(2\right)OG$$ F e 2 O G , also provides researchers with a pre-compiled list of analyzed and searchable i2OGdd-like sequences, many of which may be clinically relevant. $$Fe(2)OG$$ F e ( 2 ) O G , is freely available (http://204.152.217.16/Fe2OG.html) and supersedes all previous versions, i.e., H2OGpred, DB2OG.

scholarly journals Point Mutations in Transmembrane Helices 2 and 3 of ExbB and TolQ Affect Their Activities in Escherichia coli K-12

2004 ◽  
Vol 186 (13) ◽  
pp. 4402-4406 ◽  
Author(s):  
Volkmar Braun ◽  
Christina Herrmann
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Transmembrane Helix ◽  
Point Mutations ◽  
Transmembrane Helices ◽  
The Third ◽  
Form Part ◽  
K 12

ABSTRACT Replacement of glutamate 176, the only charged amino acid in the third transmembrane helix of ExbB, with alanine (E176A) abolished ExbB activity in all determined ExbB-dependent functions of Escherichia coli. Combination of the mutations T148A in the second transmembrane helix and T181A in the third transmembrane helix, proposed to form part of a proton pathway through ExbB, also resulted in inactive ExbB. E176 and T148 are strictly conserved in ExbB and TolQ proteins, and T181 is almost strictly conserved in ExbB, TolQ, and MotA.

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