This Shapleigh_et_al_2018_Environ_Sci_Technol_NcycleData_Readme.txt file was generated on 20180731 by Sarah J. Wright


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GENERAL INFORMATION
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1. Title of Dataset 
Data used in analyses associated with: "Salinity-aided selection of progressive onset denitrifiers as a means of providing nitrite for anammox"

2. Author Information
James P. Shapleigh, C. Armanda Roco

  Principal Investigator Contact Information
        Name: James P. Shapleigh
           Institution: Cornell University, Department of Microbiology	
           Address: 257A Wing Hall; Ithaca NY 14853
           Email: jps2@cornell.edu

3. Date of data collection 

2016-2017

4. Abstract
This is the protein sequence dataset used for determining reads derived from denitrification genes in Illumina read samples.  The protein types in the dataset are the active site containing subunits from the following proteins: Nap – periplasmic nitrate reductase; Nar – membrane associated nitrate reductase; NirK – copper containing nitrite reductase; NirS- heme-containing nitrite reductase; cNor – cytochrome c oxidizing nitrite reductase; qNor – quinol oxidizing nitric oxide reductase and Nos – nitrous oxide reductase. Sequences were initially obtained from the data available from the Integrated Microbial Genomes (IMG) system (https://img.jgi.doe.gov/cgi-bin/m/main.cgi). Related proteins were then aligned and proteins predicted to not be related or that were significantly shorter in length than group average were removed. 

5. Keywords
Denitrification, active-site containing subunits, protein sequences


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SHARING/ACCESS INFORMATION
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1. Licenses/restrictions placed on the data:
Creative Commons Attribution (CC BY) 4.0 International

2. Links to publications that cite or use the data:
Wei Li, Hui Li, Yong-di Liu, Ping Zheng, James P Shapleigh (in review). Salinity-aided selection of progressive onset denitrifiers as a means of providing nitrite for anammox. Environ. Sci. Technol.

3. Data derived from:
Sequences were initially obtained from the data available from the Integrated Microbial Genomes (IMG) system (https://img.jgi.doe.gov/cgi-bin/m/main.cgi). 

4. Recommended citation for the data:
James P. Shapleigh, C. Armanda Roco. 2018. Data used in analyses associated with: "Salinity-aided selection of progressive onset denitrifiers as a means of providing nitrite for anammox". Available from Cornell University eCommons Data Repository [Internet]. [add handle]



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DATA & FILE OVERVIEW
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1. File List
   A. Filename:      Shapleigh_et_al_2018_Environ_Sci_Technol_NcycleData.fas  
      Short description:      Curated database of denitrification enzymes(Nap,Nar,Nirs,NirK,qNor,cNor,NosZ)


2. Are there multiple versions of the dataset? 
  No


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METHODOLOGICAL INFORMATION
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1. Description of methods used for collection/generation of data: 
Sequences were obtained from the data available from the Integrated Microbial Genomes (IMG) system (https://img.jgi.doe.gov/cgi-bin/m/main.cgi). 


2. Methods for processing the data: 
Related proteins were aligned and proteins predicted to not be related or that were significantly shorter in length than group average were removed. 


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DATA-SPECIFIC INFORMATION FOR:  Shapleigh_et_al_2018_Environ_Sci_Technol_NcycleData.fas  
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1. Abbreviations used:
The protein sequences in the dataset are the active site containing subunits from the following proteins:
Nap – periplasmic nitrate reductase
Nar – membrane associated nitrate reductase
NirK – copper containing nitrite reductase
NirS- heme-containing nitrite reductase
cNor – cytochrome c oxidizing nitrite reductase
qNor – quinol oxidizing nitric oxide reductase
Nos – nitrous oxide reductase