Providencia alcalifaciens—Assisted Bioremediation of Chromium-Contaminated Groundwater: A Computational Study
, Wesam M. Hussein 2, Abdel-Aziz A. A. El-Sayed 3 and Abdulwahed Alrehaily 3,*,†Round 1
Reviewer 1 Report
The complete name of the used bacteria (Providencia alcalifaciens) must be written in the title.
Author Response
Reviewer 1
Comment 1: The complete name of the used bacteria (Providencia alcalifaciens) must be written in the title.
Response: Thank you for the great suggestion. We have incorporated your suggestion and the revised title is “Providencia alcalifaciens -Assisted Bioremediation of Chromium Contaminated Groundwater: A Computational Study”.
Reviewer 2 Report
The manuscript entitled “P. alcalifaciens -Assisted Bioremediation of Chromium Con-2 taminated Groundwater: A Computational Study” is well appreciable and informative. The authors have identified key residues and their mutants to be used in bioengineering to improve the stability of the enzyme and to remove the toxicity of chromium. The manuscript is well organized, however, some minor corrections will make it easily comprehendible.
1. Abstract should be rewrite in a more compact and structured way. The sentence “this research ….and its mutants” should be rewite as in this study does not provide structure (X ray or NMR) of ChrR and 26 its mutants.
2. In figure 3, multiple sequences of three sequences is shown including the target protein sequence, however, its accession number is not shown. Please modify the figure to appropriately show the MSA.
3. For homology modeling, the authors also used the PRABI tool, however, it is not mentioned in the materials and methods section.
4. Highlight the motifs found by the authors in multiple sequence alignment
5. The URL of all tools used must be mentioned.
6. Spelling correction for Aluminum, Gram-negative, do-main, qu ality. The authors must correct the referencing of 12, 11.
Author Response
The manuscript entitled “P. alcalifaciens -Assisted Bioremediation of Chromium Con-2 taminated Groundwater: A Computational Study” is well appreciable and informative. The authors have identified key residues and their mutants to be used in bioengineering to improve the stability of the enzyme and to remove the toxicity of chromium. The manuscript is well organized, however, some minor corrections will make it easily comprehendible.
Comment 1: Abstract should be rewrite in a more compact and structured way. The sentence “this research ….and its mutants” should be rewite as in this study does not provide structure (X ray or NMR) of ChrR and 26 its mutants.
Response: We are thankful to the reviewer. We have improvised the whole abstract and mentioned the homology modeling used for three-dimensional structure prediction.
Comment 2: In figure 3, multiple sequences of three sequences is shown including the target protein sequence, however, its accession number is not shown. Please modify the figure to appropriately show the MSA.
Response: Thank you for the observation. We have revised the Figure 3 as advised. In figure we mentioned the NCBI accession number, in the revised figure we have mentioned the Uniprot Id and highlighted the motifs.
Comment 3: For homology modeling, the authors also used the PRABI tool, however, it is not mentioned in the materials and methods section.
Response: We used Geno3D tool from PRABI (Pole Rhone Alpes de Bioinformatique). We apologize for the inconvenience and have updated each section with “Geno3D”, wherever PRABI was used.
Comment 4: Highlight the motifs found by the authors in multiple sequence alignment
Response: Thank you for the suggestion. We have incorporated your suggestion in Figure 3, in which multiple sequence alignment is shown.
Comment 5: The URL of all tools used must be mentioned.
Response: Thank you so much for pointing out the missing URLs. We have incorporated the URLs of all the tools.
ProtParam (https://web.expasy.org/protparam/)
InterProscan (https://www.ebi.ac.uk/interpro/about/interproscan/) and HMMER (http://hmmer.org/)
Pfam (http://pfam-legacy.xfam.org/)
CATH (http://cathdb.info/)
PANNZER (Protein ANNotation with Z-scoRE) (http://ekhidna2.biocenter.helsinki.fi/sanspanz/)
DeepGoWEb (https://deepgo.cbrc.kaust.edu.sa/deepgo/).
Multiple sequence alignment (MSA), Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/) and Phylogeny.fr (https://www.phylogeny.fr/)
PhyML (http://www.atgc-montpellier.fr/phyml/)
NetSurfP-2.0 (https://services.healthtech.dtu.dk/services/NetSurfP-2.0/)
GENO3D (geno3d-prabi.ibcp.fr ) (https://geno3d-prabi.ibcp.fr/cgi-bin/geno3d_automat.pl?page=/GENO3D/geno3d_home.html)
IntFOLD (https://www.reading.ac.uk/bioinf/IntFOLD/)
Protein Structure Validation Suite (PSVS) (https://montelionelab.chem.rpi.edu/PSVS/psvs2/),
Comment 6: Spelling correction for Aluminum, Gram-negative, do-main, qu ality. The authors must correct the referencing of 12, 11.
Response: Thank you for noticing the errors. We have rectified the typographical errors.
