Promals3d flowchart

Pei et al.

PROMALS3D (PRofile Multiple Alignments with Predicted Local Structures and 3D constraints) takes into account the sequence identity, secondary structure and 3D arrangement in predicting similarities between related proteins. 1PROMALS3D was particularly helpful(for me) in designing primers to insert certain protein sequences in creating a chimera motor construct.
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PROMALS3D website. The protein sequences can be copied and pasted onto the section headed "FASTA" sequences. NCBI or other sequencing programs can be used to obtain the amino acid sequences.

Step 1: Finding the sequencesEdit

One can find the protein sequences of interest from NCBI, or from other sequencing programs that would translate the cDNA into amino acid sequences. Once sequences are obtained, one can copy and paste the sequences into the PROMALS3D website, preceding with >seq(insert name here). An example is shown below. 

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A screenshot of how to input the amino acid sequences into website. Each sequence should start with >seq(name here) and can either be the whole protein, sections, etc.

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A representative page on the protein data bank. The ID code is highlighted in red.

Step 2: Selecting the corresponding structureEdit

By inputing the structural information, one can reduce 'incorrect' alignment of protein sequences that may have structural homology, but not necessarily sequence homology. Once the related structural information is obtained from the Protein Data Bank(PDB ), ID codes corresponding to the sequences can be added (in order). The PDB includes x ray crystallographic data that has been published by other scientists all around the world. This angstrom-scale resolution provides lots of structural information that would otherwise be lost or not accounted for in a normal protein sequence alignment.

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PROMALS3D uses a combination of several databases with a unique algorithm. The output is given in three different ways. Click "Show" next to any one of the databases to see the results.

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A section of the PROMALS3D alignment of 9 different kinesin-like motor protein sequences. The names in pink are representative sequences. Red letters indicate alpha helices and blue represent beta strands. Different letters underneath the sequences in green are different types of amino acids- hydrophobic, aromatic, small, charged, bulky, etc. The sequences in black represent the sequences from the published structure from the PDB. The missing sequences are usually artifacts of crystallography/EM structure determination. Disordered regions usually lack electron density, therefore the sequences cannot be ascertained.

Step 3: AlignmentEdit

After all the information has been entered, an email address can be submitted, and a link will be sent in the email, and the alignment can be obtained from there. 


1 Pei J, Kim BH, & Grishin NV (2008) PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic acids research 36(7):2295-2300